@article {pmid29098814, year = {2017}, author = {Sun, HB and Jiang, SY and Sun, H and Zhou, Y and Zhu, WT}, title = {[Cultural regionalization for Notopterygium incisum based on 3S technology platform Ⅱ. Evaluation for quality suitability for N. incisum based on collocated Cokriging].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {14}, pages = {2633-2638}, doi = {10.19540/j.cnki.cjcmm.20170614.008}, pmid = {29098814}, issn = {1001-5302}, mesh = {Apiaceae/*chemistry ; *Crop Production ; Drugs, Chinese Herbal/*standards ; Ecology ; Geographic Information Systems ; Medicine, Chinese Traditional ; Plant Roots ; Plants, Medicinal/*chemistry ; Rhizome ; Spatial Analysis ; }, abstract = {Quality characteristics based on active substance are focused for in the cultivation of traditional Chinese medicine(TCM) plants due to their economic values. However, ecological and quality suitability are not always a coincidence, which makes traditional cultural regionalization for TCM cultivation based on ecological suitability have great limitations in practical applications. A regionalization method integrated GIS and medicinal plants quality have been analyzed by using field quality data of Notopterygii Rhizoma et Radix as a case study. Spatial interpolation based on medicine quality by Cokriging method is reasonable, and the predicted values of interpolation are correlated with measured values significantly, which shows that cultural regionalization for TCM cultivation based on spatial quality suitability is possible theoretically. The results indicate that the most suitable areas for quality suitability were mainly distributed in Sichuan province (29.42%), while the spatial distribution of quality suitability and ecological suitability was not coincidence. The cultivation regionalization of TCM plants based on quality suitability is helpful to high quality and quantity cultivation of those TCM plants which spatial distribution of geoherbalism and ecological suitability is separated.}, }
@article {pmid29090545, year = {2017}, author = {Tang, C and Wen, J and Zhang, W and Su, JS and Xie, CX and Zhang, Y}, title = {[Potential distribution of the traditional Tibetan herb Pterocephalus hookeri by Maxent model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {10}, pages = {1871-1876}, doi = {10.19540/j.cnki.cjcmm.20170222.018}, pmid = {29090545}, issn = {1001-5302}, mesh = {Caprifoliaceae/*growth & development ; China ; *Climate ; *Ecology ; Geographic Information Systems ; Plant Dispersal ; Plants, Medicinal/*growth & development ; Soil ; Tibet ; }, abstract = {In order to study the ecology suitability of Pterocephalus hookeri, and provide a reference for GAP planting location and regional development, the Maxent model and GIS technology were used to investigate ecology suitability regions for P. hookeri based on the distribution points collected from Chinese virtual herbarium, the references and field trips. The potential distribution areas mainly concentrated in the eastern Tibet, western Sichuan, southern Qinghai, northwest Yunnan, and southern Gansu. There were 7 major environmental factors to have obvious influence on ecology suitability distributions of P. hookeri, including altitude (contribution rate of 62%), precipitation of warmest quarter (contribution rate of 14.4%), coefficient of variation of precipitation seasonality (contribution rate of 7.2%), mean temperature of driest quarter (contribution rate of 3.5%), the electrical conductivity of top and sub-soil (contribution rate of 3%), the total exchangeable bases in the top- and subsoil (contribution rate of 2.4%) and SD of temperature seasonality (contribution rate of 2.2%). The study of the ecological suitability regionalization of P. hookeri based on Maxent model can provide scientific basis for the selection of artificial planting base and GAP planting location.}, }
@article {pmid30846683, year = {2019}, author = {George, PBL and Lallias, D and Creer, S and Seaton, FM and Kenny, JG and Eccles, RM and Griffiths, RI and Lebron, I and Emmett, BA and Robinson, DA and Jones, DL}, title = {Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1107}, doi = {10.1038/s41467-019-09031-1}, pmid = {30846683}, issn = {2041-1723}, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA Barcoding, Taxonomic ; *Ecosystem ; Microbiota/genetics ; *Soil ; *Soil Microbiology ; Wales ; }, abstract = {Soil biota accounts for ~25% of global biodiversity and is vital to nutrient cycling and primary production. There is growing momentum to study total belowground biodiversity across large ecological scales to understand how habitat and soil properties shape belowground communities. Microbial and animal components of belowground communities follow divergent responses to soil properties and land use intensification; however, it is unclear whether this extends across heterogeneous ecosystems. Here, a national-scale metabarcoding analysis of 436 locations across 7 different temperate ecosystems shows that belowground animal and microbial (bacteria, archaea, fungi, and protists) richness follow divergent trends, whereas β-diversity does not. Animal richness is governed by intensive land use and unaffected by soil properties, while microbial richness was driven by environmental properties across land uses. Our findings demonstrate that established divergent patterns of belowground microbial and animal diversity are consistent across heterogeneous land uses and are detectable using a standardised metabarcoding approach.}, }
@article {pmid28839161, year = {2017}, author = {Cai, L and Zhou, G and Tian, RM and Tong, H and Zhang, W and Sun, J and Ding, W and Wong, YH and Xie, JY and Qiu, JW and Liu, S and Huang, H and Qian, PY}, title = {Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9320}, pmid = {28839161}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Caribbean Region ; Chlorobi/*classification/genetics/*physiology ; Cluster Analysis ; Computational Biology ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Phylogeny ; *Symbiosis ; Whole Genome Sequencing ; }, abstract = {Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.}, }
@article {pmid30587126, year = {2018}, author = {Bochkareva, OO and Moroz, EV and Davydov, II and Gelfand, MS}, title = {Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {965}, doi = {10.1186/s12864-018-5245-1}, pmid = {30587126}, issn = {1471-2164}, support = {18-14-00358//Russian Science Foundation/ ; 16-54-21004//Russian Foundation of Basic Research/ ; IZLRZ3\163872//Swiss National Science Foundation/ ; }, mesh = {Burkholderia/classification/*genetics ; *Chromosomes, Bacterial ; Databases, Genetic ; Gene Rearrangement/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.<br><br>RESULTS: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.<br><br>CONCLUSIONS: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.}, }
@article {pmid30565882, year = {2019}, author = {Haller, BC and Galloway, J and Kelleher, J and Messer, PW and Ralph, PL}, title = {Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {552-566}, doi = {10.1111/1755-0998.12968}, pmid = {30565882}, issn = {1755-0998}, support = {//Alfred P. Sloan Foundation/ ; 100956/Z/13/Z//Wellcome Trust/United Kingdom ; DBI-1262645//National Science Foundation/ ; SS/05/01//Predator Free 2050/ ; R21AI130635//National Institutes of Health/ ; //College of Agriculture and Life Sciences, Cornell University/ ; //Wellcome Trust/United Kingdom ; R01 GM127418/GM/NIGMS NIH HHS/United States ; R21 AI130635/AI/NIAID NIH HHS/United States ; R01GM127418//National Institutes of Health/ ; }, mesh = {*Biological Evolution ; Computational Biology ; Computer Simulation ; Genetics, Population/*methods ; Software ; }, abstract = {There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, &amp; Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using &quot;recapitation&quot;; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.}, }
@article {pmid30011006, year = {2018}, author = {Garamszegi, LZ and Donald, J and Francis, CD and Fuxjager, MJ and Goymann, W and Hau, M and Husak, JF and Johnson, MA and Kircher, B and Knapp, R and Martin, LB and Miller, ET and Schoenle, LA and Vitousek, MN and Williams, TD}, title = {Species-Specific Means and Within-Species Variance in Glucocorticoid Hormones and Speciation Rates in Birds.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {763-776}, doi = {10.1093/icb/icy086}, pmid = {30011006}, issn = {1557-7023}, mesh = {Animals ; Birds/*physiology ; Databases as Topic ; Ecosystem ; *Genetic Speciation ; Glucocorticoids/*metabolism ; Species Specificity ; }, abstract = {At macroevolutionary scales, stress physiology may have consequences for species diversification and subspecies richness. Populations that exploit new resources or undergo range expansion should cope with new environmental challenges, which could favor higher mean stress responses. Within-species variation in the stress response may also play a role in mediating the speciation process: in species with broad variation, there will always be some individuals that can tolerate an unpredictable environment, whereas in species with narrow variation there will be fewer individuals that are able to thrive in a new ecological niche. We tested for the evolutionary relationship between stress response, speciation rate, and subspecies richness in birds by relying on the HormoneBase repository, from which we calculated within- and among-species variation in baseline (BL) and stress-induced (SI) corticosterone levels. To estimate speciation rates, we applied Bayesian analysis of macroevolutionary mixtures that can account for variation in diversification rate among clades and through time. Contrary to our predictions, lineages with higher diversification rates were not characterized by higher BL or SI levels of corticosterone either at the tips or at the deeper nodes of the phylogeny. We also found no association between mean hormone levels and subspecies richness. Within-species variance in corticosterone levels showed close to zero repeatability, thus it is highly unlikely that this is a species-specific trait that influences diversification rates. These results imply that stress physiology may play a minor, if any, role in determining speciation rates in birds.}, }
@article {pmid29736651, year = {2018}, author = {He, K and Zhang, J and Wang, X and Zeng, Y and Zhang, L}, title = {A scientometric review of emerging trends and new developments in agricultural ecological compensation.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {17}, pages = {16522-16532}, pmid = {29736651}, issn = {1614-7499}, support = {71703051//Natural Sciences Foundation of China/ ; 71333006//Natural Sciences Foundation of China/ ; 41501213//Natural Sciences Foundation of China/ ; 2662017QD009//Fundamental Research Funds for the Central Universities/ ; 15JZD014//Key Program of Philosophy and Social Sciences Research, Ministry of Education of China/ ; 2018ADC036//Soft Science Research Project of Technology Innovation in Hubei Province/ ; }, mesh = {Agriculture/*economics/*trends ; Compensation and Redress ; Conservation of Natural Resources/*economics/*trends ; Databases, Factual ; Ecology ; Ecosystem ; Humans ; }, abstract = {Agricultural ecological compensation has drawn an increasingly broad range of interest since early 1990s. In recent years, the volume of the literature grows rapidly. As a result, a systematic review of the diverse research field and its current trends becomes essential. This paper surveys the literature of agricultural ecological compensation between 1990 and 2016. Specifically, by employing CiteSpace information visualization software, we firstly identified the research hotspots and evolution path and then illustrated the frontier and developing trend of the domain in core and broader perspectives. It is found that the focus of the academic community has always been researches on the theoretical policy and application of the payment for agro-ecosystem services, agricultural ecological compensation based on contingent valuation method, and ecological compensation of farmland landscape and organic food production as well as willingness to accept/pay for land use and ecological protection. Meanwhile, we also found that, in recent years, qualitative research has received more and more attention in the field of agricultural ecological compensation, since global warming, agricultural carbon emissions, and other emerging environmental issues have aroused widespread concern of the people around the world. Moreover, we believed that more and more scholars will employ case study methodology to analyze agricultural ecological compensation in specific systems, regions, or circumstances in the future.}, }
@article {pmid30918448, year = {2019}, author = {Stucky, BJ and Balhoff, JP and Barve, N and Barve, V and Brenskelle, L and Brush, MH and Dahlem, GA and Gilbert, JDJ and Kawahara, AY and Keller, O and Lucky, A and Mayhew, PJ and Plotkin, D and Seltmann, KC and Talamas, E and Vaidya, G and Walls, R and Yoder, M and Zhang, G and Guralnick, R}, title = {Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.}, journal = {Biodiversity data journal}, volume = {7}, number = {}, pages = {e33303}, doi = {10.3897/BDJ.7.e33303}, pmid = {30918448}, issn = {1314-2828}, abstract = {Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.}, }
@article {pmid30918402, year = {2019}, author = {Peters, MK and Hemp, A and Appelhans, T and Becker, JN and Behler, C and Classen, A and Detsch, F and Ensslin, A and Ferger, SW and Frederiksen, SB and Gebert, F and Gerschlauer, F and Gütlein, A and Helbig-Bonitz, M and Hemp, C and Kindeketa, WJ and Kühnel, A and Mayr, AV and Mwangomo, E and Ngereza, C and Njovu, HK and Otte, I and Pabst, H and Renner, M and Röder, J and Rutten, G and Schellenberger Costa, D and Sierra-Cornejo, N and Vollstädt, MGR and Dulle, HI and Eardley, CD and Howell, KM and Keller, A and Peters, RS and Ssymank, A and Kakengi, V and Zhang, J and Bogner, C and Böhning-Gaese, K and Brandl, R and Hertel, D and Huwe, B and Kiese, R and Kleyer, M and Kuzyakov, Y and Nauss, T and Schleuning, M and Tschapka, M and Fischer, M and Steffan-Dewenter, I}, title = {Climate-land-use interactions shape tropical mountain biodiversity and ecosystem functions.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-019-1048-z}, pmid = {30918402}, issn = {1476-4687}, abstract = {Agriculture and the exploitation of natural resources have transformed tropical mountain ecosystems across the world, and the consequences of these transformations for biodiversity and ecosystem functioning are largely unknown1-3. Conclusions that are derived from studies in non-mountainous areas are not suitable for predicting the effects of land-use changes on tropical mountains because the climatic environment rapidly changes with elevation, which may mitigate or amplify the effects of land use4,5. It is of key importance to understand how the interplay of climate and land use constrains biodiversity and ecosystem functions to determine the consequences of global change for mountain ecosystems. Here we show that the interacting effects of climate and land use reshape elevational trends in biodiversity and ecosystem functions on Africa's largest mountain, Mount Kilimanjaro (Tanzania). We find that increasing land-use intensity causes larger losses of plant and animal species richness in the arid lowlands than in humid submontane and montane zones. Increases in land-use intensity are associated with significant changes in the composition of plant, animal and microorganism communities; stronger modifications of plant and animal communities occur in arid and humid ecosystems, respectively. Temperature, precipitation and land use jointly modulate soil properties, nutrient turnover, greenhouse gas emissions, plant biomass and productivity, as well as animal interactions. Our data suggest that the response of ecosystem functions to land-use intensity depends strongly on climate; more-severe changes in ecosystem functioning occur in the arid lowlands and the cold montane zone. Interactions between climate and land use explained-on average-54% of the variation in species richness, species composition and ecosystem functions, whereas only 30% of variation was related to single drivers. Our study reveals that climate can modulate the effects of land use on biodiversity and ecosystem functioning, and points to a lowered resistance of ecosystems in climatically challenging environments to ongoing land-use changes in tropical mountainous regions.}, }
@article {pmid30658302, year = {2019}, author = {Liu, Z and Tai, P and Li, X and Kong, L and Matthews, TG and Lester, RE and Mondon, JA}, title = {Deriving site-specific water quality criteria for ammonia from national versus international toxicity data.}, journal = {Ecotoxicology and environmental safety}, volume = {171}, number = {}, pages = {665-676}, doi = {10.1016/j.ecoenv.2018.12.078}, pmid = {30658302}, issn = {1090-2414}, mesh = {Ammonia/*toxicity ; Animals ; China ; Chironomidae/drug effects ; Copepoda/drug effects ; Daphnia/drug effects ; Databases, Factual ; Endpoint Determination ; Fishes ; Fresh Water/chemistry ; Geologic Sediments/chemistry ; Models, Theoretical ; Palaemonidae/drug effects ; Rivers/chemistry ; Toxicity Tests ; Water Pollutants, Chemical/*toxicity ; Water Quality/*standards ; }, abstract = {A key question to be asked when developing regional water quality criteria with scarce toxicity data is whether such data need to be locally derived. To address this, ammonia toxicity data from local aquatic species in the Liao River were compared against data from species native and non-native to China, based on comparisons of the overall trends of species sensitivity distributions and derived water quality criteria. Liao River data were acquired by acute and chronic tests using five local freshwater invertebrate species, and then compiled alongside published data from Chinese national guidelines and international literature. Models of best fit using three species sensitivity distribution approaches (log-logistic, log-normal, and Burr III) did not vary markedly (r2 >0.9), and no specific model provided a best fit across all data sets. The comparisons of the overall trend of species sensitivity distribution curves showed no significant differences at either a national (Chinese native taxa tested in China versus non-native taxa) or regional level (Liao River taxa versus non-Liao River taxa). The comparisons also revealed that the inclusion or exclusions of different ecological groups had little influence on the overall trends of species sensitivity distributions. These findings suggested data on non-local and non-native species, and data from local species tested elsewhere, could be appropriate for guiding the derivation of ammonia water quality criteria for regions such as Liao River. However, caution is needed when using hazardous concentration 5% values in the development of site-specific water quality criteria for a river basin due to the considerable variation observed for ammonia (16.8-56.6 mg/L), although these differences were not statistically significant. Based on the toxicity test evaluation, a preliminary acute value of 10.0 mg/L and chronic value of 1.7 mg/L (at pH of 7.0 and 20 °C) are proposed as site-specific ammonia water quality criteria for the Liao River, China.}, }
@article {pmid30782660, year = {2019}, author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S}, title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02852-18}, pmid = {30782660}, issn = {2150-7511}, mesh = {Aquaculture ; Aquatic Organisms/microbiology ; Cluster Analysis ; Computational Biology ; *Ecotype ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Phenotype ; Recombination, Genetic ; Vibrio vulnificus/*classification/*genetics/isolation &amp; purification/physiology ; }, abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel &quot;chromids,&quot; or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.}, }
@article {pmid30897417, year = {2019}, author = {Szabó, B and Lang, Z and Bakonyi, G and Mariën, J and Roelofs, D and van Gestel, CAM and Seres, A}, title = {Transgenerational and multigenerational stress gene responses to the insecticide etofenprox in Folsomia candida (Collembola).}, journal = {Ecotoxicology and environmental safety}, volume = {175}, number = {}, pages = {181-191}, doi = {10.1016/j.ecoenv.2019.03.052}, pmid = {30897417}, issn = {1090-2414}, abstract = {Insecticide exposure may cause both transgenerational and multigenerational effects on populations, but the molecular mechanisms of these changes remain largely unclear. Many studies have focused on either transgenerational or multigenerational mechanisms but did neglect the comparative aspects. This study assessed whether the pyrethroid insecticide etofenprox (formulation Trebon® 30 EC) shows transgenerational and/or multigenerational effects on the survival and reproduction of Folsomia candida (Collembola). The activation of stress-related genes was studied to detect whether etofenprox modifies the expression of reproduction-associated genes in trans- and multigenerational treatments. A laboratory study was carried out for three generations with five insecticide concentrations in LUFA 2.2 soil. In the transgenerational treatment, only the parent generation (P) was exposed, but the subsequent generations were not. In the multigenerational treatment, all three generations were exposed to the insecticide in the same manner. Multigenerational exposure resulted in reduced reproduction effects over generations, suggesting that F. candida is capable of acclimating to enhanced concentration levels of etofenprox during prolonged exposure over multiple generations. In the transgenerational treatment, the heat shock protein 70 was up-regulated and cytochrome oxidase 6N4v1 expression down-regulated in a dose-dependent manner in the F2 generation. This finding raises the possibility of the epigenetic inheritance of insecticide impacts on parents. Furthermore, CYP6N4v1 expression was oppositely regulated in the trans- and multigenerational treatments. Our results draw attention to the differences in molecular level responses of F. candida to trans- and multigenerational etofenprox exposure.}, }
@article {pmid30325353, year = {2018}, author = {Du, E}, title = {A database of annual atmospheric acid and nutrient deposition to China's forests.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180223}, pmid = {30325353}, issn = {2052-4463}, mesh = {Acid Rain ; Air Pollutants/*analysis ; China ; *Databases, Factual ; *Environmental Monitoring ; *Forests ; }, abstract = {Anthropogenic emissions have substantially altered atmospheric acid and nutrient deposition in China. Understanding the status and characteristics of acid and nutrient deposition to China's forests is crucial to assess the consequent impacts, and to better guide forest management options. Based on a comprehensive literature review, here I present an updated database for annual acid and nutrient deposition during the period 1991-2015 in China's forests (CFAND 2.0). The database includes information from 56 forested sites on the water fluxes of bulk precipitation and throughfall, the concentrations of H+ (pH), dissolved inorganic nitrogen (N) (NH4+ and NO3-), sulfur (S), dissolved phosphorus (P), potassium (K+), calcium (Ca2+) and magnesium (Mg2+) in bulk precipitation and throughfall, and the fluxes of dissolved inorganic N, S, dissolved P, K+, Ca2+ and Mg2+ in bulk deposition and throughfall. This database will help to understand the spatial patterns of acid and nutrient deposition, validate modelling results of acid and nutrient deposition and assess the ecological effects of acid and nutrient deposition in China's forests.}, }
@article {pmid30884039, year = {2019}, author = {Piao, S and Liu, Q and Chen, A and Janssens, IA and Fu, Y and Dai, J and Liu, L and Lian, X and Shen, M and Zhu, X}, title = {Plant phenology and global climate change: current progresses and challenges.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.14619}, pmid = {30884039}, issn = {1365-2486}, abstract = {Plant phenology, the annually recurring sequence of plant developmental stages, is important for plant functioning and ecosystem services and their biophysical and biogeochemical feedbacks to the climate system. Plant phenology depends on temperature, and the current rapid climate change has revived interest in understanding and modelling the responses of plant phenology to the warming trend and the consequences thereof for ecosystems. Here, we review recent progresses in plant phenology and its interactions with climate change. Focusing on the start (leaf unfolding) and end (leaf coloring) of plant growing seasons, we show that the recent rapid expansion in ground- and remote sensing- based phenology data acquisition has been highly beneficial and has supported major advances in plant phenology research. Studies using multiple data sources and methods generally agree on the trends of advanced leaf unfolding and delayed leaf coloring due to climate change, yet these trends appear to have decelerated or even reversed in recent years. Our understanding of the mechanisms underlying the plant phenology responses to climate warming is still limited. The interactions between multiple drivers complicates the modelling and prediction of plant phenology changes. Furthermore, changes in plant phenology have important implications for ecosystem carbon cycles and ecosystem feedbacks to climate, yet the quantification of such impacts remains challenging. We suggest that future studies should primarily focus on using new observation tools to improve the understanding of tropical plant phenology, on improving process-based phenology modelling, and on the scaling of phenology from species to landscape-level. This article is protected by copyright. All rights reserved.}, }
@article {pmid30883574, year = {2019}, author = {Giezendanner, J and Bertuzzo, E and Pasetto, D and Guisan, A and Rinaldo, A}, title = {A minimalist model of extinction and range dynamics of virtual mountain species driven by warming temperatures.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213775}, doi = {10.1371/journal.pone.0213775}, pmid = {30883574}, issn = {1932-6203}, abstract = {A longstanding question in ecology concerns the prediction of the fate of mountain species under climate change, where climatic and geomorphic factors but also endogenous species characteristics are jointly expected to control species distributions. A significant step forward would single out reliably landscape effects, given their constraining role and relative ease of theoretical manipulation. Here, we address population dynamics in ecosystems where the substrates for ecological interactions are mountain landscapes subject to climate warming. We use a minimalist model of metapopulation dynamics based on virtual species (i.e. a suitable assemblage of focus species) where dispersal processes interact with the spatial structure of the landscape. Climate warming is subsumed by an upward shift of species habitat altering the metapopulation capacity of the landscape and hence species viability. We find that the landscape structure is a powerful determinant of species survival, owing to the specific role of the predictably evolving connectivity of the various habitats. Range shifts and lags in tracking suitable habitat experienced by virtual species under warming conditions are singled out in different landscapes. The range of parameters is identified for which these virtual species (characterized by comparable viability thus restricting their possible fitnesses and niche widths) prove unable to cope with environmental change. The statistics of the proportion of species bound to survive is identified for each landscape, providing the temporal evolution of species range shifts and the related expected occupation patterns. A baseline dynamic model for predicting species fates in evolving habitats is thus provided.}, }
@article {pmid29652093, year = {2018}, author = {Wilson, K and Sheldon, BC and Gaillard, JM and Sanders, NJ and Hoggart, SPG and Newton, E}, title = {And the winner of the inaugural Sidnie Manton Award is….}, journal = {The Journal of animal ecology}, volume = {87}, number = {3}, pages = {527-529}, doi = {10.1111/1365-2656.12825}, pmid = {29652093}, issn = {1365-2656}, mesh = {Animals ; *Awards and Prizes ; Ecology/*history ; History, 21st Century ; Image Interpretation, Computer-Assisted/*methods ; Oregon ; Societies, Scientific ; United Kingdom ; }, }
@article {pmid29111567, year = {2018}, author = {Weinstein, BG}, title = {A computer vision for animal ecology.}, journal = {The Journal of animal ecology}, volume = {87}, number = {3}, pages = {533-545}, doi = {10.1111/1365-2656.12780}, pmid = {29111567}, issn = {1365-2656}, mesh = {Animals ; Ecology/*methods ; Image Interpretation, Computer-Assisted/*methods ; }, abstract = {A central goal of animal ecology is to observe species in the natural world. The cost and challenge of data collection often limit the breadth and scope of ecological study. Ecologists often use image capture to bolster data collection in time and space. However, the ability to process these images remains a bottleneck. Computer vision can greatly increase the efficiency, repeatability and accuracy of image review. Computer vision uses image features, such as colour, shape and texture to infer image content. I provide a brief primer on ecological computer vision to outline its goals, tools and applications to animal ecology. I reviewed 187 existing applications of computer vision and divided articles into ecological description, counting and identity tasks. I discuss recommendations for enhancing the collaboration between ecologists and computer scientists and highlight areas for future growth of automated image analysis.}, }
@article {pmid30721227, year = {2019}, author = {Marsland, R and Cui, W and Goldford, J and Sanchez, A and Korolev, K and Mehta, P}, title = {Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.}, journal = {PLoS computational biology}, volume = {15}, number = {2}, pages = {e1006793}, doi = {10.1371/journal.pcbi.1006793}, pmid = {30721227}, issn = {1553-7358}, support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Databases, Factual ; *Ecosystem ; Energy Metabolism/*physiology ; Microbial Consortia/*physiology ; Models, Biological ; Stochastic Processes ; Thermodynamics ; }, abstract = {A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a &quot;resource-limited&quot; regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.}, }
@article {pmid30106390, year = {2018}, author = {Duarte, G and Moreira, M and Branco, P and da Costa, L and Ferreira, MT and Segurado, P}, title = {One millennium of historical freshwater fish occurrence data for Portuguese rivers and streams.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180163}, pmid = {30106390}, issn = {2052-4463}, mesh = {Animals ; Databases, Factual ; Ecology/history ; Ecosystem ; *Fishes ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Medieval ; Portugal ; Rivers ; }, abstract = {The insights that historical evidence of human presence and man-made documents provide are unique. For example, using historical data may be critical to adequately understand the ecological requirements of species. However, historical information about freshwater species distribution remains largely a knowledge gap. In this Data Descriptor, we present the Portuguese Historical Fish Database (PHish-DB), a compilation of 2214 records (557 at the basin scale, 184 at the sub-basin scale and 1473 at the segment scale) resulting from a survey of 194 historical documents. The database was developed using a three-scale approach that maximises the inclusion of information by allowing different degrees of spatial acuity. PHish database contains records of 25 taxonomical groups and covers a time span of one millennium, from the 11th until the 20th century. This database has already proven useful for two scientific studies, and PHish further use will contribute to correctly assess the full range of conditions tolerated by species, by establishing adequate benchmark conditions, and/or to improve existing knowledge of the species distribution limits.}, }
@article {pmid30842894, year = {2019}, author = {Sumsion, GR and Bradshaw, MS and Hill, KT and Pinto, LDG and Piccolo, SR}, title = {Remote sensing tree classification with a multilayer perceptron.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6101}, doi = {10.7717/peerj.6101}, pmid = {30842894}, issn = {2167-8359}, abstract = {To accelerate scientific progress on remote tree classification-as well as biodiversity and ecology sampling-The National Institute of Science and Technology created a community-based competition where scientists were invited to contribute informatics methods for classifying tree species and genus using crown-level images of trees. We classified tree species and genus at the pixel level using hyperspectral and LiDAR observations. We compared three algorithms that have been implemented extensively across a broad range of research applications: support vector machines, random forests, and multilayer perceptron. At the pixel level, the multilayer perceptron algorithm classified species or genus with high accuracy (92.7% and 95.9%, respectively) on the training data and performed better than the other two algorithms (85.8-93.5%). This indicates promise for the use of the multilayer perceptron (MLP) algorithm for tree-species classification based on hyperspectral and LiDAR observations and coincides with a growing body of research in which neural network-based algorithms outperform other types of classification algorithm for machine vision. To aggregate patterns across the images, we used an ensemble approach that averages the pixel-level outputs of the MLP algorithm to classify species at the crown level. The average accuracy of these classifications on the test set was 68.8% for the nine species.}, }
@article {pmid29989590, year = {2018}, author = {Tavşanoğlu, Ç and Pausas, JG}, title = {A functional trait database for Mediterranean Basin plants.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180135}, pmid = {29989590}, issn = {2052-4463}, mesh = {*Databases, Factual ; Ecosystem ; Mediterranean Region ; *Plants ; }, abstract = {Functional trait databases are emerging as crucial tools for a wide range of ecological studies across the world. Here, we provide a database of functional traits for vascular plant species of the Mediterranean Basin. The database includes 25,764 individual records of 44 traits from 2,457 plant taxa distributed in 119 taxonomic families. This database (BROT 2.0) is an updated and enlarged version of a previous database (BROT 1.0; 8,263 records, 14 traits, 952 taxa). Trait data were obtained from a comprehensive literature review, plus some field and experimental observations. All records are fully referenced and, in many cases, include geographic coordinates. The database is structured to include different levels of accuracy of trait information for each entry. BROT 2.0 should facilitate testing hypotheses on plant functional ecology within the Mediterranean Basin, and comparing this region with other ecosystems worldwide. The BROT 2.0 database and its trait definitions can be used as a template for creating similar trait databases in other regions of the world.}, }
@article {pmid30832282, year = {2019}, author = {Wu, Z and Lei, S and He, BJ and Bian, Z and Wang, Y and Lu, Q and Peng, S and Duo, L}, title = {Assessment of Landscape Ecological Health: A CaseStudy of a Mining City in a Semi-Arid Steppe.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/ijerph16050752}, pmid = {30832282}, issn = {1660-4601}, support = {2016YFC0501107//China University of Mining and Technology/ ; U1710120//China University of Mining and Technology/ ; 2014FY110800//China University of Mining and Technology/ ; }, abstract = {The ecological status of the semi-arid steppes in China is fragile. Under the long-term and high-intensity development of mining, the ecological integrity and biodiversity of steppe landscapes have been destroyed, causing soil pollution, grassland degradation, landscape function defect, and so on. Previous studies have mainly focused on ecosystem health assessment in mining areas. Landscape ecological health (LEH) pays more attention to the interactions between different ecosystems. Therefore, the ecological assessment of mining cities is more suitable on a landscape scale. Meanwhile, the existing LEH assessment index systems are not applicable in ecologically fragile areas with sparse population, underdeveloped economy, and in relatively small research areas. The purpose of this study was to construct a LEH assessment index system and evaluate the LEH of a mining city located in a semi-arid steppe. Xilinhot is a typical semi-arid steppe mining city in China. The contradictions between the human, land and ecological environment are serious. A new model Condition, Vigor, Organization, Resilience, and Ecosystem (CVORE) model was constructed that integrated five subsystems (services) from the perspectives of ecology, landscape ecology, mining science, and geography. This study used the CVORE model to systematically evaluate the LEH in Xilinhot city in terms of five LEH levels, including very healthy, healthy, sub-healthy, unhealthy and morbid landscape. Research results show that the areas of the very healthy, healthy, sub-healthy, unhealthy and morbid landscapes are 13.23, 736.35, 184.5, 66.76 and 20.63 km², respectively. The healthy landscapes area accounts for 72.08% and most grasslands are healthy. The sub-healthy landscapes are mainly located around areas with higher disturbances due to human activities. The morbid or unhealthy landscapes are concentrated in the mining areas. The proposed CVORE model can enrich the foundations for the quantitative assessment of Landscape Ecological Health of Mining Cities in Semi-arid Steppe (LEHMCSS). This study provided a new LEH assessment approach (CVORE model), which can support landscape ecological restoration, ecological environmental protection and urban planning of the semi-arid steppe mining cities.}, }
@article {pmid28743947, year = {2017}, author = {Santos, CD and Hanssen, F and Muñoz, AR and Onrubia, A and Wikelski, M and May, R and Silva, JP}, title = {Match between soaring modes of black kites and the fine-scale distribution of updrafts.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6421}, pmid = {28743947}, issn = {2045-2322}, mesh = {Animals ; Falconiformes/*physiology ; Flight, Animal/*physiology ; Geographic Information Systems ; Models, Biological ; Spain ; }, abstract = {Understanding how soaring birds use updrafts at small spatial scales is important to identify ecological constraints of movement, and may help to prevent conflicts between wind-energy development and the conservation of wildlife. We combined high-frequency GPS animal tracking and fine-spatial-scale uplift modelling to establish a link between flight behaviour of soaring birds and the distribution of updrafts. We caught 21 black kites (Milvus migrans) and GPS-tracked them while flying over the Tarifa region, on the Spanish side of the Strait of Gibraltar. This region has a diverse topography and land cover, favouring a heterogeneous updraft spatial distribution. Bird tracks were segmented and classified into flight modes from motion parameters. Thermal and orographic uplift velocities were modelled from publically available remote-sensing and meteorological data. We found that birds perform circular soaring in areas of higher predicted thermal uplift and linear soaring in areas of higher predicted orographic uplift velocity. We show that updraft maps produced from publically available data can be used to predict where soaring birds will concentrate their flight paths and how they will behave in flight. We recommend the use of this methodological approach to improve environmental impact assessments of new wind-energy installations.}, }
@article {pmid30096816, year = {2018}, author = {Liu, Y and Liu, Y and Li, J and Lu, W and Wei, X and Sun, C}, title = {Evolution of Landscape Ecological Risk at the Optimal Scale: A Case Study of the Open Coastal Wetlands in Jiangsu, China.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {8}, pages = {}, pmid = {30096816}, issn = {1660-4601}, mesh = {China ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geological Phenomena ; Human Activities ; Humans ; Remote Sensing Technology ; Risk ; *Wetlands ; }, abstract = {Detailed analysis of the evolution characteristics of landscape ecological risk is crucial for coastal sustainable management and for understanding the potential environmental impacts of a man-made landform landscapes (MMLL). As a typical open coastal wetland, large-scale human activities (e.g., tidal reclamation, fishery activities, wind farm construction, and port construction) have substantially affected the evolution of the coastal ecological environment. Previous landscape ecological risk assessment studies have documented the effectiveness of assessing the quality of ecological environment processes. However, these studies have either focused on the noncoastal zone, or they have not considered the evolution of the spatial characteristics and ecological risk evolution of the landscape at an optimal scale. Here, we present a landscape ecological risk pattern (LERP) evolution model, based on two successive steps: first, we constructed an optimal scale method with an appropriate extent and grain using multi⁻temporal Landsat TM/OLI images acquired in the years 2000, 2004, 2008, 2013 and 2017, and then we calculated landscape ecological risk indices. Based on this model, the entire process of the spatiotemporal evolution of ecological risk patterns of the open coastal wetlands in Jiangsu, China, was determined. The principal findings are as follows: (1) The main landscape types in the study area are tidal flats and farmland, and the main features of the landscape evolution are a significant increase in aquafarming and a substantial decrease in the tidal flat area, while the landscape heterogeneity increased; (2) In the past 20 years, the areas of low and relatively low ecological risk in the study region were greatly reduced, while the areas of medium, relatively high, and high ecological risk greatly increased; the areas of high-grade ecological risk areas are mainly around Dongtai and Dafeng; (3) The area of ecological risk from low-grade to high-grade occupied 71.75% of the study area during 2000⁻2017. During the previous periods (2000⁻2004 and 2004⁻2008), the areas of low-grade ecological risk were transformed to areas of middle-grade ecological risk area, while during the later periods (2008⁻2013 and 2013⁻2017) there was a substantial increase in the proportion of areas of high-grade ecological risk. Our results complement the official database of coastal landscape planning, and provide important information for assessing the potential effects of MMLL processes on coastal environments.}, }
@article {pmid28602241, year = {2017}, author = {Giles, KL and McCornack, BP and Royer, TA and Elliott, NC}, title = {Incorporating biological control into IPM decision making.}, journal = {Current opinion in insect science}, volume = {20}, number = {}, pages = {84-89}, doi = {10.1016/j.cois.2017.03.009}, pmid = {28602241}, issn = {2214-5753}, mesh = {Animals ; Crop Production/methods ; *Decision Support Techniques ; Ecology ; Pest Control/methods ; Pest Control, Biological/*methods ; Plants ; }, abstract = {Of the many ways biological control can be incorporated into Integrated Pest Management (IPM) programs, natural enemy thresholds are arguably most easily adopted by stakeholders. Integration of natural enemy thresholds into IPM programs requires ecological and cost/benefit crop production data, threshold model validation, and an understanding of the socioeconomic factors that influence stakeholder decisions about biological control. These thresholds are more likely to be utilized by stakeholders when integrated into dynamic web-based IPM decision support systems that summarize pest management data and push site-specific biological control management recommendations to decision-makers. We highlight recent literature on topics related to natural enemy thresholds and how findings may allow pest suppression services to be incorporated into advanced IPM programs.}, }
@article {pmid30571696, year = {2018}, author = {Somveille, M and Firth, JA and Aplin, LM and Farine, DR and Sheldon, BC and Thompson, RN}, title = {Movement and conformity interact to establish local behavioural traditions in animal populations.}, journal = {PLoS computational biology}, volume = {14}, number = {12}, pages = {e1006647}, doi = {10.1371/journal.pcbi.1006647}, pmid = {30571696}, issn = {1553-7358}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Behavior, Animal ; Computational Biology ; Ecosystem ; England ; Learning ; *Models, Biological ; Models, Psychological ; Passeriformes/physiology ; Population Dynamics ; *Social Behavior ; }, abstract = {The social transmission of information is critical to the emergence of animal culture. Two processes are predicted to play key roles in how socially-transmitted information spreads in animal populations: the movement of individuals across the landscape and conformist social learning. We develop a model that, for the first time, explicitly integrates these processes to investigate their impacts on the spread of behavioural preferences. Our results reveal a strong interplay between movement and conformity in determining whether locally-variable traditions establish across a landscape or whether a single preference dominates the whole population. The model is able to replicate a real-world cultural diffusion experiment in great tits Parus major, but also allows for a range of predictions for the emergence of animal culture under various initial conditions, habitat structure and strength of conformist bias to be made. Integrating social behaviour with ecological variation will be important for understanding the stability and diversity of culture in animals.}, }
@article {pmid30055354, year = {2018}, author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andújar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP}, title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {1-11}, doi = {10.1016/j.ympev.2018.07.008}, pmid = {30055354}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; Base Sequence ; Coleoptera/classification/*genetics ; Databases, Genetic ; *Metagenomics ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.}, }
@article {pmid29334414, year = {2018}, author = {Fišer, C and Robinson, CT and Malard, F}, title = {Cryptic species as a window into the paradigm shift of the species concept.}, journal = {Molecular ecology}, volume = {27}, number = {3}, pages = {613-635}, doi = {10.1111/mec.14486}, pmid = {29334414}, issn = {1365-294X}, mesh = {Amphipoda/physiology ; Animals ; Biodiversity ; Databases as Topic ; *Genetic Speciation ; Phylogeny ; Species Specificity ; }, abstract = {The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new &quot;species&quot; paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a &quot;process&quot; counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.}, }
@article {pmid30208069, year = {2018}, author = {Mariac, C and Vigouroux, Y and Duponchelle, F and García-Dávila, C and Nunez, J and Desmarais, E and Renno, JF}, title = {Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0202976}, pmid = {30208069}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Fishes/*classification/genetics ; High-Throughput Nucleotide Sequencing ; Larva/*genetics ; }, abstract = {The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.}, }
@article {pmid29673182, year = {2018}, author = {Li, C and Liu, M and Hu, Y and Shi, T and Zong, M and Walter, MT}, title = {Assessing the Impact of Urbanization on Direct Runoff Using Improved Composite CN Method in a Large Urban Area.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {4}, pages = {}, pmid = {29673182}, issn = {1660-4601}, mesh = {China ; Geographic Information Systems ; Hydrology ; *Models, Theoretical ; Remote Sensing Technology ; Urbanization/*trends ; }, abstract = {Urbanization is one of the most widespread anthropogenic activities, which brings a range of physical and biochemical changes to hydrological system and processes. Increasing direct runoff caused by land use change has become a major challenge for urban ecological security. Reliable prediction of the quantity and rate of surface runoff is an inherently difficult and time-consuming task for large ungauged urban areas. In this study, we combined Geographic Information System and remote sensing technology with an improved Soil Conservation Service curve number model to evaluate the effects of land use change on direct runoff volume of the four-ring area in Shenyang, China, and analyzed trends of direct runoff at different scales. Through analyzing trends of direct runoff from 1984 to 2015 at different scales, we explored how urbanization and other potential factors affect direct runoff changes. Total direct runoff volume increased over time, and trends varied from the inner urban area to suburban area. Zones 1 and 2 had a tendency toward decreasing direct runoff volume and risks, while Zones 3 and 4 showed gradual increases at both regional and pixel scales. The most important influence on direct runoff change was urban surface change caused by urbanization. This study presents a framework for identifying hotspots of runoff increase, which can provide important guidance to urban managers in future green infrastructure planning, in the hopes of improving the security of urban water ecological patterns.}, }
@article {pmid30216600, year = {2018}, author = {Lennox, GD and Gardner, TA and Thomson, JR and Ferreira, J and Berenguer, E and Lees, AC and Mac Nally, R and Aragão, LEOC and Ferraz, SFB and Louzada, J and Moura, NG and Oliveira, VHF and Pardini, R and Solar, RRC and Vaz-de Mello, FZ and Vieira, ICG and Barlow, J}, title = {Second rate or a second chance? Assessing biomass and biodiversity recovery in regenerating Amazonian forests.}, journal = {Global change biology}, volume = {24}, number = {12}, pages = {5680-5694}, doi = {10.1111/gcb.14443}, pmid = {30216600}, issn = {1365-2486}, mesh = {Animals ; *Biodiversity ; *Biomass ; Birds/physiology ; Carbon Cycle ; Coleoptera/physiology ; Conservation of Natural Resources ; Datasets as Topic ; Ecosystem ; *Forests ; Trees ; Tropical Climate ; }, abstract = {Secondary forests (SFs) regenerating on previously deforested land account for large, expanding areas of tropical forest cover. Given that tropical forests rank among Earth's most important reservoirs of carbon and biodiversity, SFs play an increasingly pivotal role in the carbon cycle and as potential habitat for forest biota. Nevertheless, their capacity to regain the biotic attributes of undisturbed primary forests (UPFs) remains poorly understood. Here, we provide a comprehensive assessment of SF recovery, using extensive tropical biodiversity, biomass, and environmental datasets. These data, collected in 59 naturally regenerating SFs and 30 co-located UPFs in the eastern Amazon, cover >1,600 large- and small-stemmed plant, bird, and dung beetles species and a suite of forest structure, landscape context, and topoedaphic predictors. After up to 40 years of regeneration, the SFs we surveyed showed a high degree of biodiversity resilience, recovering, on average among taxa, 88% and 85% mean UPF species richness and composition, respectively. Across the first 20 years of succession, the period for which we have accurate SF age data, biomass recovered at 1.2% per year, equivalent to a carbon uptake rate of 2.25 Mg/ha per year, while, on average, species richness and composition recovered at 2.6% and 2.3% per year, respectively. For all taxonomic groups, biomass was strongly associated with SF species distributions. However, other variables describing habitat complexity-canopy cover and understory stem density-were equally important occurrence predictors for most taxa. Species responses to biomass revealed a successional transition at approximately 75 Mg/ha, marking the influx of high-conservation-value forest species. Overall, our results show that naturally regenerating SFs can accumulate substantial amounts of carbon and support many forest species. However, given that the surveyed SFs failed to return to a typical UPF state, SFs are not substitutes for UPFs.}, }
@article {pmid30713051, year = {2019}, author = {Reiczigel, J and Marozzi, M and Fábián, I and Rózsa, L}, title = {Biostatistics for Parasitologists - A Primer to Quantitative Parasitology.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2019.01.003}, pmid = {30713051}, issn = {1471-5007}, abstract = {The aggregated distributions of host-parasite systems require several different infection parameters to characterize them. We advise readers how to choose infection indices with clear and distinct biological interpretations, and recommend statistical tests to compare them across samples. A user-friendly and free software is available online to overcome technical difficulties.}, }
@article {pmid29936291, year = {2018}, author = {Venter, PC and Nitsche, F and Scherwass, A and Arndt, H}, title = {Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe.}, journal = {Protist}, volume = {169}, number = {4}, pages = {521-538}, doi = {10.1016/j.protis.2018.04.001}, pmid = {29936291}, issn = {1618-0941}, mesh = {Ciliophora/*classification ; *Databases, Factual/standards ; Databases, Genetic ; Europe ; *Grassland ; High-Throughput Nucleotide Sequencing ; Molecular Typing ; *Soil Microbiology ; }, abstract = {By measuring the change in soil protist communities, the effect of human land use on grasslands can be monitored to promote sustainable ecosystem functioning. Protists form the active link in the rhizosphere between the plant roots and higher trophic organisms; however, only few morphological species and their ecological values have yet been described in this context. To investigate the communicability between morphological and molecular databases used in the molecular barcoding of protists and in the biomonitoring of grassland soil, the present high-throughput sequencing (HTS) study (N=150) covered the area of central Europe (mesoscale) known to be well studied for ciliated protists. HTS delivered 2,404 unique reads identifying taxa in all major ciliophoran classes but exact reference matches were few. The study identified clear discrepancies between databases for well-studied taxa, where molecular databases contained multiple gene variants for single morphospecies of dominant taxa. Gene variants presented own biogeography - the eukaryotic microdiversity along gradients (e.g., land-use intensity, soil water). It is possible that many of the so called novel phylogenetic lineages and hidden diversity pointed out in environmental surveys could be evidence for the severe lack of molecular data for already known and morphologically described species, present in morphological databases.}, }
@article {pmid30695030, year = {2019}, author = {Yenni, GM and Christensen, EM and Bledsoe, EK and Supp, SR and Diaz, RM and White, EP and Ernest, SKM}, title = {Developing a modern data workflow for regularly updated data.}, journal = {PLoS biology}, volume = {17}, number = {1}, pages = {e3000125}, doi = {10.1371/journal.pbio.3000125}, pmid = {30695030}, issn = {1545-7885}, abstract = {Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.}, }
@article {pmid29930200, year = {2018}, author = {Venturelli, OS and Carr, AC and Fisher, G and Hsu, RH and Lau, R and Bowen, BP and Hromada, S and Northen, T and Arkin, AP}, title = {Deciphering microbial interactions in synthetic human gut microbiome communities.}, journal = {Molecular systems biology}, volume = {14}, number = {6}, pages = {e8157}, pmid = {29930200}, issn = {1744-4292}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Physiological Phenomena ; Computational Biology/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics ; *Microbial Interactions ; Models, Biological ; }, abstract = {The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.}, }
@article {pmid30413903, year = {2019}, author = {Sánchez-Giraldo, C and Daza, JM}, title = {Getting better temporal and spatial ecology data for threatened species: using lightweight GPS devices for small primate monitoring in the northern Andes of Colombia.}, journal = {Primates; journal of primatology}, volume = {60}, number = {1}, pages = {93-102}, doi = {10.1007/s10329-018-0696-1}, pmid = {30413903}, issn = {1610-7365}, mesh = {Animals ; Colombia ; Ecology/*methods ; Endangered Species ; Female ; Geographic Information Systems/*instrumentation ; *Homing Behavior ; Male ; Saguinus/*physiology ; }, abstract = {The use of GPS telemetry has been a reliable research tool for the study of primate biology in recent years. Although in the past technological restrictions limited its use mainly to large primates, recent improvements in battery size make it possible to use this technology for small species. We used GPS devices for monitoring two adult white-footed tamarins (Saguinus leucopus) from a free-ranging group, and assessed its applicability for recording spatial and ecological data. GPS devices were operational for 66 and 85 days, recording 221 positions (36.6% acquisition rate; 73% of which were highly accurate) and 3195 activity values for both individuals. Depending on the estimation method, we calculated the home range size for the group to be 19.4 and 22.9 ha, which were within the range for the species in other localities. The animals were active each day for 11 h, with high activity during the early morning. The monkeys showed a constant and alternate use of four sleeping sites with a limited reuse of the same site on consecutive nights. These daily activity and sleeping site use patterns are similar to those reported for other Saguinus species. Based on the kind and quality of the data recorded, we consider GPS telemetry to be an efficient and advantageous method for tracking and obtaining ecological information from S. leucopus. In comparison to other data collection methods, GPS telemetry required fewer personnel and less time commitment to record data without compromising the accuracy of the spatial and activity information we obtained.}, }
@article {pmid30651533, year = {2019}, author = {Perkins, DM and Perna, A and Adrian, R and Cermeño, P and Gaedke, U and Huete-Ortega, M and White, EP and Yvon-Durocher, G}, title = {Energetic equivalence underpins the size structure of tree and phytoplankton communities.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {255}, doi = {10.1038/s41467-018-08039-3}, pmid = {30651533}, issn = {2041-1723}, abstract = {The size structure of autotroph communities - the relative abundance of small vs. large individuals - shapes the functioning of ecosystems. Whether common mechanisms underpin the size structure of unicellular and multicellular autotrophs is, however, unknown. Using a global data compilation, we show that individual body masses in tree and phytoplankton communities follow power-law distributions and that the average exponents of these individual size distributions (ISD) differ. Phytoplankton communities are characterized by an average ISD exponent consistent with three-quarter-power scaling of metabolism with body mass and equivalence in energy use among mass classes. Tree communities deviate from this pattern in a manner consistent with equivalence in energy use among diameter size classes. Our findings suggest that whilst universal metabolic constraints ultimately underlie the emergent size structure of autotroph communities, divergent aspects of body size (volumetric vs. linear dimensions) shape the ecological outcome of metabolic scaling in forest vs. pelagic ecosystems.}, }
@article {pmid30016947, year = {2018}, author = {Song, Z and Stajich, JE and Xie, Y and Liu, X and He, Y and Chen, J and Hicks, GR and Wang, G}, title = {Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {541}, pmid = {30016947}, issn = {1471-2164}, support = {IOS-1027542//National Science Foundation/ ; CA-R-PPA-5062-H//National Institute of Food and Agriculture Hatch project/ ; 31670044//National Natural Science Foundation of China/ ; 91751115//National Natural Science Foundation of China/ ; S10 OD016290/OD/NIH HHS/United States ; # 2016YFA0601401//The National Key Research Program of China/ ; 201305022//National Marine Public Welfare Industry Special Scientific Research Project/ ; }, mesh = {Biosynthetic Pathways/genetics ; Docosahexaenoic Acids/*biosynthesis ; Ecological and Environmental Phenomena ; Fatty Acids, Unsaturated/biosynthesis ; Gene Ontology ; *Genome ; Genomics ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Stramenopiles/classification/enzymology/*genetics/metabolism ; }, abstract = {BACKGROUND: Thraustochytrids are unicellular fungal-like marine protists with ubiquitous existence in marine environments. They are well-known for their ability to produce high-valued omega-3 polyunsaturated fatty acids (ω-3-PUFAs) (e.g., docosahexaenoic acid (DHA)) and hydrolytic enzymes. Thraustochytrid biomass has been estimated to surpass that of bacterioplankton in both coastal and oceanic waters indicating they have an important role in microbial food-web. Nevertheless, the molecular pathway and regulatory network for PUFAs production and the molecular mechanisms underlying ecological functions of thraustochytrids remain largely unknown.<br><br>RESULTS: The genomes of two thraustochytrids strains (Mn4 and SW8) with ability to produce DHA were sequenced and assembled with a hybrid sequencing approach utilizing Illumina short paired-end reads and Pacific Biosciences long reads to generate a highly accurate genome assembly. Phylogenomic and comparative genomic analyses found that DHA-producing thraustochytrid strains were highly similar and possessed similar gene content. Analysis of the conventional fatty acid synthesis (FAS) and the polyketide synthase (PKS) systems for PUFAs production only detected incomplete and fragmentary pathways in the genome of these two strains. Surprisingly, secreted carbohydrate active enzymes (CAZymes) were found to be significantly depleted in the genomes of these 2 strains as compared to other sequenced relatives. Furthermore, these two strains possess an expanded gene repertoire for signal transduction and self-propelled movement, which could be important for their adaptations to dynamic marine environments.<br><br>CONCLUSIONS: Our results demonstrate the possibility of a third PUFAs synthesis pathway besides previously described FAS and PKS pathways encoded in the genome of these two thraustochytrid strains. Moreover, lack of a complete set of hydrolytic enzymatic machinery for degrading plant-derived organic materials suggests that these two DHA-producing strains play an important role as a nutritional source rather than a nutrient-producer in marine microbial-food web. Results of this study suggest the existence of two types of saprobic thraustochytrids in the world's ocean. The first group, which does not produce cellulosic enzymes and live as 'left-over' scavenger of bacterioplankton, serves as a dietary source for the plankton of higher trophic levels and the other possesses capacity to live on detrital organic matters in the marine ecosystems.}, }
@article {pmid30625219, year = {2019}, author = {Ožana, S and Burda, M and Hykel, M and Malina, M and Prášek, M and Bárta, D and Dolný, A}, title = {Dragonfly Hunter CZ: Mobile application for biological species recognition in citizen science.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210370}, doi = {10.1371/journal.pone.0210370}, pmid = {30625219}, issn = {1932-6203}, abstract = {Citizen science and data collected from various volunteers have an interesting potential in aiding the understanding of many biological and ecological processes. We describe a mobile application that allows the public to map and report occurrences of the odonata species (dragonflies and damselflies) found in the Czech Republic. The application also helps in species classification based on observation details such as date, GPS coordinates, and the altitude, biotope, suborder, and colour. Dragonfly Hunter CZ is a free Android application built on the open-source framework NativeScript using the JavaScript programming language which is now fully available on Google Play. The server side is powered by Apache Server with PHP and MariaDB SQL database. A mobile application is a fast and accurate way to obtain data pertaining to the odonata species, which can be used after expert verification for ecological studies and conservation basis like Red Lists and policy instruments. We expect it to be effective in encouraging Citizen Science and in promoting the proactive reporting of odonates. It can also be extended to the reporting and monitoring of other plant and animal species.}, }
@article {pmid30061690, year = {2018}, author = {Horsthemke, B}, title = {A critical view on transgenerational epigenetic inheritance in humans.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2973}, pmid = {30061690}, issn = {2041-1723}, mesh = {Animals ; Biological Evolution ; Culture ; *DNA Methylation ; Databases, Genetic ; Drosophila ; Ecology ; *Epigenesis, Genetic ; Gene-Environment Interaction ; Germ Cells ; Humans ; *Inheritance Patterns ; Models, Genetic ; Mutation ; Nematoda ; Phenotype ; Plants/genetics ; Proteome ; Proteomics ; }, abstract = {Transgenerational epigenetic inheritance refers to the transmission of epigenetic information through the germline. While it has been observed in plants, nematodes and fruit flies, its occurrence in mammals-and humans in particular-is the matter of controversial debate, mostly because the study of transgenerational epigenetic inheritance is confounded by genetic, ecological and cultural inheritance. In this comment, I discuss the phenomenon of transgenerational epigenetic inheritance and the difficulty of providing conclusive proof for it in experimental and observational studies.}, }
@article {pmid30061657, year = {2018}, author = {Butler, S and O'Dwyer, JP}, title = {Stability criteria for complex microbial communities.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2970}, pmid = {30061657}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology ; *Ecology ; *Microbiota ; Models, Biological ; Software ; *Symbiosis ; }, abstract = {Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated through the mechanism of crossfeeding. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, positive equilibria remain stable whenever mutualistic interactions are either sufficiently weak, or when all pairs of taxa reciprocate each other's assistance.}, }
@article {pmid29642940, year = {2018}, author = {Dai, Z and Coker, OO and Nakatsu, G and Wu, WKK and Zhao, L and Chen, Z and Chan, FKL and Kristiansen, K and Sung, JJY and Wong, SH and Yu, J}, title = {Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {70}, pmid = {29642940}, issn = {2049-2618}, support = {766613, 14106145, 14111216//RGC-GRF/International ; 2016YFC1303200//135 Program Project China/International ; 2013CB531401//973 Program China/International ; 2014BAI09B05//National Key Technology R&amp;D Program/International ; }, mesh = {Aged ; Bacteria/*classification/*genetics ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/diagnosis/*etiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Gene Ontology ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; }, abstract = {BACKGROUND: Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort the structure of microbial dysbiosis in CRC and lead to inconsistent results among studies. In this regard, our study targeted at exploring changes in gut microbiota that are universal across populations at species level.<br><br>RESULTS: Based on the combined analysis of 526 metagenomic samples from Chinese, Austrian, American, and German and French cohorts, seven CRC-enriched bacteria (Bacteroides fragilis, Fusobacterium nucleatum, Porphyromonas asaccharolytica, Parvimonas micra, Prevotella intermedia, Alistipes finegoldii, and Thermanaerovibrio acidaminovorans) have been identified across populations. The seven enriched bacterial markers classified cases from controls with an area under the receiver-operating characteristics curve (AUC) of 0.80 across the different populations. Abundance correlation analysis demonstrated that CRC-enriched and CRC-depleted bacteria respectively formed their own mutualistic networks, in which the latter was disjointed in CRC. The CRC-enriched bacteria have been found to be correlated with lipopolysaccharide and energy biosynthetic pathways.<br><br>CONCLUSIONS: Our study identified potential diagnostic bacterial markers that are robust across populations, indicating their potential universal use for non-invasive CRC diagnosis. We also elucidated the ecological networks and functional capacities of CRC-associated microbiota.}, }
@article {pmid28634367, year = {2017}, author = {Gao, X and Wang, C and Dai, W and Ren, S and Tao, F and He, X and Han, G and Wang, W}, title = {Proteomic analysis reveals large amounts of decomposition enzymes and major metabolic pathways involved in algicidal process of Trametes versicolor F21a.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3907}, pmid = {28634367}, issn = {2045-2322}, mesh = {*Antibiosis ; Biomass ; Chlorophyll/metabolism ; Chromatography, Liquid ; Computational Biology/methods ; Cyanobacteria ; Fungal Proteins/*metabolism ; Metabolic Networks and Pathways ; *Proteome ; *Proteomics/methods ; Tandem Mass Spectrometry ; Trametes/*metabolism ; }, abstract = {A recent algicidal mode indicates that fungal mycelia can wrap and eliminate almost all co-cultivated algal cells within a short time span. However, the underlying molecular mechanism is rarely understood. We applied proteomic analysis to investigate the algicidal process of Trametes versicolor F21a and identified 3,754 fungal proteins. Of these, 30 fungal enzymes with endo- or exoglycosidase activities such as β-1,3-glucanase, α-galactosidase, α-glucosidase, alginate lyase and chondroitin lyase were significantly up-regulated. These proteins belong to Glycoside Hydrolases, Auxiliary Activities, Carbohydrate Esterases and Polysaccharide Lyases, suggesting that these enzymes may degrade lipopolysaccharides, peptidoglycans and alginic acid of algal cells. Additionally, peptidase, exonuclease, manganese peroxidase and cytochrome c peroxidase, which decompose proteins and DNA or convert other small molecules of algal cells, could be other major decomposition enzymes. Gene Ontology and KEGG pathway enrichment analysis demonstrated that pyruvate metabolism and tricarboxylic acid cycle pathways play a critical role in response to adverse environment via increasing energy production to synthesize lytic enzymes or uptake molecules. Carbon metabolism, selenocompound metabolism, sulfur assimilation and metabolism, as well as several amino acid biosynthesis pathways could play vital roles in the synthesis of nutrients required by fungal mycelia.}, }
@article {pmid29602265, year = {2018}, author = {Stanford, BCM and Rogers, SM}, title = {R(NA)-tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {827-830}, doi = {10.1111/mec.14419}, pmid = {29602265}, issn = {1365-294X}, mesh = {Animals ; *Daphnia ; Ecology ; Gene Ontology ; Genomics ; *RNA, Messenger ; }, abstract = {A challenge of modern ecological genomics is reducing uncertainty surrounding the biological inferences from gene expression. For example, approximately 40% of proteins in eukaryotic model organisms do not contain characterized domains (Gollery et al., 2006). Even proteins of &quot;known function&quot; are typically only characterized in the sense that they have a domain function, but provide no information on their biological role within the cell (e.g., activation, pathways or targets). Yet, as molecular ecologists, a common objective is to elucidate how organisms respond to environmental variation through changes in gene expression, including homoeostatic, acclimatory, and adaptive responses to environmental stressors, a challenge increased by poor protein ecological annotation. Now, in this issue of Molecular Ecology, Orsini et al. (2017) use the quintessential Daphnia system to characterize the differences in stress response in three genotypic backgrounds to common biotic and abiotic stressors found in nature. Using an optimized weighted gene co-expression network analysis, they link genes of unknown function to genes that they co-activate with and enrich for gene ontology. Determining the functional networks of genes that behave in genotype- and treatment-specific responses gives insight into possible pathways and respective ecological roles, helping pave the way for the next generation of transcriptomic studies in molecular ecology.}, }
@article {pmid30568285, year = {2019}, author = {Strassburg, BBN and Beyer, HL and Crouzeilles, R and Iribarrem, A and Barros, F and de Siqueira, MF and Sánchez-Tapia, A and Balmford, A and Sansevero, JBB and Brancalion, PHS and Broadbent, EN and Chazdon, RL and Filho, AO and Gardner, TA and Gordon, A and Latawiec, A and Loyola, R and Metzger, JP and Mills, M and Possingham, HP and Rodrigues, RR and Scaramuzza, CAM and Scarano, FR and Tambosi, L and Uriarte, M}, title = {Strategic approaches to restoring ecosystems can triple conservation gains and halve costs.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {1}, pages = {62-70}, doi = {10.1038/s41559-018-0743-8}, pmid = {30568285}, issn = {2397-334X}, abstract = {International commitments for ecosystem restoration add up to one-quarter of the world's arable land. Fulfilling them would ease global challenges such as climate change and biodiversity decline but could displace food production and impose financial costs on farmers. Here, we present a restoration prioritization approach capable of revealing these synergies and trade-offs, incorporating ecological and economic efficiencies of scale and modelling specific policy options. Using an actual large-scale restoration target of the Atlantic Forest hotspot, we show that our approach can deliver an eightfold increase in cost-effectiveness for biodiversity conservation compared with a baseline of non-systematic restoration. A compromise solution avoids 26% of the biome's current extinction debt of 2,864 plant and animal species (an increase of 257% compared with the baseline). Moreover, this solution sequesters 1 billion tonnes of CO2-equivalent (a 105% increase) while reducing costs by US$28 billion (a 57% decrease). Seizing similar opportunities elsewhere would offer substantial contributions to some of the greatest challenges for humankind.}, }
@article {pmid30533308, year = {2018}, author = {Jenkins, MF and White, EP and Hurlbert, AH}, title = {The proportion of core species in a community varies with spatial scale and environmental heterogeneity.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6019}, pmid = {30533308}, issn = {2167-8359}, abstract = {Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species.}, }
@article {pmid30499218, year = {2018}, author = {Taylor, SD and Meiners, JM and Riemer, K and Orr, MC and White, EP}, title = {Comparison of large-scale citizen science data and long-term study data for phenology modeling.}, journal = {Ecology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ecy.2568}, pmid = {30499218}, issn = {0012-9658}, abstract = {Large-scale observational data from citizen science efforts are becoming increasingly common in ecology, and researchers often choose between these and data from intensive local-scale studies for their analyses. This choice has trade-offs related to spatial scale, observer variance, and inter-annual variability. Here we explored this issue with phenology by comparing models built using data from the large-scale, citizen science USA National Phenology Network (USANPN) effort with models built using data from more intensive studies at Long Term Ecological Research (LTER) sites. We built statistical and process based phenology models for species common to each dataset. From these models we compared parameter estimates, estimates of phenological events, and out-of-sample errors between models derived from both USA-NPN and LTER data. We found that model parameter estimates for the same species were most similar between the two datasets when using simple models, but parameter estimates varied widely as model complexity increased. Despite this, estimates for the date of phenological events and out-of-sample errors were similar, regardless of the model. Predictions for USA-NPN data had the lowest error using models built from the USA-NPN data, while LTER predictions were best made using LTER-derived models, confirming that models perform best when applied at the same scale they were built. This difference in the cross-scale model comparison is likely due to variation in phenological requirements within species. Models using the USA-NPN dataset can integrate parameters over a large spatial scale while those using an LTER dataset can only estimate parameters for a single location. Accordingly, the choice of dataset depends on the research question. Inferences about species-specific phenological requirements are best made with LTER data, and if USA-NPN or similar data are all that is available, then analyses should be limited to simple models. Large-scale predictive modeling is best done with the larger-scale USA-NPN data, which has high spatial representation and a large regional species pool. LTER datasets, on the other hand, have high site fidelity and thus characterize inter-annual variability extremely well. Future research aimed at forecasting phenology events for particular species over larger scales should develop models which integrate the strengths of both datasets. This article is protected by copyright. All rights reserved.}, }
@article {pmid30446752, year = {2018}, author = {Felipe-Lucia, MR and Soliveres, S and Penone, C and Manning, P and van der Plas, F and Boch, S and Prati, D and Ammer, C and Schall, P and Gossner, MM and Bauhus, J and Buscot, F and Blaser, S and Blüthgen, N and de Frutos, A and Ehbrecht, M and Frank, K and Goldmann, K and Hänsel, F and Jung, K and Kahl, T and Nauss, T and Oelmann, Y and Pena, R and Polle, A and Renner, S and Schloter, M and Schöning, I and Schrumpf, M and Schulze, ED and Solly, E and Sorkau, E and Stempfhuber, B and Tschapka, M and Weisser, WW and Wubet, T and Fischer, M and Allan, E}, title = {Multiple forest attributes underpin the supply of multiple ecosystem services.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4839}, pmid = {30446752}, issn = {2041-1723}, mesh = {Conservation of Natural Resources/*methods ; Ecosystem ; Europe ; Forestry/*methods/trends ; *Forests ; Humans ; Trees/*physiology ; }, abstract = {Trade-offs and synergies in the supply of forest ecosystem services are common but the drivers of these relationships are poorly understood. To guide management that seeks to promote multiple services, we investigated the relationships between 12 stand-level forest attributes, including structure, composition, heterogeneity and plant diversity, plus 4 environmental factors, and proxies for 14 ecosystem services in 150 temperate forest plots. Our results show that forest attributes are the best predictors of most ecosystem services and are also good predictors of several synergies and trade-offs between services. Environmental factors also play an important role, mostly in combination with forest attributes. Our study suggests that managing forests to increase structural heterogeneity, maintain large trees, and canopy gaps would promote the supply of multiple ecosystem services. These results highlight the potential for forest management to encourage multifunctional forests and suggest that a coordinated landscape-scale strategy could help to mitigate trade-offs in human-dominated landscapes.}, }
@article {pmid30431668, year = {2018}, author = {Portnoy, GA and Relyea, MR and Decker, S and Shamaskin-Garroway, A and Driscoll, M and Brandt, CA and Haskell, SG}, title = {Understanding Gender Differences in Resilience Among Veterans: Trauma History and Social Ecology.}, journal = {Journal of traumatic stress}, volume = {31}, number = {6}, pages = {845-855}, doi = {10.1002/jts.22341}, pmid = {30431668}, issn = {1573-6598}, support = {VA IIR 12-118//Health Services Research and Development/ ; }, abstract = {A social-ecological framework for resilience underscores the importance of conceptualizing individuals embedded within their context when evaluating a person's vulnerability and adaptation to stress. Despite a high level of trauma exposure, most veterans exhibit psychological resilience following a traumatic event. Interpersonal trauma is associated with poorer psychological outcomes than noninterpersonal trauma and is experienced more frequently across the lifespan by women as compared to men. In the present study, we examined gender differences in trauma exposure, resilience, and protective factors among veterans. Participants included 665 veterans who completed a baseline survey assessing traumatic events; 544 veterans (81.8%) completed a 1-year follow-up survey assessing resilience, combat exposure, deployment social support, deployment preparedness, and military sexual trauma (MST). Principal component analyses revealed the Traumatic Life Events Questionnaire categorized into four meaningful components: sexual abuse, interpersonal violence, stranger violence, and accidents/unexpected trauma. Women reported greater exposure to sexual abuse, d = 0.76; interpersonal violence, d = 0.31; and MST, Cramer's V = 0.54; men reported greater exposure to stranger violence, accidents/unexpected trauma, and combat exposure, ds = 0.24-0.55. Compared to women, men also reported greater social support during deployment, d = 0.46. Hierarchical linear regression indicated that men's resilience scores were higher than women's, β = .10, p = .032, yet this association was no longer significant once we accounted for trauma type, β = .07, p = .197. Results indicate that trauma type is central to resilience and suggest one must consider the social-ecological context that can promote or inhibit resilient processes.}, }
@article {pmid30417109, year = {2018}, author = {Mazel, F and Davis, KM and Loudon, A and Kwong, WK and Groussin, M and Parfrey, LW}, title = {Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, pmid = {30417109}, issn = {2379-5077}, abstract = {Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as &quot;phylosymbiosis.&quot; Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.}, }
@article {pmid30413098, year = {2018}, author = {Trotter, RT and Lininger, MR and Camplain, R and Fofanov, VY and Camplain, C and Baldwin, JA}, title = {A Survey of Health Disparities, Social Determinants of Health, and Converging Morbidities in a County Jail: A Cultural-Ecological Assessment of Health Conditions in Jail Populations.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {11}, pages = {}, pmid = {30413098}, issn = {1660-4601}, support = {N/A//NARBHA Institute/ ; U54MD012388/MD/NIMHD NIH HHS/United States ; }, abstract = {The environmental health status of jail populations in the United States constitutes a significant public health threat for prisoners and the general population. The ecology of jails creates a dynamic condition in relation to general population health due to the concentrated potential exposure to infectious diseases, difficult access to treatment for chronic health conditions, interruption in continuity of care for serious behavioral health conditions, as well as on-going issues for the prevention and treatment of substance abuse disorders. This paper reports on elements of a cross-sectional survey embedded in a parent project, &quot;Health Disparities in Jail Populations.&quot; The overall project includes a comprehensive secondary data analysis of the health status of county jail populations, along with primary data collection that includes a cross-sectional health and health care services survey of incarcerated individuals, coupled with collection of biological samples to investigate infectious disease characteristics of a county jail population. This paper reports on the primary results of the survey data collection that indicate that this is a population with complex and interacting co-morbidities, as well as significant health disparities compared to the general population.}, }
@article {pmid30410743, year = {2018}, author = {Munos, MK and Maiga, A and Do, M and Sika, GL and Carter, ED and Mosso, R and Dosso, A and Leyton, A and Khan, SM}, title = {Linking household survey and health facility data for effective coverage measures: a comparison of ecological and individual linking methods using the Multiple Indicator Cluster Survey in Côte d'Ivoire.}, journal = {Journal of global health}, volume = {8}, number = {2}, pages = {020803}, pmid = {30410743}, issn = {2047-2986}, mesh = {Adolescent ; Adult ; Child, Preschool ; Cote d'Ivoire ; Ecology ; Feasibility Studies ; Female ; *Health Care Surveys ; Health Services Needs and Demand ; Humans ; Infant ; Infant, Newborn ; Information Storage and Retrieval/*methods ; *Medical Record Linkage ; Middle Aged ; Patient Acceptance of Health Care/*statistics &amp; numerical data ; Pregnancy ; Quality of Health Care ; Reproducibility of Results ; Young Adult ; }, abstract = {Background: Population-based measures of intervention coverage are used in low- and middle-income countries for program planning, prioritization, and evaluation. There is increased interest in effective coverage, which integrates information about service quality or health outcomes. Approaches proposed for quality-adjusted effective coverage include linking data on need and service contact from population-based surveys with data on service quality from health facility surveys. However, there is limited evidence about the validity of different linking methods for effective coverage estimation.<br><br>Methods: We collaborated with the 2016 Côte d'Ivoire Multiple Indicator Cluster Survey (MICS) to link data from a health provider assessment to care-seeking data collected by the MICS in the Savanes region of Côte d'Ivoire. The provider assessment was conducted in a census of public and non-public health facilities and pharmacies in Savanes in May-June 2016. We also included community health workers managing sick children who served the clusters sampled for the MICS. The provider assessment collected information on structural and process quality for antenatal care, delivery and immediate newborn care, postnatal care, and sick child care. We linked the MICS and provider data using exact-match and ecological linking methods, including aggregate linking and geolinking methods. We compared the results obtained from exact-match and ecological methods.<br><br>Results: We linked 731 of 786 care-seeking episodes (93%) from the MICS to a structural quality score for the provider named by the respondent. Effective coverage estimates computed using exact-match methods were 13%-63% lower than the care-seeking estimates from the MICS. Absolute differences between exact match and ecological linking methods were ±7 percentage points for all ecological methods. Incorporating adjustments for provider category and weighting by service-specific utilization into the ecological methods generally resulted in better agreement between ecological and exact match estimates.<br><br>Conclusions: Ecological linking may be a feasible and valid approach for estimating quality-adjusted effective coverage when a census of providers is used. Adjusting for provider type and caseload may improve agreement with exact match results. There remain methodological questions to be addressed to develop guidance on using linking methods for estimating quality-adjusted effective coverage, including the effect of facility sampling and time displacement.}, }
@article {pmid30384907, year = {2018}, author = {Bamisile, BS and Dash, CK and Akutse, KS and Keppanan, R and Afolabi, OG and Hussain, M and Qasim, M and Wang, L}, title = {Prospects of endophytic fungal entomopathogens as biocontrol and plant growth promoting agents: An insight on how artificial inoculation methods affect endophytic colonization of host plants.}, journal = {Microbiological research}, volume = {217}, number = {}, pages = {34-50}, doi = {10.1016/j.micres.2018.08.016}, pmid = {30384907}, issn = {1618-0623}, mesh = {*Agricultural Inoculants ; Animals ; Beauveria/physiology ; Biological Control Agents/*pharmacology ; Databases, Factual ; Endophytes/growth &amp; development/*physiology ; Host-Pathogen Interactions/physiology ; Insecta/drug effects ; Pest Control, Biological/*methods ; *Plant Development ; Plant Diseases/microbiology/*prevention &amp; control ; Plant Roots/microbiology ; Plant Stems/microbiology ; Plants/*microbiology ; Seedlings/microbiology ; Soil ; Sorghum/microbiology ; }, abstract = {Entomopathogenic fungi (EPF) can be established as endophytes in the host plants to offer a long-term preventive measure for pests and diseases. This practice serves as a better alternative to the common practice of periodic direct application of EPF on plants or the target pests as a short-term defense strategy against pests and diseases. These fungal endophytes, aside from their role in pests and diseases prevention, also act as plant growth promoters. Several fungal endophytes have been associated with improvement in plant height, dry and wet weight and other growth parameters. However, many limiting factors have been identified as mitigating the successful colonization of the host plants by EPF. The inoculation methods used have been identified as one, but sadly, this has received little or less attention. Some previous studies carried out comparison between various artificial inoculation methods; foliar application, seedling dipping, soil drenching, seed inoculation, direct injection and others. In separate studies, some authors had suggested different application methods that are best suitable for certain fungal entomopathogens. For instance, leaf inoculation with conidial suspensions was suggested to be the best inoculation method for Beauveria bassiana in sorghum, stem injection was suggested as the most suitable for coffee, while, root dipping method proved the most successful for B. bassiana colonization of tomato plants for the management of Helicoverpa armigera. Here, we discussed entomopathogenic fungal endophytes as bio-control agents, plant growth promoters and highlighted the effect of various artificial inoculation methods on their endophytic colonization of the host plants.}, }
@article {pmid30366399, year = {2018}, author = {Meng, X and Wang, F and Xie, Y and Song, G and Ma, S and Hu, S and Bai, J and Yang, Y}, title = {An Ontology-Driven Approach for Integrating Intelligence to Manage Human and Ecological Health Risks in the Geospatial Sensor Web.}, journal = {Sensors (Basel, Switzerland)}, volume = {18}, number = {11}, pages = {}, pmid = {30366399}, issn = {1424-8220}, support = {41501441//National Natural Science Foundation of China/ ; 2014HB04//Hubei Provincial Environment Protection Project/ ; GDGTKJ2017001//Guangdong Provincial Land Resource Research Project/ ; 2042017kf0212//Wuhan University Grant/ ; }, mesh = {Ecology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; Intelligence ; Software ; }, abstract = {Due to the rapid installation of a massive number of fixed and mobile sensors, monitoring machines are intentionally or unintentionally involved in the production of a large amount of geospatial data. Environmental sensors and related software applications are rapidly altering human lifestyles and even impacting ecological and human health. However, there are rarely specific geospatial sensor web (GSW) applications for certain ecological public health questions. In this paper, we propose an ontology-driven approach for integrating intelligence to manage human and ecological health risks in the GSW. We design a Human and Ecological health Risks Ontology (HERO) based on a semantic sensor network ontology template. We also illustrate a web-based prototype, the Human and Ecological Health Risk Management System (HaEHMS), which helps health experts and decision makers to estimate human and ecological health risks. We demonstrate this intelligent system through a case study of automatic prediction of air quality and related health risk.}, }
@article {pmid30344120, year = {2018}, author = {Gopalakrishnan, S and Sinding, MS and Ramos-Madrigal, J and Niemann, J and Samaniego Castruita, JA and Vieira, FG and Carøe, C and Montero, MM and Kuderna, L and Serres, A and González-Basallote, VM and Liu, YH and Wang, GD and Marques-Bonet, T and Mirarab, S and Fernandes, C and Gaubert, P and Koepfli, KP and Budd, J and Rueness, EK and Heide-Jørgensen, MP and Petersen, B and Sicheritz-Ponten, T and Bachmann, L and Wiig, Ø and Hansen, AJ and Gilbert, MTP}, title = {Interspecific Gene Flow Shaped the Evolution of the Genus Canis.}, journal = {Current biology : CB}, volume = {28}, number = {21}, pages = {3441-3449.e5}, pmid = {30344120}, issn = {1879-0445}, support = {U01 MH106874/MH/NIMH NIH HHS/United States ; }, abstract = {The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a &quot;ghost&quot; basal canid lineage.}, }
@article {pmid30269263, year = {2018}, author = {Li, W and Liu, S and Pei, Y and He, J and Wang, Q}, title = {Zoning for eco-geological environment before mining in Yushenfu mining area, northern Shaanxi, China.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {10}, pages = {619}, pmid = {30269263}, issn = {1573-2959}, support = {2015CB251601//the National Basic Research Program of China (973 Program)/ ; 41430643//the State Key Program of the National Natural Science Foundation of China/ ; }, mesh = {China ; Ecology/*methods ; Ecosystem ; Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geology ; Groundwater ; *Mining ; Remote Sensing Technology/methods ; }, abstract = {Zoning for the eco-geological environment (EGE) aims to protect and improve the regional ecological environment. It is the basis for evaluating the ecological characteristics of a mining area prior to mining activities and has the purpose of implementing water-preserved mining according to zoning type. In this study, four EGE types were proposed following field investigation in the Yushenfu mining area: oasis type with phreatic water and bottomland in desert (OTPWBD), oasis type with surface water and valley river (OTSWVR), loess gully type with surface runoff (LGTSR), and regional deep groundwater enrichment type (RDGET). Nine EGE evaluation indices were selected: rainfall, evaporation capacity, Luohe formation thickness, surface elevation, Sara Wusu aquifer water abundance, surface lithology, topography, slope, and normalized difference vegetation index (NDVI). Remote sensing technology and geographic information systems were first used to generate the evaluation index thematic maps. Then, the weight of each evaluation index was determined based on an analytic hierarchy process (AHP). Third, the index weight was used to form an improved weighted fuzzy C s clustering algorithm, and EGE zones were assigned using the MATLAB computing platform. For comparison, the AHP was also adopted for EGE zoning and a map of zoning differences was obtained. Finally, EGE field surveys of typical mines were carried out, which verified that EGE zoning using fuzzy clustering was accurate and reasonable.}, }
@article {pmid30262689, year = {2018}, author = {Song, H and Zhang, YX and Yang, MJ and Sun, JC and Zhang, T and Wang, HY}, title = {Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale.}, journal = {Journal of genetics}, volume = {97}, number = {4}, pages = {e79-e86}, pmid = {30262689}, issn = {0973-7731}, mesh = {Animals ; China ; Computational Biology ; Gastropoda/*genetics ; Genetic Variation ; Genome/*genetics ; *Genomics ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats/*genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {The veined rapa whelk (Rapana venosa) is an economically important gastropod in China, but is considered as an invasive species globally. Only a few studies have examined the R. venosa genome, a genomewide survey is necessary for improving our understanding of the genome structure and size of this organism. Microsatellite markers are powerful tools for characterizing germplasms, genetic diversity and kinship among individuals. The resultant data are applicable to breeding efforts in commercial aquaculture or for understanding invasion mechanisms. Here, we investigated the genome structure of R. venosa on an Illumina Hi-seq platform with ∼92× sequencing depth. We performed a K-mer analysis to estimate genome size, repeat sequences and heterozygosity. Clean reads were de novo assembled for the identification of simple-sequence repeat (SSR) loci that are suitable as markers. The estimated genome size of R. venosa was 2200.07 Mb, with a 1.41% heterozygosity rate and 67.04% repeats. We detected 5,477,450 simple-sequence repeats (SSRs), with 3,400,602 loci present as pure tandem repeats and 2,076,848 as compound motifs. We further selected and characterized 28 polymorphic markers in 78 individuals from Dandong, Laizhou, Weihai and Zhoushan in China. The range of alleles was 2-28 and the observed heterozygosity was 0.2857-0.8676. The data obtained from our genomic survey will aid the design of R. venosa whole-genome sequencing projects and advance the identification of SSR markers. Both these developments are valuable for further studies on ecological, evolutionary and genetic breeding in R. venosa.}, }
@article {pmid30258229, year = {2018}, author = {Bjorkman, AD and Myers-Smith, IH and Elmendorf, SC and Normand, S and Rüger, N and Beck, PSA and Blach-Overgaard, A and Blok, D and Cornelissen, JHC and Forbes, BC and Georges, D and Goetz, SJ and Guay, KC and Henry, GHR and HilleRisLambers, J and Hollister, RD and Karger, DN and Kattge, J and Manning, P and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Thomas, HJD and Vellend, M and Wilmking, M and Wipf, S and Carbognani, M and Hermanutz, L and Lévesque, E and Molau, U and Petraglia, A and Soudzilovskaia, NA and Spasojevic, MJ and Tomaselli, M and Vowles, T and Alatalo, JM and Alexander, HD and Anadon-Rosell, A and Angers-Blondin, S and Beest, MT and Berner, L and Björk, RG and Buchwal, A and Buras, A and Christie, K and Cooper, EJ and Dullinger, S and Elberling, B and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Harper, KA and Heijmans, MMPD and Hudson, J and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Johnstone, JF and Jørgensen, RH and Kaarlejärvi, E and Klady, R and Kuleza, S and Kulonen, A and Lamarque, LJ and Lantz, T and Little, CJ and Speed, JDM and Michelsen, A and Milbau, A and Nabe-Nielsen, J and Nielsen, SS and Ninot, JM and Oberbauer, SF and Olofsson, J and Onipchenko, VG and Rumpf, SB and Semenchuk, P and Shetti, R and Collier, LS and Street, LE and Suding, KN and Tape, KD and Trant, A and Treier, UA and Tremblay, JP and Tremblay, M and Venn, S and Weijers, S and Zamin, T and Boulanger-Lapointe, N and Gould, WA and Hik, DS and Hofgaard, A and Jónsdóttir, IS and Jorgenson, J and Klein, J and Magnusson, B and Tweedie, C and Wookey, PA and Bahn, M and Blonder, B and van Bodegom, PM and Bond-Lamberty, B and Campetella, G and Cerabolini, BEL and Chapin, FS and Cornwell, WK and Craine, J and Dainese, M and de Vries, FT and Díaz, S and Enquist, BJ and Green, W and Milla, R and Niinemets, Ü and Onoda, Y and Ordoñez, JC and Ozinga, WA and Penuelas, J and Poorter, H and Poschlod, P and Reich, PB and Sandel, B and Schamp, B and Sheremetev, S and Weiher, E}, title = {Plant functional trait change across a warming tundra biome.}, journal = {Nature}, volume = {562}, number = {7725}, pages = {57-62}, doi = {10.1038/s41586-018-0563-7}, pmid = {30258229}, issn = {1476-4687}, abstract = {The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature-trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.}, }
@article {pmid30194403, year = {2018}, author = {Rokas, A and Wisecaver, JH and Lind, AL}, title = {The birth, evolution and death of metabolic gene clusters in fungi.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {12}, pages = {731-744}, doi = {10.1038/s41579-018-0075-3}, pmid = {30194403}, issn = {1740-1534}, abstract = {Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.}, }
@article {pmid30181062, year = {2018}, author = {de Jonge, PA and Nobrega, FL and Brouns, SJJ and Dutilh, BE}, title = {Molecular and Evolutionary Determinants of Bacteriophage Host Range.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2018.08.006}, pmid = {30181062}, issn = {1878-4380}, abstract = {The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.}, }
@article {pmid30156039, year = {2018}, author = {An, S and Zhu, X and Shen, M and Wang, Y and Cao, R and Chen, X and Yang, W and Chen, J and Tang, Y}, title = {Mismatch in elevational shifts between satellite observed vegetation greenness and temperature isolines during 2000-2016 on the Tibetan Plateau.}, journal = {Global change biology}, volume = {24}, number = {11}, pages = {5411-5425}, doi = {10.1111/gcb.14432}, pmid = {30156039}, issn = {1365-2486}, abstract = {Climate warming on the Tibetan Plateau tends to induce an uphill shift of temperature isolines. Observations and process-based models have both shown that climate warming has resulted in an increase in vegetation greenness on the Tibetan Plateau in recent decades. However, it is unclear whether the uphill shift of temperature isolines has caused greenness isolines to shift upward and whether the two shifts match each other. Our analysis of satellite observed vegetation greenness during the growing season (May-Sep) and gridded climate data for 2000-2016 documented a substantial mismatch between the elevational shifts of greenness and temperature isolines. This mismatch is probably associated with a lagging response of greenness to temperature change and with the elevational gradient of greenness. The lagging response of greenness may be associated with water limitation, resources availability, and acclimation. This lag may weaken carbon sequestration by Tibetan ecosystems, given that greenness is closely related to primary carbon uptake and ecosystem respiration increases exponentially with temperature. We also found that differences in terrain slope angle accounted for large spatial variations in the elevational gradient of greenness and thus the velocity of elevational shifts of greenness isolines and the sensitivity of elevational shifts of greenness isolines to temperature, highlighting the role of terrain effects on the elevational shifts of greenness isolines. The mismatches and the terrain effect found in this study suggest that there is potentially large micro-topographical difference in response and acclimation/adaptation of greenness to temperature changes in plants. More widespread in situ measurements and fine-resolution remote sensing observations and fine-gridded climate data are required to attribute the mismatch to specific environmental drivers and ecological processes such as vertical changes in community structure, plant physiology, and distribution of species.}, }
@article {pmid30147447, year = {2018}, author = {Dornelas, M and Antão, LH and Moyes, F and Bates, AE and Magurran, AE and Adam, D and Akhmetzhanova, AA and Appeltans, W and Arcos, JM and Arnold, H and Ayyappan, N and Badihi, G and Baird, AH and Barbosa, M and Barreto, TE and Bässler, C and Bellgrove, A and Belmaker, J and Benedetti-Cecchi, L and Bett, BJ and Bjorkman, AD and Błażewicz, M and Blowes, SA and Bloch, CP and Bonebrake, TC and Boyd, S and Bradford, M and Brooks, AJ and Brown, JH and Bruelheide, H and Budy, P and Carvalho, F and Castañeda-Moya, E and Chen, CA and Chamblee, JF and Chase, TJ and Siegwart Collier, L and Collinge, SK and Condit, R and Cooper, EJ and Cornelissen, JHC and Cotano, U and Kyle Crow, S and Damasceno, G and Davies, CH and Davis, RA and Day, FP and Degraer, S and Doherty, TS and Dunn, TE and Durigan, G and Duffy, JE and Edelist, D and Edgar, GJ and Elahi, R and Elmendorf, SC and Enemar, A and Ernest, SKM and Escribano, R and Estiarte, M and Evans, BS and Fan, TY and Turini Farah, F and Loureiro Fernandes, L and Farneda, FZ and Fidelis, A and Fitt, R and Fosaa, AM and Daher Correa Franco, GA and Frank, GE and Fraser, WR and García, H and Cazzolla Gatti, R and Givan, O and Gorgone-Barbosa, E and Gould, WA and Gries, C and Grossman, GD and Gutierréz, JR and Hale, S and Harmon, ME and Harte, J and Haskins, G and Henshaw, DL and Hermanutz, L and Hidalgo, P and Higuchi, P and Hoey, A and Van Hoey, G and Hofgaard, A and Holeck, K and Hollister, RD and Holmes, R and Hoogenboom, M and Hsieh, CH and Hubbell, SP and Huettmann, F and Huffard, CL and Hurlbert, AH and Macedo Ivanauskas, N and Janík, D and Jandt, U and Jażdżewska, A and Johannessen, T and Johnstone, J and Jones, J and Jones, FAM and Kang, J and Kartawijaya, T and Keeley, EC and Kelt, DA and Kinnear, R and Klanderud, K and Knutsen, H and Koenig, CC and Kortz, AR and Král, K and Kuhnz, LA and Kuo, CY and Kushner, DJ and Laguionie-Marchais, C and Lancaster, LT and Min Lee, C and Lefcheck, JS and Lévesque, E and Lightfoot, D and Lloret, F and Lloyd, JD and López-Baucells, A and Louzao, M and Madin, JS and Magnússon, B and Malamud, S and Matthews, I and McFarland, KP and McGill, B and McKnight, D and McLarney, WO and Meador, J and Meserve, PL and Metcalfe, DJ and Meyer, CFJ and Michelsen, A and Milchakova, N and Moens, T and Moland, E and Moore, J and Mathias Moreira, C and Müller, J and Murphy, G and Myers-Smith, IH and Myster, RW and Naumov, A and Neat, F and Nelson, JA and Paul Nelson, M and Newton, SF and Norden, N and Oliver, JC and Olsen, EM and Onipchenko, VG and Pabis, K and Pabst, RJ and Paquette, A and Pardede, S and Paterson, DM and Pélissier, R and Peñuelas, J and Pérez-Matus, A and Pizarro, O and Pomati, F and Post, E and Prins, HHT and Priscu, JC and Provoost, P and Prudic, KL and Pulliainen, E and Ramesh, BR and Mendivil Ramos, O and Rassweiler, A and Rebelo, JE and Reed, DC and Reich, PB and Remillard, SM and Richardson, AJ and Richardson, JP and van Rijn, I and Rocha, R and Rivera-Monroy, VH and Rixen, C and Robinson, KP and Ribeiro Rodrigues, R and de Cerqueira Rossa-Feres, D and Rudstam, L and Ruhl, H and Ruz, CS and Sampaio, EM and Rybicki, N and Rypel, A and Sal, S and Salgado, B and Santos, FAM and Savassi-Coutinho, AP and Scanga, S and Schmidt, J and Schooley, R and Setiawan, F and Shao, KT and Shaver, GR and Sherman, S and Sherry, TW and Siciński, J and Sievers, C and da Silva, AC and Rodrigues da Silva, F and Silveira, FL and Slingsby, J and Smart, T and Snell, SJ and Soudzilovskaia, NA and Souza, GBG and Maluf Souza, F and Castro Souza, V and Stallings, CD and Stanforth, R and Stanley, EH and Mauro Sterza, J and Stevens, M and Stuart-Smith, R and Rondon Suarez, Y and Supp, S and Yoshio Tamashiro, J and Tarigan, S and Thiede, GP and Thorn, S and Tolvanen, A and Teresa Zugliani Toniato, M and Totland, Ø and Twilley, RR and Vaitkus, G and Valdivia, N and Vallejo, MI and Valone, TJ and Van Colen, C and Vanaverbeke, J and Venturoli, F and Verheye, HM and Vianna, M and Vieira, RP and Vrška, T and Quang Vu, C and Van Vu, L and Waide, RB and Waldock, C and Watts, D and Webb, S and Wesołowski, T and White, EP and Widdicombe, CE and Wilgers, D and Williams, R and Williams, SB and Williamson, M and Willig, MR and Willis, TJ and Wipf, S and Woods, KD and Woehler, EJ and Zawada, K and Zettler, ML and Hickler, T}, title = {BioTIME: A database of biodiversity time series for the Anthropocene.}, journal = {Global ecology and biogeography : a journal of macroecology}, volume = {27}, number = {7}, pages = {760-786}, pmid = {30147447}, issn = {1466-822X}, support = {//Wellcome Trust/United Kingdom ; 250189//European Research Council/International ; }, abstract = {Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.<br><br>The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.<br><br>Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).<br><br>Time period and grain: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.<br><br>BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.<br><br>Software format: .csv and .SQL.}, }
@article {pmid30145518, year = {2018}, author = {D'Alessandro, M and Esposito, V and Porporato, EMD and Berto, D and Renzi, M and Giacobbe, S and Scotti, G and Consoli, P and Valastro, G and Andaloro, F and Romeo, T}, title = {Relationships between plastic litter and chemical pollutants on benthic biodiversity.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {242}, number = {Pt B}, pages = {1546-1556}, doi = {10.1016/j.envpol.2018.08.002}, pmid = {30145518}, issn = {1873-6424}, mesh = {Animals ; *Biodiversity ; Ecology ; Environmental Monitoring ; Introduced Species ; Mediterranean Sea ; Mollusca/classification ; Plastics/*analysis ; Polychaeta/classification ; Water Pollutants, Chemical/*analysis ; }, abstract = {Five Descriptors (D) of Marine Strategy Framework Directive (MSFD): marine litter (D10), non-indigenous species (D2) and organic and inorganic pollutants (D8), were estimated in a coastal area of GSA 16 (Augusta harbour, Central Mediterranean Sea) in order to study their effects on the biodiversity (D1) of the benthic community D6) and to improve data for the MSFD. Investigation of plastic debris had led to the identification of 38 fragments divided into four categories, among which microplastics resulted as the most abundant. Six non-indigenous species, belonging to Polychaeta (Kirkegaardia dorsobranchialis, Notomastus aberans, Pista unibranchia, Pseudonereis anomala, Branchiomma bairdi) and Mollusca (Brachidontes pharaonis) were found. Biodiversity and benthic indices suggested a generalised, slightly disturbed ecological status. Anthracene, Zinc and Chrome were the most abundant chemical compounds in analysed sediments. Significant correlations were found between the abundance of trace elements vs biotic indices and between plastic debris vs biodiversity and benthic indices. This study represents the first report about the abundance of plastic debris and its relationship to contaminants and infauna in Augusta harbour. Our results can provide useful information for national and international laws and directives.}, }
@article {pmid30108295, year = {2018}, author = {Liebhold, AM and Yamanaka, T and Roques, A and Augustin, S and Chown, SL and Brockerhoff, EG and Pyšek, P}, title = {Plant diversity drives global patterns of insect invasions.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12095}, pmid = {30108295}, issn = {2045-2322}, abstract = {During the last two centuries, thousands of insect species have been transported (largely inadvertently) and established outside of their native ranges worldwide, some with catastrophic ecological and economic impacts. Global variation in numbers of invading species depends on geographic variation in propagule pressure and heterogeneity of environmental resistance to invasions. Elton's diversity-invasibility hypothesis, proposed over sixty years ago, has been widely explored for plants but little is known on how biodiversity affects insect invasions. Here we use species inventories from 44 land areas, ranging from small oceanic islands to entire continents in various world regions, to show that numbers of established insect species are primarily driven by diversity of plants, with both native and non-native plant species richness being the strongest predictor of insect invasions. We find that at large spatial scales, plant diversity directly explains variation in non-native insect species richness among world regions, while geographic factors such as land area, climate and insularity largely affect insect invasions indirectly via their effects on local plant richness.}, }
@article {pmid30107371, year = {2018}, author = {Wang, Q and Xiong, X and Wang, X and Tu, Q and Li, J and Ding, X and Li, Y and Huang, P and He, S and Yin, Y and Yang, H}, title = {Suckling Piglet Intestinal Enterocyte Nutrient Metabolism Changes.}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology}, volume = {48}, number = {5}, pages = {2103-2113}, doi = {10.1159/000492552}, pmid = {30107371}, issn = {1421-9778}, mesh = {Amino Acids/analysis/metabolism ; Animals ; Animals, Suckling ; Cells, Cultured ; Chromatography, High Pressure Liquid ; Citric Acid Cycle/genetics ; Databases, Factual ; Enterocytes/cytology/*metabolism ; Fatty Acids/analysis/metabolism ; Glucose/analysis/metabolism ; Jejunum/cytology ; Peptides/analysis ; Swine ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND/AIMS: Intestinal morphology and the types of enterocytes are changed in piglets during the suckling period, but it is unclear whether these changes are associated with metabolic changes in epithelium. The present study was conducted to test the hypothesis that glucose, fatty acids, and amino acid metabolism in differentiated piglet enterocytes changed during suckling.<br><br>METHODS: Twenty-four piglets (Duroc × [Landrace × Yorkshire]) from 8 litters (3 piglets/litter) were selected. A single piglet from each litter was randomly selected and euthanized at days 7, 14, and 21. Differentiated enterocytes (DE) were isolated from their mid-jejunum. Isobaric tags for relative and absolute quantification and subsequent liquid chromatography-tandem mass spectrometry were used to identify and measure protein synthesis.<br><br>RESULTS: The results showed that various activities, including: cellular processes; metabolic processes; biological regulation; pigmentation; and, localization, in DEs changed during suckling. Metabolic process analyses revealed that protein expression related to glycolysis and citrate cycle was decreased from day 7 to day 14. The number of differentiated enterocytes of 21 d piglets increased compared to 7 d piglets. Most of the proteins involved in fatty acid and amino acids metabolism had decreased DE expression between day 7 and day 14. Some, but not all, detected proteins down-regulated in DEs of 21 day piglets compared to 7 day piglets.<br><br>CONCLUSION: These results indicate that glucose, fatty acids, and amino acids metabolism changed during suckling. This may provide useful information for designing feed formulas and regulating piglet intestinal growth and development.}, }
@article {pmid30093613, year = {2018}, author = {Albrecht, J and Classen, A and Vollstädt, MGR and Mayr, A and Mollel, NP and Schellenberger Costa, D and Dulle, HI and Fischer, M and Hemp, A and Howell, KM and Kleyer, M and Nauss, T and Peters, MK and Tschapka, M and Steffan-Dewenter, I and Böhning-Gaese, K and Schleuning, M}, title = {Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3177}, pmid = {30093613}, issn = {2041-1723}, support = {For1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; }, abstract = {Species' functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird-fruit, bird-flower and insect-flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant-animal interaction networks.}, }
@article {pmid30046636, year = {2018}, author = {Bird, SM and King, R}, title = {Multiple Systems Estimation (or Capture-Recapture Estimation) to Inform Public Policy.}, journal = {Annual review of statistics and its application}, volume = {5}, number = {}, pages = {95-118}, pmid = {30046636}, issn = {2326-8298}, support = {MC_U105260794//Medical Research Council/United Kingdom ; }, abstract = {Estimating population sizes has long been of interest, from the estimation of the human or ecological population size within regions or countries to the hidden number of civilian casualties in a war. Total enumeration of the population, for example, via a census, is often infeasible or simply impractical. However, a series of partial enumerations or observations of the population is often possible. This has led to the ideas of capture-recapture methods, which have been extensively used within ecology to estimate the size of wildlife populations, with an associated measure of uncertainty, and are most effectively applied when there are multiple capture occasions. Capture-recapture ideology can be more widely applied to multiple data-sources, by the linkage of individuals across the multiple lists. This is often referred to as Multiple Systems Estimation (MSE). The MSE approach has been preferred when estimating &quot;capture-shy&quot; or hard-to-reach populations, including those caught up in the criminal justice system; or homeless; or trafficked; or civilian casualties of war. Motivated by a range of public policy applications of MSE, each briefly introduced, we discuss practical problems with potentially substantial methodological implications. They include: &quot;period&quot; definition; &quot;case&quot; definition; when an observed count is not a true count of the population of interest but an upper bound due to mismatched definitions; exact or probabilistic matching of &quot;cases&quot; across different lists; demographic or other information about the &quot;case&quot; which may influence capture-propensities; required permissions to access extant-lists; list-creation by research-teams or interested parties; referrals (if presence on list A results - almost surely - in presence on list B); different mathematical models leading to widely different estimated population sizes; uncertainty in estimation; computational efficiency; external validation; hypothesis-generation; and additional independent external information. Returning to our motivational applications, we focus on whether the uncertainty which qualified their estimates was sufficiently narrow to orient public policy; and, if not, what options were available and/or taken to reduce the uncertainty or to seek external validation. We also consider whether MSE was hypothesis-generating: in the sense of having spawned new lines of inquiry.}, }
@article {pmid30029348, year = {2018}, author = {Ridding, LE and Redhead, JW and Oliver, TH and Schmucki, R and McGinlay, J and Graves, AR and Morris, J and Bradbury, RB and King, H and Bullock, JM}, title = {The importance of landscape characteristics for the delivery of cultural ecosystem services.}, journal = {Journal of environmental management}, volume = {206}, number = {}, pages = {1145-1154}, doi = {10.1016/j.jenvman.2017.11.066}, pmid = {30029348}, issn = {1095-8630}, mesh = {*Conservation of Natural Resources ; Ecology ; *Ecosystem ; England ; *Geographic Information Systems ; Humans ; }, abstract = {The importance of Cultural Ecosystem Services (CES) to human wellbeing is widely recognised. However, quantifying these non-material benefits is challenging and consequently they are often not assessed. Mapping approaches are increasingly being used to understand the spatial distribution of different CES and how this relates to landscape characteristics. This study uses an online Public Participation Geographic Information System (PPGIS) to elicit information on outdoor locations important to respondents in Wiltshire, a dynamic lowland landscape in southern England. We analysed these locations in a GIS with spatial datasets representing potential influential factors, including protected areas, land use, landform, and accessibility. We assess these characteristics at different spatial and visual scales for different types of cultural engagement. We find that areas that are accessible, near to urban centres, with larger views, and a high diversity of protected habitats, are important for the delivery of CES. Other characteristics including a larger area of woodland and the presence of sites of historic interest in the surrounding landscape were also influential. These findings have implications for land-use planning and the management of ecosystems, by demonstrating the benefits of high quality ecological sites near to towns. The importance of maintaining and restoring landscape features, such as woodlands, to enhance the delivery of CES were also highlighted.}, }
@article {pmid30029345, year = {2018}, author = {He, L and Shen, J and Zhang, Y}, title = {Ecological vulnerability assessment for ecological conservation and environmental management.}, journal = {Journal of environmental management}, volume = {206}, number = {}, pages = {1115-1125}, doi = {10.1016/j.jenvman.2017.11.059}, pmid = {30029345}, issn = {1095-8630}, mesh = {China ; *Climate Change ; *Conservation of Natural Resources ; Ecology ; Ecosystem ; *Geographic Information Systems ; Humans ; }, abstract = {Identifying ecological vulnerable regions is a significant aspect in ecological conservation and environmental management. This paper presents a first attempt to provide a prototype framework that can assess ecological vulnerability and evaluate potential impacts of natural, social, economic, environmental pollution, and human health elements on ecological vulnerability with integrating spatial analysis of Geographic Information System (GIS) method and multi-criteria decision analysis (MCDA). A general ecological vulnerability index was constructed to describe the vulnerability status in an ecological hotspot of China. The assessment results of this study confirm the poor ecological vulnerability in China that only 1.32% of the China's population lives in not vulnerable ecosystem. A very high percentage (98.68%) of Chinese with 1.34 billion people lives in vulnerable and highly vulnerable area. This situation is mainly caused by increasing population pressure, exhausted nature resources, extensive economic growth, severe environmental pollution, insufficient environmental protection investment, and accelerating population aging. The spatial comparison indicates that spatial disparity existed in China with the central and northwestern provinces showing higher ecological vulnerability than the northeastern and southern provinces. The results of ecological vulnerability assessment can support effective guidance for mid- or long-term ecologic management. The developed framework can be replicated at different spatial and temporal scales using context-specific datasets to support ecological managers and government with decision-making. With available robust climate change models, future research might incorporate climate change into the ecological vulnerability framework.}, }
@article {pmid30029326, year = {2018}, author = {Djikanović, V and Skorić, S and Spasić, S and Naunovic, Z and Lenhardt, M}, title = {Ecological risk assessment for different macrophytes and fish species in reservoirs using biota-sediment accumulation factors as a useful tool.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {241}, number = {}, pages = {1167-1174}, doi = {10.1016/j.envpol.2018.06.054}, pmid = {30029326}, issn = {1873-6424}, mesh = {Animals ; Aquatic Organisms/*chemistry ; Biota ; Canada ; Catfishes ; Cyprinidae ; Ecology ; Environmental Monitoring/*methods ; Gills/chemistry ; Liver/chemistry ; Metals/analysis ; Metals, Heavy/analysis ; Muscles/chemistry ; Netherlands ; Risk Assessment ; Serbia ; Trace Elements/analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Metal content was evaluated in the sediment, macrophytes and fish in the Medjuvršje reservoir (Western Serbia). Concentrations of 16 trace elements (Ag; Al; As; B; Ba; Cd; Co; Cr; Cu; Fe; Li; Mn; Ni; Pb; Sr; Zn) were analysed in the sediment, macrophytes and fish of an aquatic ecosystem. Five macrophyte species and three fish tissues (liver, muscle, gills) from five fish species (freshwater bream, common nase, Prussian carp, chub, wels catfish) were sampled and the metal content was analysed with ICP-OES. The sediment concentrations of Cu, Cd, and Zn exceeded the Canadian sediment quality guidelines while concentrations of Cr and Ni were above the Netherlands' target values. Bioaccumulation factors (BSAF) were calculated for analysed macrophytes and fish tissue. The BSAF had higher values for macrophytes for all investigated elements except for Cu and Zn; Cu had a higher value in the liver of the freshwater bream (0.823) and Zn had a higher value in the liver of freshwater bream (0.914) and chub (0.834) as well as in gills of Prussian carp (2.58) and chub (1.26). Potamogeton pectinatus, Ceratophylum demersum and the root of Phragmites communis showed higher accumulation of elements than Trapa natans and Potamogeton fluitans and the body of P. communis. The highest BSAF values for Ba, Mn, Sr and Ni were recorded in the gills. Cd and Cu had the highest BSAF values in the liver. Results confirmed that particular macrophyte and fish species could be a good indicator of reservoir water and sediment pollution.}, }
@article {pmid30026187, year = {2018}, author = {Bradburd, GS and Coop, GM and Ralph, PL}, title = {Inferring Continuous and Discrete Population Genetic Structure Across Space.}, journal = {Genetics}, volume = {210}, number = {1}, pages = {33-52}, pmid = {30026187}, issn = {1943-2631}, support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cluster Analysis ; Data Interpretation, Statistical ; Gene Flow/genetics ; Genetic Variation/genetics ; Genetics, Population/*methods/*statistics &amp; numerical data ; Humans ; Models, Genetic ; North America ; Population Groups/genetics ; Populus/genetics ; Ursidae/genetics ; }, abstract = {A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the &quot;clines versus clusters&quot; problem in modeling population genetic variation, and remedies some of the overfitting to which nonspatial models are prone. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.}, }
@article {pmid30020436, year = {2018}, author = {Chen, F and Zhang, J and Chen, J and Li, X and Dong, W and Hu, J and Lin, M and Liu, Y and Li, G and Wang, Z and Zhang, L}, title = {realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta).}, journal = {Database : the journal of biological databases and curation}, volume = {2018}, number = {}, pages = {}, pmid = {30020436}, issn = {1758-0463}, mesh = {Algal Proteins/chemistry/genetics/metabolism ; *Databases, Genetic ; *Genome ; Internet ; Molecular Sequence Annotation ; Rhodophyta/*genetics ; Sequence Alignment ; Transcriptome/*genetics ; }, abstract = {With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development.Database URL: http://realdb.algaegenome.org/.}, }
@article {pmid30017551, year = {2018}, author = {Longbottom, J and Shearer, FM and Devine, M and Alcoba, G and Chappuis, F and Weiss, DJ and Ray, SE and Ray, N and Warrell, DA and Ruiz de Castañeda, R and Williams, DJ and Hay, SI and Pigott, DM}, title = {Vulnerability to snakebite envenoming: a global mapping of hotspots.}, journal = {Lancet (London, England)}, volume = {392}, number = {10148}, pages = {673-684}, pmid = {30017551}, issn = {1474-547X}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Africa, Northern/epidemiology ; Animals ; Antivenins/therapeutic use ; Geographic Mapping ; Health Resources/economics/statistics &amp; numerical data ; Health Services Accessibility/standards ; Humans ; Indonesia/epidemiology ; Neglected Diseases/drug therapy/epidemiology/prevention &amp; control ; Public Health/education ; Quality of Health Care/standards ; Snake Bites/*drug therapy/*epidemiology/mortality/prevention &amp; control ; Snakes/*classification/injuries ; Vulnerable Populations/*statistics &amp; numerical data ; }, abstract = {BACKGROUND: Snakebite envenoming is a frequently overlooked cause of mortality and morbidity. Data for snake ecology and existing snakebite interventions are scarce, limiting accurate burden estimation initiatives. Low global awareness stunts new interventions, adequate health resources, and available health care. Therefore, we aimed to synthesise currently available data to identify the most vulnerable populations at risk of snakebite, and where additional data to manage this global problem are needed.<br><br>METHODS: We assembled a list of snake species using WHO guidelines. Where relevant, we obtained expert opinion range (EOR) maps from WHO or the Clinical Toxinology Resources. We also obtained occurrence data for each snake species from a variety of websites, such as VertNet and iNaturalist, using the spocc R package (version 0.7.0). We removed duplicate occurrence data and categorised snakes into three groups: group A (no available EOR map or species occurrence records), group B (EOR map but <5 species occurrence records), and group C (EOR map and ≥5 species occurrence records). For group C species, we did a multivariate environmental similarity analysis using the 2008 WHO EOR maps and newly available evidence. Using these data and the EOR maps, we produced contemporary range maps for medically important venomous snake species at a 5 × 5 km resolution. We subsequently triangulated these data with three health system metrics (antivenom availability, accessibility to urban centres, and the Healthcare Access and Quality [HAQ] Index) to identify the populations most vulnerable to snakebite morbidity and mortality.<br><br>FINDINGS: We provide a map showing the ranges of 278 snake species globally. Although about 6·85 billion people worldwide live within range of areas inhabited by snakes, about 146·70 million live within remote areas lacking quality health-care provisioning. Comparing opposite ends of the HAQ Index, 272·91 million individuals (65·25%) of the population within the lowest decile are at risk of exposure to any snake for which no effective therapy exists compared with 519·46 million individuals (27·79%) within the highest HAQ Index decile, showing a disproportionate coverage in reported antivenom availability. Antivenoms were available for 119 (43%) of 278 snake species evaluated by WHO, while globally 750·19 million (10·95%) of those living within snake ranges live more than 1 h from population centres. In total, we identify about 92·66 million people living within these vulnerable geographies, including many sub-Saharan countries, Indonesia, and other parts of southeast Asia.<br><br>INTERPRETATION: Identifying exact populations vulnerable to the most severe outcomes of snakebite envenoming at a subnational level is important for prioritising new data collection and collation, reinforcing envenoming treatment, existing health-care systems, and deploying currently available and future interventions. These maps can guide future research efforts on snakebite envenoming from both ecological and public health perspectives and better target future estimates of the burden of this neglected tropical disease.<br><br>FUNDING: Bill &amp; Melinda Gates Foundation.}, }
@article {pmid29985552, year = {2018}, author = {Ma, ZS and Li, L}, title = {Measuring metagenome diversity and similarity with Hill numbers.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1339-1355}, doi = {10.1111/1755-0998.12923}, pmid = {29985552}, issn = {1755-0998}, support = {//Industry Technology Talent Grant/ ; //A China-US International Collaborative Project/ ; 71473243//National Science Foundation of China/ ; }, mesh = {Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; *Metagenome ; Metagenomics/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The first step of any metagenome sequencing project is to get the inventory of OTU abundances (operational taxonomic units) and/or metagenomic gene abundances. The former is generated with 16S-rRNA-tagged amplicon sequencing technology, and the latter can be generated from either gene-targeted or whole-sample shotgun metagenomics technologies. With 16S-rRNA data sets, measuring community diversity with diversity indexes such as species richness and Shannon's index has been a de facto standard analysis; nevertheless, similarly comprehensive approaches to metagenomic gene abundances are still largely missing, despite that both OTU and gene abundances are DNA reads. Here, we adapt the Hill numbers, which were reintroduced to macrocommunity ecology recently and are now widely regarded as a most appropriate measure system for ecological diversity, for measuring metagenome alpha-, beta- and gamma-diversities, and similarity. Our proposal includes the following: (a) Metagenomic gene (MG) diversity measures the single-gene-level metagenome diversity; (b) Type-I metagenome functional gene cluster (MFGC) diversity measures the diversity of functional gene clusters but ignoring within-cluster gene abundance information; (c) Type-II MFGC diversity considers within-cluster gene abundances information and integrates gene-cluster-level metagenome diversity and functional gene redundancy information; and (d) Four classes of Hill-numbers-based similarity metrics, including local gene overlap, regional gene overlap, gene homogeneity measure and gene turnover complement, were introduced in terms of MG and MFGC, respectively. We demonstrate the proposal with the gut metagenomes from healthy and IBD (inflammatory bowel disease) cohorts. The Hill numbers offer a unified approach to cohesively and comprehensively measuring the ecological and metagenome diversities of microbiomes.}, }
@article {pmid29981010, year = {2018}, author = {Lant, C and Baggio, J and Konar, M and Mejia, A and Ruddell, B and Rushforth, R and Sabo, JL and Troy, TJ}, title = {The U.S. food-energy-water system: A blueprint to fill the mesoscale gap for science and decision-making.}, journal = {Ambio}, volume = {}, number = {}, pages = {}, doi = {10.1007/s13280-018-1077-0}, pmid = {29981010}, issn = {1654-7209}, support = {1639529//National Science Foundation/ ; }, abstract = {Food, energy, and water (FEW) are interdependent and must be examined as a coupled natural-human system. This perspective essay defines FEW systems and outlines key findings about them as a blueprint for future models to satisfy six key objectives. The first three focus on linking the FEW production and consumption to impacts on Earth cycles in a spatially specific manner in order to diagnose problems and identify potential solutions. The second three focus on describing the evolution of FEW systems to identify risks, thus empowering the FEW actors to better achieve the goals of resilience and sustainability. Four key findings about the FEW systems that guide future model development are (1) that they engage ecological, carbon, water, and nutrient cycles most powerfully among all human systems; (2) that they operate primarily at a mesoscale best captured by counties, districts, and cities; (3) that cities are hubs within the FEW system; and (4) that the FEW system forms a complex network.}, }
@article {pmid29973596, year = {2018}, author = {Bramon Mora, B and Gravel, D and Gilarranz, LJ and Poisot, T and Stouffer, DB}, title = {Identifying a common backbone of interactions underlying food webs from different ecosystems.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2603}, pmid = {29973596}, issn = {2041-1723}, mesh = {Animals ; Competitive Behavior/*physiology ; Datasets as Topic ; Ecosystem ; *Food Chain ; *Models, Statistical ; Predatory Behavior/*physiology ; Principal Component Analysis ; }, abstract = {Although the structure of empirical food webs can differ between ecosystems, there is growing evidence of multiple ways in which they also exhibit common topological properties. To reconcile these contrasting observations, we postulate the existence of a backbone of interactions underlying all ecological networks-a common substructure within every network comprised of species playing similar ecological roles-and a periphery of species whose idiosyncrasies help explain the differences between networks. To test this conjecture, we introduce a new approach to investigate the structural similarity of 411 food webs from multiple environments and biomes. We first find significant differences in the way species in different ecosystems interact with each other. Despite these differences, we then show that there is compelling evidence of a common backbone of interactions underpinning all food webs. We expect that identifying a backbone of interactions will shed light on the rules driving assembly of different ecological communities.}, }
@article {pmid29923321, year = {2018}, author = {Keck, F and Vasselon, V and Rimet, F and Bouchez, A and Kahlert, M}, title = {Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1299-1309}, doi = {10.1111/1755-0998.12919}, pmid = {29923321}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Diatoms/classification/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Microscopy ; Phylogeny ; Rivers/microbiology ; Sensitivity and Specificity ; }, abstract = {DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.}, }
@article {pmid29917104, year = {2018}, author = {Celis, JS and Wibberg, D and Ramírez-Portilla, C and Rupp, O and Sczyrba, A and Winkler, A and Kalinowski, J and Wilke, T}, title = {Binning enables efficient host genome reconstruction in cnidarian holobionts.}, journal = {GigaScience}, volume = {7}, number = {7}, pages = {}, pmid = {29917104}, issn = {2047-217X}, mesh = {Algorithms ; Animals ; Anthozoa/*physiology ; Cnidaria/*genetics ; Computational Biology ; Coral Reefs ; DNA/analysis ; Ecology ; *Genome ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Symbiosis ; Transcriptome ; }, abstract = {Background: Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities-together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.<br><br>Results: Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.<br><br>Conclusions: Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.}, }
@article {pmid29898550, year = {2018}, author = {Mirtl, M and T Borer, E and Djukic, I and Forsius, M and Haubold, H and Hugo, W and Jourdan, J and Lindenmayer, D and McDowell, WH and Muraoka, H and Orenstein, DE and Pauw, JC and Peterseil, J and Shibata, H and Wohner, C and Yu, X and Haase, P}, title = {Genesis, goals and achievements of Long-Term Ecological Research at the global scale: A critical review of ILTER and future directions.}, journal = {The Science of the total environment}, volume = {626}, number = {}, pages = {1439-1462}, doi = {10.1016/j.scitotenv.2017.12.001}, pmid = {29898550}, issn = {1879-1026}, abstract = {Since its founding in 1993 the International Long-term Ecological Research Network (ILTER) has gone through pronounced development phases. The current network comprises 44 active member LTER networks representing 700 LTER Sites and ~80 LTSER Platforms across all continents, active in the fields of ecosystem, critical zone and socio-ecological research. The critical challenges and most important achievements of the initial phase have now become state-of-the-art in networking for excellent science. At the same time increasing integration, accelerating technology, networking of resources and a strong pull for more socially relevant scientific information have been modifying the mission and goals of ILTER. This article provides a critical review of ILTER's mission, goals, development and impacts. Major characteristics, tools, services, partnerships and selected examples of relative strengths relevant for advancing ILTER are presented. We elaborate on the tradeoffs between the needs of the scientific community and stakeholder expectations. The embedding of ILTER in an increasingly collaborative landscape of global environmental observation and ecological research networks and infrastructures is also reflected by developments of pioneering regional and national LTER networks such as SAEON in South Africa, CERN/CEOBEX in China, TERN in Australia or eLTER RI in Europe. The primary role of ILTER is currently seen as a mechanism to investigate ecosystem structure, function, and services in response to a wide range of environmental forcings using long-term, place-based research. We suggest four main fields of activities and advancements for the next decade through development/delivery of a: (1) Global multi-disciplinary community of researchers and research institutes; (2) Strategic global framework and strong partnerships in ecosystem observation and research; (3) Global Research Infrastructure (GRI); and (4) a scientific knowledge factory for societally relevant information on sustainable use of natural resources.}, }
@article {pmid29890590, year = {2018}, author = {Dick, J and Orenstein, DE and Holzer, JM and Wohner, C and Achard, AL and Andrews, C and Avriel-Avni, N and Beja, P and Blond, N and Cabello, J and Chen, C and Díaz-Delgado, R and Giannakis, GV and Gingrich, S and Izakovicova, Z and Krauze, K and Lamouroux, N and Leca, S and Melecis, V and Miklós, K and Mimikou, M and Niedrist, G and Piscart, C and Postolache, C and Psomas, A and Santos-Reis, M and Tappeiner, U and Vanderbilt, K and Van Ryckegem, G}, title = {What is socio-ecological research delivering? A literature survey across 25 international LTSER platforms.}, journal = {The Science of the total environment}, volume = {622-623}, number = {}, pages = {1225-1240}, doi = {10.1016/j.scitotenv.2017.11.324}, pmid = {29890590}, issn = {1879-1026}, abstract = {With an overarching goal of addressing global and regional sustainability challenges, Long Term Socio-Ecological Research Platforms (LTSER) aim to conduct place-based research, to collect and synthesize both environmental and socio-economic data, and to involve a broader stakeholder pool to set the research agenda. To date there have been few studies examining the output from LTSER platforms. In this study we enquire if the socio-ecological research from 25 self-selected LTSER platforms of the International Long-Term Ecological Research (ILTER) network has produced research products which fulfil the aims and ambitions of the paradigm shift from ecological to socio-ecological research envisaged at the turn of the century. In total we assessed 4983 publically available publications, of which 1112 were deemed relevant to the socio-ecological objectives of the platform. A series of 22 questions were scored for each publication, assessing relevance of responses in terms of the disciplinary focus of research, consideration of human health and well-being, degree of stakeholder engagement, and other relevant variables. The results reflected the diverse origins of the individual platforms and revealed a wide range in foci, temporal periods and quantity of output from participating platforms, supporting the premise that there is a growing trend in socio-ecological research at long-term monitoring platforms. Our review highlights the challenges of realizing the top-down goal to harmonize international network activities and objectives and the need for bottom-up, self-definition for research platforms. This provides support for increasing the consistency of LTSER research while preserving the diversity of regional experiences.}, }
@article {pmid29847023, year = {2018}, author = {Dellicour, S and Flot, JF}, title = {The hitchhiker's guide to single-locus species delimitation.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1234-1246}, doi = {10.1111/1755-0998.12908}, pmid = {29847023}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Metagenomics/*methods ; *Phylogeny ; }, abstract = {Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single-gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species-poor samples and/or tree-based approaches: as a result, travellers in the land of single-locus species delimitation lack a comprehensive &quot;hitchhiker's guide&quot; highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance-based (ABGD, &quot;automatic barcode gap discovery&quot;), allele sharing-based (haplowebs) and tree-based approaches (GMYC, &quot;generalized mixed Yule-coalescent&quot; and PTP, &quot;Poisson tree processes&quot;) to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree-based approaches. The latter's error type was mostly oversplitting, whereas ABGD chiefly overlumped and haplowebs leaned either way depending on simulation parameters: such widely divergent error patterns suggest that, if all three types of methods agree, then the resulting delimitation is probably correct. Perfect congruence being quite rare, travellers in search of a one-size-fit-all approach to single-locus species delimitation should forget it; however, our hitchhiker's guide raises hope that such species delimitation's Holy Grail may be found in the relatively uncharted nearby land of multilocus species delimitation.}, }
@article {pmid29802772, year = {2018}, author = {Snell Taylor, SJ and Evans, BS and White, EP and Hurlbert, AH}, title = {The prevalence and impact of transient species in ecological communities.}, journal = {Ecology}, volume = {99}, number = {8}, pages = {1825-1835}, doi = {10.1002/ecy.2398}, pmid = {29802772}, issn = {0012-9658}, abstract = {Transient species occur infrequently in a community over time and do not maintain viable local populations. Because transient species interact differently than non-transients with their biotic and abiotic environment, it is important to characterize the prevalence of these species and how they impact our understanding of ecological systems. We quantified the prevalence and impact of transient species in communities using data on over 19,000 community time series spanning an array of ecosystems, taxonomic groups, and spatial scales. We found that transient species are a general feature of communities regardless of taxa or ecosystem. The proportion of these species decreases with increasing spatial scale leading to a need to control for scale in comparative work. Removing transient species from analyses influences the form of a suite of commonly studied ecological patterns including species-abundance distributions, species-energy relationships, species-area relationships, and temporal turnover. Careful consideration should be given to whether transient species are included in analyses depending on the theoretical and practical relevance of these species for the question being studied.}, }
@article {pmid29794166, year = {2018}, author = {Couger, MB and Arévalo, L and Campbell, P}, title = {A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {7}, pages = {2145-2152}, pmid = {29794166}, issn = {2160-1836}, mesh = {Animals ; Computational Biology/methods ; Ecology ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Geography ; Hungary ; Mice ; Molecular Sequence Annotation ; Phylogeny ; Species Specificity ; Transcriptome ; }, abstract = {Genomic data for the closest relatives of house mice (Mus musculus species complex) are surprisingly limited. Here, we present the first complete genome for a behaviorally and ecologically unique member of the sister clade to house mice, the mound-building mouse, Mus spicilegus Using read cloud sequencing and de novo assembly we produced a 2.50 Gbp genome with a scaffold N50 of 2.27 Mbp. We constructed >25 000 gene models, of which the majority had high homology to other Mus species. To evaluate the utility of the M. spicilegus genome for behavioral and ecological genomics, we extracted 196 vomeronasal receptor (VR) sequences from our genome and analyzed phylogenetic relationships between M. spicilegus VRs and orthologs from M. musculus and the Algerian mouse, M. spretus While most M. spicilegus VRs clustered with orthologs in M. musculus and M. spretus, 10 VRs with evidence of rapid divergence in M. spicilegus are strong candidate modulators of species-specific chemical communication. A high quality assembly and genome for M. spicilegus will help to resolve discordant ancestry patterns in house mouse genomes, and will provide an essential foundation for genetic dissection of phenotypes that distinguish commensal from non-commensal species, and the social and ecological characteristics that make M. spicilegus unique.}, }
@article {pmid29751427, year = {2018}, author = {Meng, L and Huang, J and Dong, J}, title = {Assessment of rural ecosystem health and type classification in Jiangsu province, China.}, journal = {The Science of the total environment}, volume = {615}, number = {}, pages = {1218-1228}, doi = {10.1016/j.scitotenv.2017.09.312}, pmid = {29751427}, issn = {1879-1026}, mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Urbanization ; }, abstract = {Quantitative analysis of rural ecosystem health (REH) is required to comprehend the spatial differentiation of rural landscape and promote rural sustainable development under the pressure of urbanization and industrialization, especially those with dramatic changes in rural ecology of China and other developing countries. In this study, taking Jiangsu province as the case study, appropriate indicators were selected in the perspective of compound ecosystem and the rural ecosystem health index (REHI) was developed including four rural ecological subsystems of resource, environmental, social and economic. The comprehensive indicator assessment models and geographic information system (GIS) spatial methods were used to analyze the REH status and spatial differentiation of 57 counties in Jiangsu province. The REH scores of 57 rural counties were in a higher range of 0.686-0.882 and fluctuating increased from north to south, indicating that the rural ecosystem in Jiangsu province was at a relatively healthy level and counties in southern Jiangsu were healthier than those in central and northern regions. The spatial concentration of REH in Jiangsu was poor and the spatial distribution of four subsystems health levels were significantly different by spatial Gini coefficient analysis. The REH of 57 counties in Jiangsu province were classified into 13 types according to the identification of the health levels and quantity of four subsystems. Moreover, we analyzed the influencing factors of each type and proposed paths to promote the development and management of rural ecosystem.}, }
@article {pmid29734799, year = {2018}, author = {Peters, K and Worrich, A and Weinhold, A and Alka, O and Balcke, G and Birkemeyer, C and Bruelheide, H and Calf, OW and Dietz, S and Dührkop, K and Gaquerel, E and Heinig, U and Kücklich, M and Macel, M and Müller, C and Poeschl, Y and Pohnert, G and Ristok, C and Rodríguez, VM and Ruttkies, C and Schuman, M and Schweiger, R and Shahaf, N and Steinbeck, C and Tortosa, M and Treutler, H and Ueberschaar, N and Velasco, P and Weiß, BM and Widdig, A and Neumann, S and Dam, NMV}, title = {Current Challenges in Plant Eco-Metabolomics.}, journal = {International journal of molecular sciences}, volume = {19}, number = {5}, pages = {}, pmid = {29734799}, issn = {1422-0067}, mesh = {*Ecology ; Metabolomics/*trends ; Plants/*genetics/metabolism ; }, abstract = {The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.}, }
@article {pmid29717679, year = {2019}, author = {Toni, M and Manciocco, A and Angiulli, E and Alleva, E and Cioni, C and Malavasi, S}, title = {Review: Assessing fish welfare in research and aquaculture, with a focus on European directives.}, journal = {Animal : an international journal of animal bioscience}, volume = {13}, number = {1}, pages = {161-170}, doi = {10.1017/S1751731118000940}, pmid = {29717679}, issn = {1751-732X}, abstract = {The number of farmed fish in the world has increased considerably. Aquaculture is a growing industry that will in the future provide a large portion of fishery products. Moreover, in recent years, the number of teleost fish used as animal models for scientific research in both biomedical and ecological fields has increased. Therefore, it is increasingly important to implement measures designed to enhance the welfare of these animals. Currently, a number of European rules exist as requirements for the establishment, care and accommodation of fish maintained for human purposes. As far as (teleost) fish are concerned, the fact that the number of extant species is much greater than that of all other vertebrates must be considered. Of further importance is that each species has its own specific physical and chemical requirements. These factors make it difficult to provide generalized recommendations or requirements for all fish species. An adequate knowledge is required of the physiology and ecology of each species bred. This paper integrates and discusses, in a single synthesis, the current issues related to fish welfare, considering that teleosts are target species for both aquaculture and experimental models in biological and biomedical research. We first focus on the practical aspects, which must be considered when assessing fish welfare in both research and aquaculture contexts. Next, we address husbandry and the care of fish housed in research laboratories and aquaculture facilities in relation to their physiological and behavioural requirements, as well as in reference to the suggestions provided by European regulations. Finally, to evaluate precisely which parameters described by Directive 2010/63/EU are reported in scientific papers, we analysed 82 articles published by European researchers in 2014 and 2015. This review found that there is a general lack of information related to the optimal environmental conditions that should be provided for the range of species covered by this directive.}, }
@article {pmid29686079, year = {2018}, author = {Muscente, AD and Prabhu, A and Zhong, H and Eleish, A and Meyer, MB and Fox, P and Hazen, RM and Knoll, AH}, title = {Quantifying ecological impacts of mass extinctions with network analysis of fossil communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {20}, pages = {5217-5222}, pmid = {29686079}, issn = {1091-6490}, mesh = {Animals ; *Biodiversity ; Biological Evolution ; *Databases, Factual ; *Ecosystem ; *Extinction, Biological ; *Fossils ; Geology ; Invertebrates ; *Paleontology ; }, abstract = {Mass extinctions documented by the fossil record provide critical benchmarks for assessing changes through time in biodiversity and ecology. Efforts to compare biotic crises of the past and present, however, encounter difficulty because taxonomic and ecological changes are decoupled, and although various metrics exist for describing taxonomic turnover, no methods have yet been proposed to quantify the ecological impacts of extinction events. To address this issue, we apply a network-based approach to exploring the evolution of marine animal communities over the Phanerozoic Eon. Network analysis of fossil co-occurrence data enables us to identify nonrandom associations of interrelated paleocommunities. These associations, or evolutionary paleocommunities, dominated total diversity during successive intervals of relative community stasis. Community turnover occurred largely during mass extinctions and radiations, when ecological reorganization resulted in the decline of one association and the rise of another. Altogether, we identify five evolutionary paleocommunities at the generic and familial levels in addition to three ordinal associations that correspond to Sepkoski's Cambrian, Paleozoic, and Modern evolutionary faunas. In this context, we quantify magnitudes of ecological change by measuring shifts in the representation of evolutionary paleocommunities over geologic time. Our work shows that the Great Ordovician Biodiversification Event had the largest effect on ecology, followed in descending order by the Permian-Triassic, Cretaceous-Paleogene, Devonian, and Triassic-Jurassic mass extinctions. Despite its taxonomic severity, the Ordovician extinction did not strongly affect co-occurrences of taxa, affirming its limited ecological impact. Network paleoecology offers promising approaches to exploring ecological consequences of extinctions and radiations.}, }
@article {pmid29668682, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Koutra, D and Schloss, PD}, title = {Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006099}, pmid = {29668682}, issn = {1553-7358}, support = {T32AI007528/NH/NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; P30DK034933/NH/NIH HHS/United States ; U01AI124255/NH/NIH HHS/United States ; U19AI09087/NH/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Bacteriophages/*genetics/*physiology ; Computational Biology ; Diet ; Humans ; Metagenomics ; Microbial Consortia/genetics/physiology ; Microbiota/*genetics/*physiology ; Models, Biological ; Phylogeography ; Skin/microbiology/virology ; }, abstract = {Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.}, }
@article {pmid29666315, year = {2018}, author = {Chen, S and Wang, W and Xu, W and Wang, Y and Wan, H and Chen, D and Tang, Z and Tang, X and Zhou, G and Xie, Z and Zhou, D and Shangguan, Z and Huang, J and He, JS and Wang, Y and Sheng, J and Tang, L and Li, X and Dong, M and Wu, Y and Wang, Q and Wang, Z and Wu, J and Chapin, FS and Bai, Y}, title = {Plant diversity enhances productivity and soil carbon storage.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {16}, pages = {4027-4032}, pmid = {29666315}, issn = {1091-6490}, mesh = {*Biodiversity ; Biomass ; Carbon/*analysis ; *Carbon Sequestration ; China ; Conservation of Natural Resources ; Datasets as Topic ; *Ecosystem ; Farms ; Forests ; Grassland ; Human Activities ; Humans ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Plant Dispersal ; Plants/chemistry/classification/*metabolism ; Rain ; Soil/*chemistry ; Temperature ; }, abstract = {Despite evidence from experimental grasslands that plant diversity increases biomass production and soil organic carbon (SOC) storage, it remains unclear whether this is true in natural ecosystems, especially under climatic variations and human disturbances. Based on field observations from 6,098 forest, shrubland, and grassland sites across China and predictions from an integrative model combining multiple theories, we systematically examined the direct effects of climate, soils, and human impacts on SOC storage versus the indirect effects mediated by species richness (SR), aboveground net primary productivity (ANPP), and belowground biomass (BB). We found that favorable climates (high temperature and precipitation) had a consistent negative effect on SOC storage in forests and shrublands, but not in grasslands. Climate favorability, particularly high precipitation, was associated with both higher SR and higher BB, which had consistent positive effects on SOC storage, thus offsetting the direct negative effect of favorable climate on SOC. The indirect effects of climate on SOC storage depended on the relationships of SR with ANPP and BB, which were consistently positive in all biome types. In addition, human disturbance and soil pH had both direct and indirect effects on SOC storage, with the indirect effects mediated by changes in SR, ANPP, and BB. High soil pH had a consistently negative effect on SOC storage. Our findings have important implications for improving global carbon cycling models and ecosystem management: Maintaining high levels of diversity can enhance soil carbon sequestration and help sustain the benefits of plant diversity and productivity.}, }
@article {pmid29618526, year = {2018}, author = {Ching, T and Himmelstein, DS and Beaulieu-Jones, BK and Kalinin, AA and Do, BT and Way, GP and Ferrero, E and Agapow, PM and Zietz, M and Hoffman, MM and Xie, W and Rosen, GL and Lengerich, BJ and Israeli, J and Lanchantin, J and Woloszynek, S and Carpenter, AE and Shrikumar, A and Xu, J and Cofer, EM and Lavender, CA and Turaga, SC and Alexandari, AM and Lu, Z and Harris, DJ and DeCaprio, D and Qi, Y and Kundaje, A and Peng, Y and Wiley, LK and Segler, MHS and Boca, SM and Swamidass, SJ and Huang, A and Gitter, A and Greene, CS}, title = {Opportunities and obstacles for deep learning in biology and medicine.}, journal = {Journal of the Royal Society, Interface}, volume = {15}, number = {141}, pages = {}, pmid = {29618526}, issn = {1742-5662}, support = {DP2 GM123485/GM/NIGMS NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; R01 GM089753/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; }, abstract = {Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.}, }
@article {pmid29590103, year = {2018}, author = {Emery, M and Willis, MMS and Hao, Y and Barry, K and Oakgrove, K and Peng, Y and Schmutz, J and Lyons, E and Pires, JC and Edger, PP and Conant, GC}, title = {Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.}, journal = {PLoS genetics}, volume = {14}, number = {3}, pages = {e1007267}, pmid = {29590103}, issn = {1553-7404}, mesh = {Brassicaceae/*genetics ; Evolution, Molecular ; *Genes, Plant ; *Genomic Imprinting ; *Hybridization, Genetic ; Models, Genetic ; *Polyploidy ; }, abstract = {Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecological success. One source of polyploid organisms' successes may be their origins in the merging and mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (the Polyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events, one from the bakers' yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsis thaliana) and one from grasses including Sorghum bicolor. Analyzing a total of 21 genomes, we assign to every gene a probability for having come from each parental subgenome (i.e., derived from the diploid progenitor species), yielding orthologous segments across all genomes. Our model detects statistically robust evidence for the existence of biased fractionation in all three lineages, whereby genes from one of the two subgenomes were more likely to be lost than those from the other subgenome. We further find that a driver of this pattern of biased losses is the co-retention of genes from the same parental genome that share functional interactions. The pattern of biased fractionation after the Arabidopsis and grass allopolyploid events was surprisingly constant in time, with the same parental genome favored throughout the lineages' history. In strong contrast, the yeast allopolyploid event shows evidence of biased fractionation only immediately after the event, with balanced gene losses more recently. The rapid loss of functionally associated genes from a single subgenome is difficult to reconcile with the action of genetic drift and suggests that selection may favor the removal of specific duplicates. Coupled to the evidence for continuing, functionally-associated biased fractionation after the A. thaliana At-α event, we suggest that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss.}, }
@article {pmid29574273, year = {2018}, author = {Psonis, N and Antoniou, A and Karameta, E and Leaché, AD and Kotsakiozi, P and Darriba, D and Kozlov, A and Stamatakis, A and Poursanidis, D and Kukushkin, O and Jablonski, D and Crnobrnja-Isailović, J and Gherghel, I and Lymberakis, P and Poulakakis, N}, title = {Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.}, journal = {Molecular phylogenetics and evolution}, volume = {125}, number = {}, pages = {100-115}, doi = {10.1016/j.ympev.2018.03.021}, pmid = {29574273}, issn = {1095-9513}, mesh = {Animals ; Balkan Peninsula ; Bayes Theorem ; Biodiversity ; Calibration ; DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Genomics ; Haplotypes/genetics ; Lizards/*classification/genetics ; Microsatellite Repeats/genetics ; *Models, Biological ; Phylogeny ; *Phylogeography ; Species Specificity ; }, abstract = {The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time.}, }
@article {pmid29569818, year = {2018}, author = {Anderegg, LDL and Berner, LT and Badgley, G and Sethi, ML and Law, BE and HilleRisLambers, J}, title = {Within-species patterns challenge our understanding of the leaf economics spectrum.}, journal = {Ecology letters}, volume = {21}, number = {5}, pages = {734-744}, doi = {10.1111/ele.12945}, pmid = {29569818}, issn = {1461-0248}, abstract = {The utility of plant functional traits for predictive ecology relies on our ability to interpret trait variation across multiple taxonomic and ecological scales. Using extensive data sets of trait variation within species, across species and across communities, we analysed whether and at what scales leaf economics spectrum (LES) traits show predicted trait-trait covariation. We found that most variation in LES traits is often, but not universally, at high taxonomic levels (between families or genera in a family). However, we found that trait covariation shows distinct taxonomic scale dependence, with some trait correlations showing opposite signs within vs. across species. LES traits responded independently to environmental gradients within species, with few shared environmental responses across traits or across scales. We conclude that, at small taxonomic scales, plasticity may obscure or reverse the broad evolutionary linkages between leaf traits, meaning that variation in LES traits cannot always be interpreted as differences in resource use strategy.}, }
@article {pmid29566054, year = {2018}, author = {Jablonski, KE and Boone, RB and Meiman, PJ}, title = {An agent-based model of cattle grazing toxic Geyer's larkspur.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194450}, pmid = {29566054}, issn = {1932-6203}, mesh = {Agriculture/*methods ; Alkaloids/toxicity ; Animals ; Behavior, Animal ; Biological Variation, Population ; Cattle ; Cattle Diseases/etiology/*prevention &amp; control ; Computational Biology ; Delphinium/chemistry/*toxicity ; *Models, Biological ; Plant Poisoning/etiology/*prevention &amp; control/veterinary ; United States ; }, abstract = {By killing cattle and otherwise complicating management, the many species of larkspur (Delphinium spp.) present a serious, intractable, and complex challenge to livestock grazing management in the western United States. Among the many obstacles to improving our understanding of cattle-larkspur dynamics has been the difficulty of testing different grazing management strategies in the field, as the risk of dead animals is too great. Agent-based models (ABMs) provide an effective method of testing alternate management strategies without risk to livestock. ABMs are especially useful for modeling complex systems such as livestock grazing management, and allow for realistic bottom-up encoding of cattle behavior. Here, we introduce a spatially-explicit, behavior-based ABM of cattle grazing in a pasture with a dangerous amount of Geyer's larkspur (D. geyeri). This model tests the role of herd cohesion and stocking density in larkspur intake, finds that both are key drivers of larkspur-induced toxicosis, and indicates that alteration of these factors within realistic bounds can mitigate risk. Crucially, the model points to herd cohesion, which has received little attention in the discipline, as playing an important role in lethal acute toxicosis. As the first ABM to model grazing behavior at realistic scales, this study also demonstrates the tremendous potential of ABMs to illuminate grazing management dynamics, including fundamental aspects of livestock behavior amidst ecological heterogeneity.}, }
@article {pmid29541867, year = {2018}, author = {Heider, K and Lopez, JMR and Scheffran, J}, title = {The potential of volunteered geographic information to investigate peri-urbanization in the conservation zone of Mexico City.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {4}, pages = {219}, pmid = {29541867}, issn = {1573-2959}, support = {10th call//Center for a Sustainable University/ ; }, mesh = {Cities ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/methods ; *Geographic Information Systems ; Mexico ; Rural Population ; Urbanization/*trends ; }, abstract = {Due to the availability of Web 2.0 technologies, volunteered geographic information (VGI) is on the rise. This new type of data is available on many topics and on different scales. Thus, it has become interesting for research. This article deals with the collective potential of VGI and remote sensing to detect peri-urbanization in the conservation zone of Mexico City. On the one hand, remote sensing identifies horizontal urban expansion, and on the other hand, VGI of ecological complaints provides data about informal settlements. This enables the combination of top-down approaches (remote sensing) and bottom-up approaches (ecological complaints). Within the analysis, we identify areas of high urbanization as well as complaint densities and bring them together in a multi-scale analysis using Geographic Information Systems (GIS). Furthermore, we investigate the influence of settlement patterns and main roads on the peri-urbanization process in Mexico City using OpenStreetMap. Peri-urbanization is detected especially in the transition zone between the urban and rural (conservation) area and near main roads as well as settlements.}, }
@article {pmid29540568, year = {2018}, author = {Liu, XY and Koba, K and Koyama, LA and Hobbie, SE and Weiss, MS and Inagaki, Y and Shaver, GR and Giblin, AE and Hobara, S and Nadelhoffer, KJ and Sommerkorn, M and Rastetter, EB and Kling, GW and Laundre, JA and Yano, Y and Makabe, A and Yano, M and Liu, CQ}, title = {Nitrate is an important nitrogen source for Arctic tundra plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {13}, pages = {3398-3403}, pmid = {29540568}, issn = {1091-6490}, mesh = {Denitrification ; Nitrates/*metabolism ; Nitrogen/*analysis ; Plant Leaves/growth &amp; development/*metabolism ; Soil/*chemistry ; *Tundra ; }, abstract = {Plant nitrogen (N) use is a key component of the N cycle in terrestrial ecosystems. The supply of N to plants affects community species composition and ecosystem processes such as photosynthesis and carbon (C) accumulation. However, the availabilities and relative importance of different N forms to plants are not well understood. While nitrate (NO3-) is a major N form used by plants worldwide, it is discounted as a N source for Arctic tundra plants because of extremely low NO3- concentrations in Arctic tundra soils, undetectable soil nitrification, and plant-tissue NO3- that is typically below detection limits. Here we reexamine NO3- use by tundra plants using a sensitive denitrifier method to analyze plant-tissue NO3- Soil-derived NO3- was detected in tundra plant tissues, and tundra plants took up soil NO3- at comparable rates to plants from relatively NO3--rich ecosystems in other biomes. Nitrate assimilation determined by 15N enrichments of leaf NO3- relative to soil NO3- accounted for 4 to 52% (as estimated by a Bayesian isotope-mixing model) of species-specific total leaf N of Alaskan tundra plants. Our finding that in situ soil NO3- availability for tundra plants is high has important implications for Arctic ecosystems, not only in determining species compositions, but also in determining the loss of N from soils via leaching and denitrification. Plant N uptake and soil N losses can strongly influence C uptake and accumulation in tundra soils. Accordingly, this evidence of NO3- availability in tundra soils is crucial for predicting C storage in tundra.}, }
@article {pmid29513661, year = {2018}, author = {Lee, EC and Arab, A and Goldlust, SM and Viboud, C and Grenfell, BT and Bansal, S}, title = {Deploying digital health data to optimize influenza surveillance at national and local scales.}, journal = {PLoS computational biology}, volume = {14}, number = {3}, pages = {e1006020}, pmid = {29513661}, issn = {1553-7358}, support = {P2C HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Bayes Theorem ; Computer Simulation ; Databases, Factual ; Humans ; Influenza A Virus, H1N1 Subtype/pathogenicity ; Influenza, Human/*epidemiology ; Medical Records ; Models, Theoretical ; Online Systems ; Pandemics ; Population Surveillance/*methods ; Selection Bias ; Sentinel Surveillance ; United States ; }, abstract = {The surveillance of influenza activity is critical to early detection of epidemics and pandemics and the design of disease control strategies. Case reporting through a voluntary network of sentinel physicians is a commonly used method of passive surveillance for monitoring rates of influenza-like illness (ILI) worldwide. Despite its ubiquity, little attention has been given to the processes underlying the observation, collection, and spatial aggregation of sentinel surveillance data, and its subsequent effects on epidemiological understanding. We harnessed the high specificity of diagnosis codes in medical claims from a database that represented 2.5 billion visits from upwards of 120,000 United States healthcare providers each year. Among influenza seasons from 2002-2009 and the 2009 pandemic, we simulated limitations of sentinel surveillance systems such as low coverage and coarse spatial resolution, and performed Bayesian inference to probe the robustness of ecological inference and spatial prediction of disease burden. Our models suggest that a number of socio-environmental factors, in addition to local population interactions, state-specific health policies, as well as sampling effort may be responsible for the spatial patterns in U.S. sentinel ILI surveillance. In addition, we find that biases related to spatial aggregation were accentuated among areas with more heterogeneous disease risk, and sentinel systems designed with fixed reporting locations across seasons provided robust inference and prediction. With the growing availability of health-associated big data worldwide, our results suggest mechanisms for optimizing digital data streams to complement traditional surveillance in developed settings and enhance surveillance opportunities in developing countries.}, }
@article {pmid29495440, year = {2018}, author = {Torina, A and Blanda, V and Blanda, M and Auteri, M and La Russa, F and Scimeca, S and D'Agostino, R and Disclafani, R and Villari, S and Currò, V and Caracappa, S}, title = {A Geographical Information System Based Approach for Integrated Strategies of Tick Surveillance and Control in the Peri-Urban Natural Reserve of Monte Pellegrino (Palermo, Southern Italy).}, journal = {International journal of environmental research and public health}, volume = {15}, number = {3}, pages = {}, pmid = {29495440}, issn = {1660-4601}, mesh = {Animals ; Conservation of Natural Resources ; *Geographic Information Systems ; Italy ; Spatio-Temporal Analysis ; Tick Control/*methods ; *Ticks ; Urban Health ; }, abstract = {Ticks (Acari: Ixodidae) are bloodsucking arthropods involved in pathogen transmission in animals and humans. Tick activity depends on various ecological factors such as vegetation, hosts, and temperature. The aim of this study was to analyse the spatial/temporal distribution of ticks in six sites within a peri-urban area of Palermo (Natural Reserve of Monte Pellegrino) and correlate it with field data using Geographical Information System (GIS) data. A total of 3092 ticks were gathered via dragging method from June 2012 to May 2014. The species collected were: Ixodes ventalloi (46.09%), Hyalomma lusitanicum (19.99%), Rhipicephalus sanguineus (17.34%), Rhipicephalus pusillus (16.11%), Haemaphisalis sulcata (0.36%), Dermacentor marginatus (0.10%), and Rhipicephalus turanicus (0.03%). GIS analysis revealed environmental characteristics of each site, and abundance of each tick species was analysed in relation to time (monthly trend) and space (site-specific abundance). A relevant presence of I. ventalloi in site 2 and H. lusitanicum in site 5 was observed, suggesting the possible exposure of animals and humans to tick-borne pathogens. Our study shows the importance of surveillance of ticks in peri-urban areas and the useful implementation of GIS analysis in vector ecology; studies on temporal and spatial distribution of ticks correlated to GIS-based ecological analysis represent an integrated strategy for decision support in public health.}, }
@article {pmid29479643, year = {2018}, author = {Hervé, MR and Nicolè, F and Lê Cao, KA}, title = {Multivariate Analysis of Multiple Datasets: a Practical Guide for Chemical Ecology.}, journal = {Journal of chemical ecology}, volume = {44}, number = {3}, pages = {215-234}, doi = {10.1007/s10886-018-0932-6}, pmid = {29479643}, issn = {1573-1561}, mesh = {*Databases, Chemical ; Ecology/*methods ; *Guidelines as Topic ; Models, Statistical ; Multivariate Analysis ; }, abstract = {Chemical ecology has strong links with metabolomics, the large-scale study of all metabolites detectable in a biological sample. Consequently, chemical ecologists are often challenged by the statistical analyses of such large datasets. This holds especially true when the purpose is to integrate multiple datasets to obtain a holistic view and a better understanding of a biological system under study. The present article provides a comprehensive resource to analyze such complex datasets using multivariate methods. It starts from the necessary pre-treatment of data including data transformations and distance calculations, to the application of both gold standard and novel multivariate methods for the integration of different omics data. We illustrate the process of analysis along with detailed results interpretations for six issues representative of the different types of biological questions encountered by chemical ecologists. We provide the necessary knowledge and tools with reproducible R codes and chemical-ecological datasets to practice and teach multivariate methods.}, }
@article {pmid29466331, year = {2018}, author = {Ma, Z and Guo, D and Xu, X and Lu, M and Bardgett, RD and Eissenstat, DM and McCormack, ML and Hedin, LO}, title = {Evolutionary history resolves global organization of root functional traits.}, journal = {Nature}, volume = {555}, number = {7694}, pages = {94-97}, pmid = {29466331}, issn = {1476-4687}, mesh = {Biodiversity ; *Biological Evolution ; Carbon/metabolism ; Databases, Factual ; Desert Climate ; *Ecosystem ; Mycorrhizae/physiology ; Photosynthesis ; Phylogeny ; Plant Roots/*anatomy &amp; histology/classification/microbiology/*physiology ; Seasons ; Soil/chemistry ; Species Specificity ; Symbiosis ; Tropical Climate ; }, abstract = {Plant roots have greatly diversified in form and function since the emergence of the first land plants, but the global organization of functional traits in roots remains poorly understood. Here we analyse a global dataset of 10 functionally important root traits in metabolically active first-order roots, collected from 369 species distributed across the natural plant communities of 7 biomes. Our results identify a high degree of organization of root traits across species and biomes, and reveal a pattern that differs from expectations based on previous studies of leaf traits. Root diameter exerts the strongest influence on root trait variation across plant species, growth forms and biomes. Our analysis suggests that plants have evolved thinner roots since they first emerged in land ecosystems, which has enabled them to markedly improve their efficiency of soil exploration per unit of carbon invested and to reduce their dependence on symbiotic mycorrhizal fungi. We also found that diversity in root morphological traits is greatest in the tropics, where plant diversity is highest and many ancestral phylogenetic groups are preserved. Diversity in root morphology declines sharply across the sequence of tropical, temperate and desert biomes, presumably owing to changes in resource supply caused by seasonally inhospitable abiotic conditions. Our results suggest that root traits have evolved along a spectrum bounded by two contrasting strategies of root life: an ancestral 'conservative' strategy in which plants with thick roots depend on symbiosis with mycorrhizal fungi for soil resources and a more-derived 'opportunistic' strategy in which thin roots enable plants to more efficiently leverage photosynthetic carbon for soil exploration. These findings imply that innovations of belowground traits have had an important role in preparing plants to colonize new habitats, and in generating biodiversity within and across biomes.}, }
@article {pmid29451365, year = {2018}, author = {Kim, HS and Lee, BY and Han, J and Jeong, CB and Hwang, DS and Lee, MC and Kang, HM and Kim, DH and Kim, HJ and Papakostas, S and Declerck, SAJ and Choi, IY and Hagiwara, A and Park, HG and Lee, JS}, title = {The genome of the freshwater monogonont rotifer Brachionus calyciflorus.}, journal = {Molecular ecology resources}, volume = {18}, number = {3}, pages = {646-655}, doi = {10.1111/1755-0998.12768}, pmid = {29451365}, issn = {1755-0998}, mesh = {Animals ; *Databases, Genetic ; *Genome ; Molecular Sequence Annotation ; Rotifera/*genetics ; Sequence Analysis, DNA ; }, abstract = {Monogononta is the most speciose class of rotifers, with more than 2,000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex and ecotoxicology. With the importance of Brachionus species in many areas of research, it is remarkable that the genome has not been characterized. This study aims to address this lacuna by presenting, for the first time, the whole-genome assembly of the freshwater species Brachionus calyciflorus. The total length of the assembled genome was 129.6 Mb, with 1,041 scaffolds. The N50 value was 786.6 kb, and the GC content was 24%. A total of 16,114 genes were annotated with repeat sequences, accounting for 21% of the assembled genome. This assembled genome may form a basis for future studies addressing key questions on the evolution of monogonont rotifers. It will also provide the necessary molecular resources to mechanistically investigate ecophysiological and ecotoxicological responses.}, }
@article {pmid29426200, year = {2018}, author = {Stefanidis, K and Panagopoulos, Y and Mimikou, M}, title = {Response of a multi-stressed Mediterranean river to future climate and socio-economic scenarios.}, journal = {The Science of the total environment}, volume = {627}, number = {}, pages = {756-769}, doi = {10.1016/j.scitotenv.2018.01.282}, pmid = {29426200}, issn = {1879-1026}, mesh = {*Climate Change ; Ecosystem ; *Environmental Monitoring ; Europe ; Greece ; Mediterranean Region ; *Models, Theoretical ; Rivers/*chemistry ; Socioeconomic Factors ; Water Pollution/*statistics &amp; numerical data ; }, abstract = {Streams and rivers are among the most threatened ecosystems in Europe due to the combined effects of multiple pressures related to anthropogenic activities. Particularly in the Mediterranean region, changes in hydromorphology along with increased nutrient loadings are known to affect the ecological functions and ecosystem services of streams and rivers with the anticipated climate change being likely to further impair their functionality and structure. In this study, we investigated the combined effects of agricultural driven stressors on the ecology and delivered services of the Pinios river basin in Greece under three future world scenarios developed within the EU funded MARS project. Scenarios are based on combinations of Representative Concentration Pathways and Shared Socioeconomic Pathways and refer to early century (2030) and mid-century (2060) representing future climate worlds with particular socioeconomic characteristics. To assess the responses of ecological and ecosystem service indicators to the scenarios we first simulated hydrology and water quality in Pinios with a process-based model. Simulated abiotic stressor parameters (predictors) were linked to two biotic indicators, the macroinvertebrate indicators ASPT and EPT, with empirical modelling based on boosted regression trees and general linear models. Our results showed that the techno world scenario driven by fast economic growth and intensive exploitation of energy resources had the largest impact on both the abiotic status (nutrient loads and concentrations in water) and the biotic indicators. In contrast, the predicted changes under the other two future worlds, consensus and fragmented, were more diverse and were mostly dictated by the projected climate. This work showed that the future scenarios, especially the mid-century ones, had significant impact on both abiotic status and biotic responses underpinning the need for implementing catchment management practices able to mitigate the ecological threat on waters in the long-term.}, }
@article {pmid29382768, year = {2018}, author = {Zachar, I and Szilágyi, A and Számadó, S and Szathmáry, E}, title = {Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {7}, pages = {E1504-E1510}, pmid = {29382768}, issn = {1091-6490}, support = {294332//European Research Council/International ; }, mesh = {Animals ; Bacteria/pathogenicity ; *Biological Evolution ; Computational Biology ; Erythrocytes/*microbiology ; Eukaryota ; Humans ; Mitochondria/*physiology ; *Models, Biological ; Predatory Behavior ; *Selection, Genetic ; Symbiosis/*physiology ; }, abstract = {The origin of mitochondria was a major evolutionary transition leading to eukaryotes, and is a hotly debated issue. It is unknown whether mitochondria were acquired early or late, and whether it was captured via phagocytosis or syntrophic integration. We present dynamical models to directly simulate the emergence of mitochondria in an ecoevolutionary context. Our results show that regulated farming of prey bacteria and delayed digestion can facilitate the establishment of stable endosymbiosis if prey-rich and prey-poor periods alternate. Stable endosymbiosis emerges without assuming any initial metabolic benefit provided by the engulfed partner, in a wide range of parameters, despite that during good periods farming is costly. Our approach lends support to the appearance of mitochondria before any metabolic coupling has emerged, but after the evolution of primitive phagocytosis by the urkaryote.}, }
@article {pmid29382745, year = {2018}, author = {Dietze, MC and Fox, A and Beck-Johnson, LM and Betancourt, JL and Hooten, MB and Jarnevich, CS and Keitt, TH and Kenney, MA and Laney, CM and Larsen, LG and Loescher, HW and Lunch, CK and Pijanowski, BC and Randerson, JT and Read, EK and Tredennick, AT and Vargas, R and Weathers, KC and White, EP}, title = {Iterative near-term ecological forecasting: Needs, opportunities, and challenges.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {7}, pages = {1424-1432}, pmid = {29382745}, issn = {1091-6490}, mesh = {Bayes Theorem ; Climate Change ; Ecology/*education/*methods/trends ; Ecosystem ; Forecasting ; Humans ; Models, Theoretical ; }, abstract = {Two foundational questions about sustainability are &quot;How are ecosystems and the services they provide going to change in the future?&quot; and &quot;How do human decisions affect these trajectories?&quot; Answering these questions requires an ability to forecast ecological processes. Unfortunately, most ecological forecasts focus on centennial-scale climate responses, therefore neither meeting the needs of near-term (daily to decadal) environmental decision-making nor allowing comparison of specific, quantitative predictions to new observational data, one of the strongest tests of scientific theory. Near-term forecasts provide the opportunity to iteratively cycle between performing analyses and updating predictions in light of new evidence. This iterative process of gaining feedback, building experience, and correcting models and methods is critical for improving forecasts. Iterative, near-term forecasting will accelerate ecological research, make it more relevant to society, and inform sustainable decision-making under high uncertainty and adaptive management. Here, we identify the immediate scientific and societal needs, opportunities, and challenges for iterative near-term ecological forecasting. Over the past decade, data volume, variety, and accessibility have greatly increased, but challenges remain in interoperability, latency, and uncertainty quantification. Similarly, ecologists have made considerable advances in applying computational, informatic, and statistical methods, but opportunities exist for improving forecast-specific theory, methods, and cyberinfrastructure. Effective forecasting will also require changes in scientific training, culture, and institutions. The need to start forecasting is now; the time for making ecology more predictive is here, and learning by doing is the fastest route to drive the science forward.}, }
@article {pmid29371471, year = {2018}, author = {Tucker, MA and Böhning-Gaese, K and Fagan, WF and Fryxell, JM and Van Moorter, B and Alberts, SC and Ali, AH and Allen, AM and Attias, N and Avgar, T and Bartlam-Brooks, H and Bayarbaatar, B and Belant, JL and Bertassoni, A and Beyer, D and Bidner, L and van Beest, FM and Blake, S and Blaum, N and Bracis, C and Brown, D and de Bruyn, PJN and Cagnacci, F and Calabrese, JM and Camilo-Alves, C and Chamaillé-Jammes, S and Chiaradia, A and Davidson, SC and Dennis, T and DeStefano, S and Diefenbach, D and Douglas-Hamilton, I and Fennessy, J and Fichtel, C and Fiedler, W and Fischer, C and Fischhoff, I and Fleming, CH and Ford, AT and Fritz, SA and Gehr, B and Goheen, JR and Gurarie, E and Hebblewhite, M and Heurich, M and Hewison, AJM and Hof, C and Hurme, E and Isbell, LA and Janssen, R and Jeltsch, F and Kaczensky, P and Kane, A and Kappeler, PM and Kauffman, M and Kays, R and Kimuyu, D and Koch, F and Kranstauber, B and LaPoint, S and Leimgruber, P and Linnell, JDC and López-López, P and Markham, AC and Mattisson, J and Medici, EP and Mellone, U and Merrill, E and de Miranda Mourão, G and Morato, RG and Morellet, N and Morrison, TA and Díaz-Muñoz, SL and Mysterud, A and Nandintsetseg, D and Nathan, R and Niamir, A and Odden, J and O'Hara, RB and Oliveira-Santos, LGR and Olson, KA and Patterson, BD and Cunha de Paula, R and Pedrotti, L and Reineking, B and Rimmler, M and Rogers, TL and Rolandsen, CM and Rosenberry, CS and Rubenstein, DI and Safi, K and Saïd, S and Sapir, N and Sawyer, H and Schmidt, NM and Selva, N and Sergiel, A and Shiilegdamba, E and Silva, JP and Singh, N and Solberg, EJ and Spiegel, O and Strand, O and Sundaresan, S and Ullmann, W and Voigt, U and Wall, J and Wattles, D and Wikelski, M and Wilmers, CC and Wilson, JW and Wittemyer, G and Zięba, F and Zwijacz-Kozica, T and Mueller, T}, title = {Moving in the Anthropocene: Global reductions in terrestrial mammalian movements.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6374}, pages = {466-469}, doi = {10.1126/science.aam9712}, pmid = {29371471}, issn = {1095-9203}, mesh = {*Animal Migration ; Animals ; Geographic Information Systems ; *Human Activities ; Humans ; *Mammals ; }, abstract = {Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral changes of individual animals and to the exclusion of species with long-range movements from areas with higher human impact. Global loss of vagility alters a key ecological trait of animals that affects not only population persistence but also ecosystem processes such as predator-prey interactions, nutrient cycling, and disease transmission.}, }
@article {pmid29362551, year = {2017}, author = {Filippova, N and Bulyonkova, T}, title = {The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia).}, journal = {Biodiversity data journal}, volume = {}, number = {5}, pages = {e20732}, doi = {10.3897/BDJ.5.e20732}, pmid = {29362551}, issn = {1314-2828}, abstract = {Background: The diversity of macrofungi in the vicinities of Khanty-Mansiysk (Yugra, Russia) was surveyed using a method of permanent sampling plots. Ten plots, each consisting of a number of micro-plots, were established in several different communities ranging from old-growth mixed taiga forest to its derivatives in cutting succession and bogged areas. For more complete registration of the mycota, plots were supplemented with random walking routes directly nearby. Survey results were subjected to various quantitative analyses which allowed not only to evaluate the diversity of fungi but also to obtain valuable information on occurrence, abundance and ecology of individual species as well as community structure and its dynamics in the course of ecological succession. The paper reports the results of the first year of observations.<br><br>New information: 460 species of terrestrial macrofungi revealed in a poorly explored area in middle taiga of West Siberia. The plot-based study revealed differences between communities of terrestrial macrofungi of old coniferous forests, their after-cutting secondary formations and bogged stages. The survey allowed to reveal records of 3 species listed in the Red Data Book of Russia and 9 species listed in the Red Data Book of Yugra.}, }
@article {pmid29315317, year = {2018}, author = {Marshall, HH and Griffiths, DJ and Mwanguhya, F and Businge, R and Griffiths, AGF and Kyabulima, S and Mwesige, K and Sanderson, JL and Thompson, FJ and Vitikainen, EIK and Cant, MA}, title = {Data collection and storage in long-term ecological and evolutionary studies: The Mongoose 2000 system.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190740}, pmid = {29315317}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; Computers ; Data Collection ; Databases, Factual ; *Ecosystem ; Environmental Monitoring/*methods ; Female ; Herpestidae ; Humans ; Male ; Pregnancy ; Smartphone ; Uganda ; }, abstract = {Studying ecological and evolutionary processes in the natural world often requires research projects to follow multiple individuals in the wild over many years. These projects have provided significant advances but may also be hampered by needing to accurately and efficiently collect and store multiple streams of the data from multiple individuals concurrently. The increase in the availability and sophistication of portable computers (smartphones and tablets) and the applications that run on them has the potential to address many of these data collection and storage issues. In this paper we describe the challenges faced by one such long-term, individual-based research project: the Banded Mongoose Research Project in Uganda. We describe a system we have developed called Mongoose 2000 that utilises the potential of apps and portable computers to meet these challenges. We discuss the benefits and limitations of employing such a system in a long-term research project. The app and source code for the Mongoose 2000 system are freely available and we detail how it might be used to aid data collection and storage in other long-term individual-based projects.}, }
@article {pmid29220487, year = {2017}, author = {Lassalle, F and Planel, R and Penel, S and Chapulliot, D and Barbe, V and Dubost, A and Calteau, A and Vallenet, D and Mornico, D and Bigot, T and Guéguen, L and Vial, L and Muller, D and Daubin, V and Nesme, X}, title = {Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3413-3431}, pmid = {29220487}, issn = {1759-6653}, mesh = {Agrobacterium/*cytology/*genetics ; *Biological Evolution ; Computational Biology ; *Ecology ; *Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Software ; }, abstract = {Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.}, }
@article {pmid29198378, year = {2018}, author = {Matz, MV}, title = {Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms.}, journal = {Trends in genetics : TIG}, volume = {34}, number = {2}, pages = {121-132}, doi = {10.1016/j.tig.2017.11.002}, pmid = {29198378}, issn = {0168-9525}, mesh = {Adaptation, Biological/genetics ; Animals ; Biological Evolution ; DNA Methylation ; Ecology ; Gene Ontology ; *Genetics, Population ; *Genome ; Genomics/instrumentation/*methods ; High-Throughput Nucleotide Sequencing/economics/*methods/trends ; *Models, Animal ; Molecular Sequence Annotation ; }, abstract = {The application of genomic approaches to 'obscure model organisms' (OMOs), meaning species with no prior genomic resources, enables increasingly sophisticated studies of the genomic basis of evolution, acclimatization, and adaptation in real ecological contexts. I consider here ecological questions that can be addressed using OMOs, and indicate optimal sequencing and data-handling solutions for each case. With this I hope to promote the diversity of OMO-based projects that would capitalize on the peculiarities of the natural history of OMOs and could feasibly be completed within the scope of a single PhD thesis.}, }
@article {pmid29186423, year = {2018}, author = {Richardson, MF and Sequeira, F and Selechnik, D and Carneiro, M and Vallinoto, M and Reid, JG and West, AJ and Crossland, MR and Shine, R and Rollins, LA}, title = {Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.}, journal = {GigaScience}, volume = {7}, number = {1}, pages = {1-7}, pmid = {29186423}, issn = {2047-217X}, mesh = {Animals ; Aquatic Organisms/*genetics/growth &amp; development ; Benchmarking ; Bufonidae/*genetics/growth &amp; development ; Chromosome Mapping ; Female ; Gene Library ; Gene Ontology ; *Genome ; High-Throughput Nucleotide Sequencing ; *Introduced Species ; Life Cycle Stages/*genetics ; Male ; Molecular Sequence Annotation ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {Background: Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range.<br><br>Findings: Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available.<br><br>Conclusions: This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers.}, }
@article {pmid29184540, year = {2017}, author = {Walter, JM and Coutinho, FH and Dutilh, BE and Swings, J and Thompson, FL and Thompson, CC}, title = {Ecogenomics and Taxonomy of Cyanobacteria Phylum.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2132}, pmid = {29184540}, issn = {1664-302X}, abstract = {Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.}, }
@article {pmid29153398, year = {2017}, author = {Dornburg, A and Townsend, JP and Wang, Z}, title = {Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data.}, journal = {Advances in genetics}, volume = {100}, number = {}, pages = {1-47}, doi = {10.1016/bs.adgen.2017.09.007}, pmid = {29153398}, issn = {0065-2660}, mesh = {Evolution, Molecular ; Fungi/*genetics ; *Genome, Fungal ; *Genomics ; Information Systems ; Models, Genetic ; *Phylogeny ; Phylogeography ; }, abstract = {Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.}, }
@article {pmid29145425, year = {2017}, author = {Mainali, KP and Bewick, S and Thielen, P and Mehoke, T and Breitwieser, FP and Paudel, S and Adhikari, A and Wolfe, J and Slud, EV and Karig, D and Fagan, WF}, title = {Statistical analysis of co-occurrence patterns in microbial presence-absence datasets.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0187132}, pmid = {29145425}, issn = {1932-6203}, mesh = {*Datasets as Topic ; *Microbiota ; }, abstract = {Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy. First, we show how Pearson's correlation coefficient (r) and Jaccard's index (J)-two of the most common metrics for correlation analysis of presence-absence data-can contradict each other when applied to a typical microbiome dataset. In our dataset, for example, 14% of species-pairs predicted to be significantly correlated by r were not predicted to be significantly correlated using J, while 37.4% of species-pairs predicted to be significantly correlated by J were not predicted to be significantly correlated using r. Mismatch was particularly common among species-pairs with at least one rare species (<10% prevalence), explaining why r and J might differ more strongly in microbiome datasets, where there are large numbers of rare taxa. Indeed 74% of all species-pairs in our study had at least one rare species. Next, we show how Pearson's correlation coefficient can result in artificial inflation of positive taxon relationships and how this is a particular problem for microbiome studies. We then illustrate how Jaccard's index of similarity (J) can yield improvements over Pearson's correlation coefficient. However, the standard null model for Jaccard's index is flawed, and thus introduces its own set of spurious conclusions. We thus identify a better null model based on a hypergeometric distribution, which appropriately corrects for species prevalence. This model is available from recent statistics literature, and can be used for evaluating the significance of any value of an empirically observed Jaccard's index. The resulting simple, yet effective method for handling correlation analysis of microbial presence-absence datasets provides a robust means of testing and finding relationships and/or shared environmental responses among microbial taxa.}, }
@article {pmid29140991, year = {2017}, author = {Schwager, E and Mallick, H and Ventz, S and Huttenhower, C}, title = {A Bayesian method for detecting pairwise associations in compositional data.}, journal = {PLoS computational biology}, volume = {13}, number = {11}, pages = {e1005852}, pmid = {29140991}, issn = {1553-7358}, support = {T32 GM074897/GM/NIGMS NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; *Bayes Theorem ; Computational Biology/*methods ; *Computer Simulation ; Ecology ; Humans ; Markov Chains ; Microbiota ; *Models, Biological ; Proteobacteria ; }, abstract = {Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix. We also use a first-order Taylor expansion to approximate the transformation from the unobserved counts to the composition in order to investigate what characteristics of the unobserved counts can make the correlations more or less difficult to infer. On simulated datasets, we show that BAnOCC infers the true network as well as previous methods while offering the advantage of posterior inference. Larger and more realistic simulated datasets further showed that BAnOCC performs well as measured by type I and type II error rates. Finally, we apply BAnOCC to a microbial ecology dataset from the Human Microbiome Project, which in addition to reproducing established ecological results revealed unique, competition-based roles for Proteobacteria in multiple distinct habitats.}, }
@article {pmid29134195, year = {2017}, author = {Crouzeilles, R and Ferreira, MS and Chazdon, RL and Lindenmayer, DB and Sansevero, JBB and Monteiro, L and Iribarrem, A and Latawiec, AE and Strassburg, BBN}, title = {Ecological restoration success is higher for natural regeneration than for active restoration in tropical forests.}, journal = {Science advances}, volume = {3}, number = {11}, pages = {e1701345}, pmid = {29134195}, issn = {2375-2548}, abstract = {Is active restoration the best approach to achieve ecological restoration success (the return to a reference condition, that is, old-growth forest) when compared to natural regeneration in tropical forests? Our meta-analysis of 133 studies demonstrated that natural regeneration surpasses active restoration in achieving tropical forest restoration success for all three biodiversity groups (plants, birds, and invertebrates) and five measures of vegetation structure (cover, density, litter, biomass, and height) tested. Restoration success for biodiversity and vegetation structure was 34 to 56% and 19 to 56% higher in natural regeneration than in active restoration systems, respectively, after controlling for key biotic and abiotic factors (forest cover, precipitation, time elapsed since restoration started, and past disturbance). Biodiversity responses were based primarily on ecological metrics of abundance and species richness (74%), both of which take far less time to achieve restoration success than similarity and composition. This finding challenges the widely held notion that natural forest regeneration has limited conservation value and that active restoration should be the default ecological restoration strategy. The proposition that active restoration achieves greater restoration success than natural regeneration may have arisen because previous comparisons lacked controls for biotic and abiotic factors; we also did not find any difference between active restoration and natural regeneration outcomes for vegetation structure when we did not control for these factors. Future policy priorities should align the identified patterns of biophysical and ecological conditions where each or both restoration approaches are more successful, cost-effective, and compatible with socioeconomic incentives for tropical forest restoration.}, }
@article {pmid29110111, year = {2017}, author = {Goleiji, E and Hosseini, SM and Khorasani, N and Monavari, SM}, title = {Forest fire risk assessment-an integrated approach based on multicriteria evaluation.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {12}, pages = {612}, pmid = {29110111}, issn = {1573-2959}, mesh = {Disasters ; Ecology ; Environmental Monitoring/methods ; Fires/statistics &amp; numerical data ; *Forests ; Fuzzy Logic ; Geographic Information Systems ; Iran ; Risk Assessment/methods ; Trees ; Wildfires/*statistics &amp; numerical data ; }, abstract = {The present study deals with application of the weighted linear combination method for zoning of forest fire risk in Dohezar and Sehezar region of Mazandaran province in northern Iran. In this study, the effective criteria for fires were identified by the Delphi method, and these included ecological and socioeconomic parameters. In this regard, the first step comprised of digital layers; the required data were provided from databases, related centers, and field data collected in the region. Then, the map of criteria was digitized in a geographic information system, and all criteria and indexes were normalized by fuzzy logic. After that, the geographic information system (GIS 10.3) was integrated with the Weighted Linear Combination and the Analytical Network Process, to produce zonation of the forest fire risk map in the Dohezar and Sehezar region. In order to analyze accuracy of the evaluation, the results obtained from the study were compared to records of former fire incidents in the region. This was done using the Kappa coefficient test and a receiver operating characteristic curve. The model showing estimations for forest fire risk explained that the prepared map had accuracy of 90% determined by the Kappa coefficient test and the value of 0.924 by receiver operating characteristic. These results showed that the prepared map had high accuracy and efficacy.}, }
@article {pmid29053868, year = {2017}, author = {Soranno, PA and Bacon, LC and Beauchene, M and Bednar, KE and Bissell, EG and Boudreau, CK and Boyer, MG and Bremigan, MT and Carpenter, SR and Carr, JW and Cheruvelil, KS and Christel, ST and Claucherty, M and Collins, SM and Conroy, JD and Downing, JA and Dukett, J and Fergus, CE and Filstrup, CT and Funk, C and Gonzalez, MJ and Green, LT and Gries, C and Halfman, JD and Hamilton, SK and Hanson, PC and Henry, EN and Herron, EM and Hockings, C and Jackson, JR and Jacobson-Hedin, K and Janus, LL and Jones, WW and Jones, JR and Keson, CM and King, KBS and Kishbaugh, SA and Lapierre, JF and Lathrop, B and Latimore, JA and Lee, Y and Lottig, NR and Lynch, JA and Matthews, LJ and McDowell, WH and Moore, KEB and Neff, BP and Nelson, SJ and Oliver, SK and Pace, ML and Pierson, DC and Poisson, AC and Pollard, AI and Post, DM and Reyes, PO and Rosenberry, DO and Roy, KM and Rudstam, LG and Sarnelle, O and Schuldt, NJ and Scott, CE and Skaff, NK and Smith, NJ and Spinelli, NR and Stachelek, JJ and Stanley, EH and Stoddard, JL and Stopyak, SB and Stow, CA and Tallant, JM and Tan, PN and Thorpe, AP and Vanni, MJ and Wagner, T and Watkins, G and Weathers, KC and Webster, KE and White, JD and Wilmes, MK and Yuan, S}, title = {LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes.}, journal = {GigaScience}, volume = {6}, number = {12}, pages = {1-22}, pmid = {29053868}, issn = {2047-217X}, mesh = {*Databases, Factual ; Lakes/*chemistry ; United States ; *Water Quality ; }, abstract = {Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many data sets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 US states.LAGOS-NE contains data for 51 101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 data modules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situ measurements of lake water quality for a subset of the lakes from the past 3 decades for approximately 2600-12 000 lakes depending on the variable. The database contains approximately 150 000 measures of total phosphorus, 200 000 measures of chlorophyll, and 900 000 measures of Secchi depth. The water quality data were compiled from 87 lake water quality data sets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This database is one of the largest and most comprehensive databases of its type because it includes both in situ measurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales.}, }
@article {pmid29038424, year = {2017}, author = {Corander, J and Fraser, C and Gutmann, MU and Arnold, B and Hanage, WP and Bentley, SD and Lipsitch, M and Croucher, NJ}, title = {Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {12}, pages = {1950-1960}, pmid = {29038424}, issn = {2397-334X}, support = {//Wellcome Trust/United Kingdom ; R01 AI048935/AI/NIAID NIH HHS/United States ; R01 AI106786/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Pneumococcal Vaccines/immunology ; Population Dynamics ; *Selection, Genetic ; Streptococcus pneumoniae/*genetics/immunology ; }, abstract = {Many bacterial species are composed of multiple lineages distinguished by extensive variation in gene content. These often cocirculate in the same habitat, but the evolutionary and ecological processes that shape these complex populations are poorly understood. Addressing these questions is particularly important for Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen, because the changes in population structure associated with the recent introduction of partial-coverage vaccines have substantially reduced pneumococcal disease. Here we show that pneumococcal lineages from multiple populations each have a distinct combination of intermediate-frequency genes. Functional analysis suggested that these loci may be subject to negative frequency-dependent selection (NFDS) through interactions with other bacteria, hosts or mobile elements. Correspondingly, these genes had similar frequencies in four populations with dissimilar lineage compositions. These frequencies were maintained following substantial alterations in lineage prevalences once vaccination programmes began. Fitting a multilocus NFDS model of post-vaccine population dynamics to three genomic datasets using Approximate Bayesian Computation generated reproducible estimates of the influence of NFDS on pneumococcal evolution, the strength of which varied between loci. Simulations replicated the stable frequency of lineages unperturbed by vaccination, patterns of serotype switching and clonal replacement. This framework highlights how bacterial ecology affects the impact of clinical interventions.}, }
@article {pmid29023475, year = {2017}, author = {Wang, D and Li, L and Wu, G and Vasseur, L and Yang, G and Huang, P}, title = {De novo transcriptome sequencing of Isaria cateniannulata and comparative analysis of gene expression in response to heat and cold stresses.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186040}, pmid = {29023475}, issn = {1932-6203}, mesh = {Cold-Shock Response/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Gene Ontology ; Heat-Shock Response/*genetics ; Hypocreales/genetics/*physiology ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Isaria cateniannulata is a very important and virulent entomopathogenic fungus that infects many insect pest species. Although I. cateniannulata is commonly exposed to extreme environmental temperature conditions, little is known about its molecular response mechanism to temperature stress. Here, we sequenced and de novo assembled the transcriptome of I. cateniannulata in response to high and low temperature stresses using Illumina RNA-Seq technology. Our assembly encompassed 17,514 unigenes (mean length = 1,197 bp), in which 11,445 unigenes (65.34%) showed significant similarities to known sequences in NCBI non-redundant protein sequences (Nr) database. Using digital gene expression analysis, 4,483 differentially expressed genes (DEGs) were identified after heat treatment, including 2,905 up-regulated genes and 1,578 down-regulated genes. Under cold stress, 1,927 DEGs were identified, including 1,245 up-regulated genes and 682 down-regulated genes. The expression patterns of 18 randomly selected candidate DEGs resulting from quantitative real-time PCR (qRT-PCR) were consistent with their transcriptome analysis results. Although DEGs were involved in many pathways, we focused on the genes that were involved in endocytosis: In heat stress, the pathway of clathrin-dependent endocytosis (CDE) was active; however at low temperature stresses, the pathway of clathrin-independent endocytosis (CIE) was active. Besides, four categories of DEGs acting as temperature sensors were observed, including cell-wall-major-components-metabolism-related (CWMCMR) genes, heat shock protein (Hsp) genes, intracellular-compatible-solutes-metabolism-related (ICSMR) genes and glutathione S-transferase (GST). These results enhance our understanding of the molecular mechanisms of I. cateniannulata in response to temperature stresses and provide a valuable resource for the future investigations.}, }
@article {pmid28972575, year = {2017}, author = {Tedesco, PA and Beauchard, O and Bigorne, R and Blanchet, S and Buisson, L and Conti, L and Cornu, JF and Dias, MS and Grenouillet, G and Hugueny, B and Jézéquel, C and Leprieur, F and Brosse, S and Oberdorff, T}, title = {A global database on freshwater fish species occurrence in drainage basins.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {170141}, pmid = {28972575}, issn = {2052-4463}, mesh = {Animals ; Biodiversity ; Databases, Factual ; Ecosystem ; *Fishes ; Fresh Water ; }, abstract = {A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth's surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources. Alone or in combination with further datasets on species biological and ecological characteristics and their evolutionary history, this database represents a highly valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation.}, }
@article {pmid28962629, year = {2017}, author = {Soltész, Z and Erdélyi, K and Bakonyi, T and Barna, M and Szentpáli-Gavallér, K and Solt, S and Horváth, É and Palatitz, P and Kotymán, L and Dán, Á and Papp, L and Harnos, A and Fehérvári, P}, title = {West Nile virus host-vector-pathogen interactions in a colonial raptor.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {449}, pmid = {28962629}, issn = {1756-3305}, mesh = {Animals ; Antibodies, Viral/blood ; Bird Diseases/blood/transmission/*virology ; Culex/physiology/*virology ; Falconiformes/blood/*virology ; Feeding Behavior ; Female ; Host-Pathogen Interactions ; Insect Vectors/physiology/*virology ; Male ; Seroepidemiologic Studies ; West Nile Fever/transmission/*veterinary/virology ; West Nile virus/genetics/isolation &amp; purification/*physiology ; }, abstract = {BACKGROUND: Avian host species have different roles in the amplification and maintenance of West Nile virus (WNV), therefore identifying key taxa is vital in understanding WNV epidemics. Here, we present a comprehensive case study conducted on red-footed falcons, where host-vector, vector-virus and host-virus interactions were simultaneously studied to evaluate host species contribution to WNV circulation qualitatively.<br><br>RESULTS: Mosquitoes were trapped inside red-footed falcon nest-boxes by a method originally developed for the capture of blackflies and midges. We showed that this approach is also efficient for trapping mosquitoes and that the number of trapped vectors is a function of host attraction. Brood size and nestling age had a positive effect on the number of attracted Culex pipiens individuals while the blood-feeding success rate of both dominant Culex species (Culex pipiens and Culex modestus) markedly decreased after the nestlings reached 14 days of age. Using RT-PCR, we showed that WNV was present in these mosquitoes with 4.2% (CI: 0.9-7.5%) prevalence. We did not detect WNV in any of the nestling blood samples. However, a relatively high seroprevalence (25.4% CI: 18.8-33.2%) was detected with an enzyme-linked immunoabsorbent assay (ELISA). Using the ELISA OD ratios as a proxy to antibody titers, we showed that older seropositive nestlings have lower antibody levels than their younger conspecifics and that hatching order negatively influences antibody levels in broods with seropositive nestlings.<br><br>CONCLUSIONS: Red-footed falcons in the studied system are exposed to a local sylvatic WNV circulation, and the risk of infection is higher for younger nestlings. However, the lack of individuals with viremia and the high WNV seroprevalence, indicate that either host has a very short viremic period or that a large percentage of nestlings in the population receive maternal antibodies. This latter assumption is supported by the age and hatching order dependence of antibody levels found for seropositive nestlings. Considering the temporal pattern in mosquito feeding success, maternal immunity may be effective in protecting progeny against WNV infection despite the short antibody half-life measured in various other species. We conclude that red-footed falcons seem to have low WNV host competence and are unlikely to be effective virus reservoirs in the studied region.}, }
@article {pmid28958130, year = {2018}, author = {Martin, RW and Waits, ER and Nietch, CT}, title = {Empirically-based modeling and mapping to consider the co-occurrence of ecological receptors and stressors.}, journal = {The Science of the total environment}, volume = {613-614}, number = {}, pages = {1228-1239}, pmid = {28958130}, issn = {1879-1026}, support = {EPA999999//Intramural EPA/United States ; }, mesh = {Animals ; Bayes Theorem ; Ecology ; Environmental Monitoring/*methods ; Fishes ; *Geographic Information Systems ; Models, Theoretical ; Ohio ; Rivers/chemistry ; Software ; }, abstract = {Part of the ecological risk assessment process involves examining the potential for environmental stressors and ecological receptors to co-occur across a landscape. In this study, we introduce a Bayesian joint modeling framework for use in evaluating and mapping the co-occurrence of stressors and receptors using empirical data, open-source statistical software, and Geographic Information Systems tools and data. To illustrate the approach, we apply the framework to bioassessment data on stream fishes and nutrients collected from a watershed in southwestern Ohio. The results highlighted the joint model's ability to parse and exploit statistical dependencies in order to provide empirical insight into the potential environmental and ecotoxicological interactions influencing co-occurrence. We also demonstrate how probabilistic predictions can be generated and mapped to visualize spatial patterns in co-occurrences. For practitioners, we believe that this data-driven approach to modeling and mapping co-occurrence can lead to more quantitatively transparent and robust assessments of ecological risk.}, }
@article {pmid28957328, year = {2017}, author = {Bauer, M and Graf, IR and Ngampruetikorn, V and Stephens, GJ and Frey, E}, title = {Exploiting ecology in drug pulse sequences in favour of population reduction.}, journal = {PLoS computational biology}, volume = {13}, number = {9}, pages = {e1005747}, pmid = {28957328}, issn = {1553-7358}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/*drug effects ; *Bacterial Infections/drug therapy/microbiology ; Caenorhabditis elegans ; Computational Biology ; Ecology ; *Models, Biological ; *Population Dynamics ; }, abstract = {A deterministic population dynamics model involving birth and death for a two-species system, comprising a wild-type and more resistant species competing via logistic growth, is subjected to two distinct stress environments designed to mimic those that would typically be induced by temporal variation in the concentration of a drug (antibiotic or chemotherapeutic) as it permeates through the population and is progressively degraded. Different treatment regimes, involving single or periodical doses, are evaluated in terms of the minimal population size (a measure of the extinction probability), and the population composition (a measure of the selection pressure for resistance or tolerance during the treatment). We show that there exist timescales over which the low-stress regime is as effective as the high-stress regime, due to the competition between the two species. For multiple periodic treatments, competition can ensure that the minimal population size is attained during the first pulse when the high-stress regime is short, which implies that a single short pulse can be more effective than a more protracted regime. Our results suggest that when the duration of the high-stress environment is restricted, a treatment with one or multiple shorter pulses can produce better outcomes than a single long treatment. If ecological competition is to be exploited for treatments, it is crucial to determine these timescales, and estimate for the minimal population threshold that suffices for extinction. These parameters can be quantified by experiment.}, }
@article {pmid28923966, year = {2017}, author = {Cardoso, D and Särkinen, T and Alexander, S and Amorim, AM and Bittrich, V and Celis, M and Daly, DC and Fiaschi, P and Funk, VA and Giacomin, LL and Goldenberg, R and Heiden, G and Iganci, J and Kelloff, CL and Knapp, S and Cavalcante de Lima, H and Machado, AFP and Dos Santos, RM and Mello-Silva, R and Michelangeli, FA and Mitchell, J and Moonlight, P and de Moraes, PLR and Mori, SA and Nunes, TS and Pennington, TD and Pirani, JR and Prance, GT and de Queiroz, LP and Rapini, A and Riina, R and Rincon, CAV and Roque, N and Shimizu, G and Sobral, M and Stehmann, JR and Stevens, WD and Taylor, CM and Trovó, M and van den Berg, C and van der Werff, H and Viana, PL and Zartman, CE and Forzza, RC}, title = {Amazon plant diversity revealed by a taxonomically verified species list.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {40}, pages = {10695-10700}, pmid = {28923966}, issn = {1091-6490}, mesh = {*Biodiversity ; Brazil ; *Databases, Factual ; Plants/*classification ; *Rainforest ; }, abstract = {Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.}, }
@article {pmid28921829, year = {2018}, author = {Fisher, RA and Koven, CD and Anderegg, WRL and Christoffersen, BO and Dietze, MC and Farrior, CE and Holm, JA and Hurtt, GC and Knox, RG and Lawrence, PJ and Lichstein, JW and Longo, M and Matheny, AM and Medvigy, D and Muller-Landau, HC and Powell, TL and Serbin, SP and Sato, H and Shuman, JK and Smith, B and Trugman, AT and Viskari, T and Verbeeck, H and Weng, E and Xu, C and Xu, X and Zhang, T and Moorcroft, PR}, title = {Vegetation demographics in Earth System Models: A review of progress and priorities.}, journal = {Global change biology}, volume = {24}, number = {1}, pages = {35-54}, doi = {10.1111/gcb.13910}, pmid = {28921829}, issn = {1365-2486}, mesh = {*Earth (Planet) ; *Ecosystem ; *Models, Biological ; *Plants ; Population Dynamics ; Uncertainty ; }, abstract = {Numerous current efforts seek to improve the representation of ecosystem ecology and vegetation demographic processes within Earth System Models (ESMs). These developments are widely viewed as an important step in developing greater realism in predictions of future ecosystem states and fluxes. Increased realism, however, leads to increased model complexity, with new features raising a suite of ecological questions that require empirical constraints. Here, we review the developments that permit the representation of plant demographics in ESMs, and identify issues raised by these developments that highlight important gaps in ecological understanding. These issues inevitably translate into uncertainty in model projections but also allow models to be applied to new processes and questions concerning the dynamics of real-world ecosystems. We argue that stronger and more innovative connections to data, across the range of scales considered, are required to address these gaps in understanding. The development of first-generation land surface models as a unifying framework for ecophysiological understanding stimulated much research into plant physiological traits and gas exchange. Constraining predictions at ecologically relevant spatial and temporal scales will require a similar investment of effort and intensified inter-disciplinary communication.}, }
@article {pmid28920370, year = {2016}, author = {Jiang, SY and Sun, HB and Qin, JH and Zhu, WT and Sun, H}, title = {[Functional production regionalization for Fritillariae Cirrhosae Bulbus based on growth and quality suitability assessment].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3194-3201}, doi = {10.4268/cjcmm20161713}, pmid = {28920370}, issn = {1001-5302}, mesh = {China ; Ecology ; Fritillaria/*growth &amp; development ; Geographic Information Systems ; Plants, Medicinal/growth &amp; development ; }, abstract = {The major contributing factors for growth of endangered medicinal plants of Fritillariae Cirrhosae Bulbus were screened on the GIS platform by using the MaxEnt model, and spatial distribution data of the medicine quality suitability were generated by geostatistics interpolation based on reported measured data of ecology and quality suitability assessment. On this basis, a functional production cultivation regionalization with high feasibility and operability were formatted for protection, wild monitoring, and cultivation of this plant by fuzzy superposition of spatial suitability data of ecology and quality, as well as integrated with land use and cover data. Therefore, a novel assessment and regionalization method were presented for ecology, growth and quality suitability of the Chinese traditional medicinal plants. This method is expected to overcome shortage of traditional regionalization methods difficult to distinguish the contribution of ecological factors and quality factors, which provide an innovative theory and methodology for regionalization, and is helpful to practical application of wild resource protection, monitoring, and commercialization cultivation for traditional Chinese medicinal plants.}, }
@article {pmid28920369, year = {2016}, author = {Liu, X and Yang, YF and Song, HP and Zhang, XB and Huang, LQ and Wu, HZ}, title = {[Cultural regionalization for Coptis chinensis based on 3S technology platform Ⅰ. Study on growth suitability for Coptis chinensis based on ecological factors analysis by Maxent and ArcGIS model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3186-3193}, doi = {10.4268/cjcmm20161712}, pmid = {28920369}, issn = {1001-5302}, mesh = {Alkaloids/analysis ; China ; Coptis/chemistry/*growth &amp; development ; Ecology ; Ecosystem ; Geographic Information Systems ; Rhizome/chemistry/growth &amp; development ; }, abstract = {At the urgent request of Coptis chinensis planting,growth suitability as assessment indicators for C. chinensis cultivation was proposed and analyzed in this paper , based on chemical quality determination and ecological fators analysis by Maxent and ArcGIS model. Its potential distribution areas at differernt suitability grade and regionalization map were formulated based on statistical theory and growth suitability theory. The results showed that the most suitable habitats is some parts of Chongqing and Hubei province, such as Shizhu, Lichuan, Wulong, Wuxi, Enshi. There are seven ecological factor is the main ecological factors affect the growth of Coptidis Rhizoma, including altitude, precipitation in February and September and the rise of precipitation and altitude is conducive to the accumulation of total alkaloid content in C. chinensis. Therefore, The results of the study not only illustrates the most suitable for the surroundings of Coptidis Rhizoma, also helpful to further research and practice of cultivation regionalization, wild resource monitoring and large-scale cultivation of traditional Chinese medicine plants.}, }
@article {pmid28920368, year = {2016}, author = {Miao, Q and Yuan, YJ and Luo, GM and Wei, CH and Rao, YQ and Gong, YH and Zhang, L and Shao, J and Dong, YK}, title = {[Study on ecological suitability of Gardenia jasminoides based on ArcGIS and Maxent model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3181-3185}, doi = {10.4268/cjcmm20161711}, pmid = {28920368}, issn = {1001-5302}, mesh = {China ; Climate ; Ecology ; Gardenia/*growth &amp; development ; Geographic Information Systems ; }, abstract = {The application of ArcGIS and Maxent modelto analyze the ecological suitability of Gardenia jasminoides.Taking 85 batches of Gardenia as the basis of analysis, the selection of ecological factors for the growth of Gardenia. The results showed that the average precipitation in April, the average precipitation in November and the average precipitation in August were the most important factors affecting the growth of Gardenia. The relative concentration of Gardenia suitable growth region,north to the south of Shaanxi province, south of Henan, central Anhui, south to the north of Hainan province, west to central Sichuan province, east of Zhejiang coastal area, northeast of Taiwan.}, }
@article {pmid28920367, year = {2016}, author = {Lu, YY and Yang, YM and Ma, XH and Zhang, XB and Zhu, SD and Jin, L}, title = {[Ecology suitability study of Chinese materia medica Gentianae Macrophyllae Radix].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3176-3180}, doi = {10.4268/cjcmm20161710}, pmid = {28920367}, issn = {1001-5302}, mesh = {Altitude ; China ; Climate ; Ecology ; Gentiana/*growth &amp; development ; Geographic Information Systems ; }, abstract = {This paper is aimed to predict ecology suitability distribution of Gentianae Macrophyllae Radix and search the main ecological factors affecting the suitability distribution. The 313 distribution information about G. macrophylla, 186 distribution information about G. straminea, 343 distribution information about G. dauricaand 131 distribution information about G. crasicaulis were collected though investigation and network sharing platform data . The ecology suitable distribution factors for production Gentianae Macrophyllae Radix was analyzed respectively by the software of ArcGIS and MaxEnt with 55 environmental factors. The result of MaxEnt prediction was very well (AUC was above 0.9). The results of predominant factors analysis showed that precipitation and altitude were all the major factors impacting the ecology suitable of Getiana Macrophylla Radix production. G. macrophylla ecology suitable region was mainly concentrated in south of Gansu, Shanxi, central of Shaanxi and east of Qinghai provinces. G. straminea ecology suitable region was mainly concentrated in southwest of Gansu, east of Qinghai, north and northwest of Sichuan, east of Xizang province. G. daurica ecology suitable region was mainly concentrated in south and southwest of Gansu, east of Qinghai, Shanxi and north of Shaanxi province. G. crasicaulis ecology suitable region was mainly concentrated in Sichuan and north of Yunnan, east of Xizang, south of Gansu and east of Qinghai province. The ecological suitability distribution result of Gentianae Macrophyllae Radix was consistent with each species actual distribution. The study could provide reference for the collection and protection of wild resources, meanwhile, provide the basis for the selection of cultivation area of Gentiana Macrophylla Radix.}, }
@article {pmid28920364, year = {2016}, author = {Shi, ZW and Ma, CJ and Kang, CZ and Wang, L and Zhang, ZH and Chen, JF and Zhang, XB and Liu, DH}, title = {[Ecological suitability regionalization for Gastrodia elata in Zhaotong based on Maxent and ArcGIS].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3155-3163}, doi = {10.4268/cjcmm20161707}, pmid = {28920364}, issn = {1001-5302}, mesh = {China ; Climate ; Ecology ; Gastrodia/*growth &amp; development ; Geographic Information Systems ; Soil ; }, abstract = {In this paper, the potential distribution information and ecological suitability regionalization for Gastrodia elata in Zhaotong were studied based on the climate, terrain, soil and vegetation factors analysis by Maxent and ArcGIS. The results showed that the highly potential distribution (suitability index>0.6) mainly located in Zhaotong, Yunnan province（Zhenxiong,Yiliang and Daguan county, with an area of 2 872 km²）, and Bijie, Guizhou province （Hezhang,Bijie,Weining county, 1 251 km²）. The AUC of ROC curve was above 0.99, indicating that the predictive results with the Maxent model were highly precise. The main ecological factors determining the potential distribution were the altitude, average rainfall in November, average rainfall in October, vegetation types, average rainfall in March, average rainfall in April,soil types,isothermal characteristic and average rainfall in June. The environmental variables in the highly potential areas were determined as altitude around 1 450-2 200 m,annual average temperature around 18.0-20.4 ℃,annual average precipitation around 900 mm,yellow soil or yellow brown soil,and acid sandy loam or slightly acidic sandy loam.The results will provide valuable references for plantation regionalization and the siting for imitation wild planting of G. elata in Zhaotong.}, }
@article {pmid28920360, year = {2016}, author = {Wang, HQ and Wang, Q and Ma, L and Ding, R and Di, TY and An, W and Zhang, XB and Wang, YH}, title = {[Production regionalization study of Lycii Fructus].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3127-3131}, doi = {10.4268/cjcmm20161703}, pmid = {28920360}, issn = {1001-5302}, mesh = {China ; Climate ; Ecosystem ; Geographic Information Systems ; Lycium/*growth &amp; development ; Soil ; }, abstract = {The distribution information of Lycii Fructus was collected by interview investigation and field survey, and 46 related environmental factors were collected, some kinds of functional chemical constituents the of Lycii Fructus were analyzed. Integrated climate, topography and other related ecological factors, the habitat suitability study was conducted based on Arc geographic information system(ArcGIS),and maximum entropy model. The AUC of ROC curve was both above 0.95, indicating that the predictive results with the maximum model were highly precise. The results showed that 5 major ecological factors had obvious influence on ecology suitability distributions of Lycii Fructus, including soil pH, soil subclass, vegetation type and in August the average temperature et al. It is suitable for the living habits of the Lycii Fructus, dry, cool weather, more hardy, drought-resistant, alkali soil, which is suitable for distribution in the northern temperate plains. In addition, the ecological suitability regionalization based on the chemical constituents of Lycii Fructus also provides a new suitable distribution area other than the traditional distribution area, which provides a scientific basis for the reasonable introduction of Lycii Fructus.}, }
@article {pmid28886010, year = {2017}, author = {Joshi, J and Couzin, ID and Levin, SA and Guttal, V}, title = {Mobility can promote the evolution of cooperation via emergent self-assortment dynamics.}, journal = {PLoS computational biology}, volume = {13}, number = {9}, pages = {e1005732}, pmid = {28886010}, issn = {1553-7358}, mesh = {Animals ; *Biological Evolution ; Cell Movement ; Computational Biology ; *Cooperative Behavior ; Locomotion ; *Models, Biological ; Selection, Genetic ; }, abstract = {The evolution of costly cooperation, where cooperators pay a personal cost to benefit others, requires that cooperators interact more frequently with other cooperators. This condition, called positive assortment, is known to occur in spatially-structured viscous populations, where individuals typically have low mobility and limited dispersal. However many social organisms across taxa, from cells and bacteria, to birds, fish and ungulates, are mobile, and live in populations with considerable inter-group mixing. In the absence of information regarding others' traits or conditional strategies, such mixing may inhibit assortment and limit the potential for cooperation to evolve. Here we employ spatially-explicit individual-based evolutionary simulations to incorporate costs and benefits of two coevolving costly traits: cooperative and local cohesive tendencies. We demonstrate that, despite possessing no information about others' traits or payoffs, mobility (via self-propulsion or environmental forcing) facilitates assortment of cooperators via a dynamically evolving difference in the cohesive tendencies of cooperators and defectors. We show analytically that this assortment can also be viewed in a multilevel selection framework, where selection for cooperation among emergent groups can overcome selection against cooperators within the groups. As a result of these dynamics, we find an oscillatory pattern of cooperation and defection that maintains cooperation even in the absence of well known mechanisms such as kin interactions, reciprocity, local dispersal or conditional strategies that require information on others' strategies or payoffs. Our results offer insights into differential adhesion based mechanisms for positive assortment and reveal the possibility of cooperative aggregations in dynamic fission-fusion populations.}, }
@article {pmid28873454, year = {2017}, author = {Müller, M and Seifert, S and Lübbe, T and Leuschner, C and Finkeldey, R}, title = {De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184167}, pmid = {28873454}, issn = {1932-6203}, mesh = {*Droughts ; Fagus/*genetics/*physiology ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Genotype ; Microsatellite Repeats/genetics ; Molecular Sequence Annotation ; Plant Stomata/physiology ; RNA, Messenger/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, RNA ; Stress, Physiological/genetics ; Transcriptome/*genetics ; }, abstract = {Despite the ecological and economic importance of European beech (Fagus sylvatica L.) genomic resources of this species are still limited. This hampers an understanding of the molecular basis of adaptation to stress. Since beech will most likely be threatened by the consequences of climate change, an understanding of adaptive processes to climate change-related drought stress is of major importance. Here, we used RNA-seq to provide the first drought stress-related transcriptome of beech. In a drought stress trial with beech saplings, 50 samples were taken for RNA extraction at five points in time during a soil desiccation experiment. De novo transcriptome assembly and analysis of differential gene expression revealed 44,335 contigs, and 662 differentially expressed genes between the stress and normally watered control group. Gene expression was specific to the different time points, and only five genes were significantly differentially expressed between the stress and control group on all five sampling days. GO term enrichment showed that mostly genes involved in lipid- and homeostasis-related processes were upregulated, whereas genes involved in oxidative stress response were downregulated in the stressed seedlings. This study gives first insights into the genomic drought stress response of European beech, and provides new genetic resources for adaptation research in this species.}, }
@article {pmid28872632, year = {2017}, author = {Oliveira, BF and São-Pedro, VA and Santos-Barrera, G and Penone, C and Costa, GC}, title = {AmphiBIO, a global database for amphibian ecological traits.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {170123}, pmid = {28872632}, issn = {2052-4463}, mesh = {*Amphibians ; Animals ; Databases, Factual ; Ecosystem ; Phylogeny ; }, abstract = {Current ecological and evolutionary research are increasingly moving from species- to trait-based approaches because traits provide a stronger link to organism's function and fitness. Trait databases covering a large number of species are becoming available, but such data remains scarce for certain groups. Amphibians are among the most diverse vertebrate groups on Earth, and constitute an abundant component of major terrestrial and freshwater ecosystems. They are also facing rapid population declines worldwide, which is likely to affect trait composition in local communities, thereby impacting ecosystem processes and services. In this context, we introduce AmphiBIO, a comprehensive database of natural history traits for amphibians worldwide. The database releases information on 17 traits related to ecology, morphology and reproduction features of amphibians. We compiled data from more than 1,500 literature sources, and for more than 6,500 species of all orders (Anura, Caudata and Gymnophiona), 61 families and 531 genera. This database has the potential to allow unprecedented large-scale analyses in ecology, evolution, and conservation of amphibians.}, }
@article {pmid28852870, year = {2017}, author = {Tumolo, BB and Flinn, MB}, title = {Top-down effects of an invasive omnivore: detection in long-term monitoring of large-river reservoir chlorophyll-a.}, journal = {Oecologia}, volume = {185}, number = {2}, pages = {293-303}, pmid = {28852870}, issn = {1432-1939}, support = {F13AP00999//U.S. Fish and Wildlife Service/ ; }, mesh = {Animals ; Carps/*physiology ; Chlorophyll/*analysis ; Chlorophyll A ; Databases, Factual ; *Food Chain ; *Introduced Species ; Kentucky ; *Lakes ; Phytoplankton/chemistry/growth &amp; development ; *Rivers ; }, abstract = {Invasive species are capable of altering ecosystems through the consumption of basal resources. However, quantifying the effects of invasive species in large ecosystems is challenging. Measuring changes in basal resources (i.e., phytoplankton) at an ecosystem scale is an important and potentially translatable response vital to the understanding of how introduced species influence ecosystems. In this study, we analyzed patterns of early summer chlorophyll-a in a large-river reservoir in response to invasion of silver carp (Hypophthalmichthys molitrix). We used 25 years of ecological data from a 30-km reach of Kentucky Lake collected before and after silver carp establishment. We found significant decreases in chlorophyll-a within certain reservoir habitats since establishment of silver carp. Additionally, environmental and biological drivers of phytoplankton production showed no significant differences before and after invasion. These results suggest seasonal, and habitat-specific consumptive effects of invasive silver carp on an important basal food web resource. Further, our results convey the utility of long-term quantitative biological and physiochemical data in understanding ecosystem responses to elements of global change (i.e., species invasions). Importantly, the observed changes in the basal food web resource of Kentucky Lake may apply to other ecosystems facing invasion by silver carp (e.g., Laurentian Great Lakes). Our study offers insight into the mechanisms by which silver carp may influence ecosystems and furthers our understanding of invasive omnivores.}, }
@article {pmid28813450, year = {2017}, author = {Chen, H and Peng, S and Dai, L and Zou, Q and Yi, B and Yang, X and Ma, ZS}, title = {Oral microbial community assembly under the influence of periodontitis.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182259}, pmid = {28813450}, issn = {1932-6203}, mesh = {Algorithms ; *Biodiversity ; Case-Control Studies ; Datasets as Topic ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Mouth Mucosa/*microbiology ; Periodontitis/*microbiology ; }, abstract = {Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.'s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li &amp; Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher's exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or 'phenotype' of community assembly), it does not seem to cause the 'mutation' of the 'genotype&quot; (mechanism) of community assembly. We argue that the 'phenotypic' changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.}, }
@article {pmid28783034, year = {2017}, author = {Reiczigel, J and Rozsa, L}, title = {Do small samples underestimate mean abundance? It depends on what type of bias we consider.}, journal = {Folia parasitologica}, volume = {64}, number = {}, pages = {}, doi = {10.14411/fp.2017.025}, pmid = {28783034}, issn = {0015-5683}, abstract = {Former authors claimed that, due to parasites' aggregated distribution, small samples underestimate the true population mean abundance. Here we show that this claim is false or true, depending on what is meant by 'underestimate' or, mathematically speaking, how we define 'bias'. The 'how often' and 'on average' views lead to different conclusions because sample mean abundance itself exhibits an aggregated distribution: most often it falls slightly below the true population mean, while sometimes greatly exceeds it. Since the several small negative deviations are compensated by a few greater positive ones, the average of sample means approximates the true population mean.}, }
@article {pmid28766908, year = {2018}, author = {Kissling, WD and Ahumada, JA and Bowser, A and Fernandez, M and Fernández, N and García, EA and Guralnick, RP and Isaac, NJB and Kelling, S and Los, W and McRae, L and Mihoub, JB and Obst, M and Santamaria, M and Skidmore, AK and Williams, KJ and Agosti, D and Amariles, D and Arvanitidis, C and Bastin, L and De Leo, F and Egloff, W and Elith, J and Hobern, D and Martin, D and Pereira, HM and Pesole, G and Peterseil, J and Saarenmaa, H and Schigel, D and Schmeller, DS and Segata, N and Turak, E and Uhlir, PF and Wee, B and Hardisty, AR}, title = {Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {1}, pages = {600-625}, doi = {10.1111/brv.12359}, pmid = {28766908}, issn = {1469-185X}, abstract = {Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence-absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.}, }
@article {pmid28747480, year = {2017}, author = {Votier, SC and Fayet, AL and Bearhop, S and Bodey, TW and Clark, BL and Grecian, J and Guilford, T and Hamer, KC and Jeglinski, JWE and Morgan, G and Wakefield, E and Patrick, SC}, title = {Effects of age and reproductive status on individual foraging site fidelity in a long-lived marine predator.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1859}, pages = {}, pmid = {28747480}, issn = {1471-2954}, mesh = {*Age Factors ; Animals ; *Appetitive Behavior ; Birds/*physiology ; Ecology ; Feeding Behavior ; Geographic Information Systems ; *Reproduction ; }, abstract = {Individual foraging specializations, where individuals use a small component of the population niche width, are widespread in nature with important ecological and evolutionary implications. In long-lived animals, foraging ability develops with age, but we know little about the ontogeny of individuality in foraging. Here we use precision global positioning system (GPS) loggers to examine how individual foraging site fidelity (IFSF), a common component of foraging specialization, varies between breeders, failed breeders and immatures in a long-lived marine predator-the northern gannet Morus bassanus Breeders (aged 5+) showed strong IFSF: they had similar routes and were faithful to distal points during successive trips. However, centrally placed immatures (aged 2-3) were far more exploratory and lacked route or foraging site fidelity. Failed breeders were intermediate: some with strong fidelity, others being more exploratory. Individual foraging specializations were previously thought to arise as a function of heritable phenotypic differences or via social transmission. Our results instead suggest a third alternative-in long-lived species foraging sites are learned during exploratory behaviours early in life, which become canalized with age and experience, and refined where possible-the exploration-refinement foraging hypothesis. We speculate similar patterns may be present in other long-lived species and moreover that long periods of immaturity may be a consequence of such memory-based individual foraging strategies.}, }
@article {pmid28746735, year = {2018}, author = {Orsini, L and Brown, JB and Shams Solari, O and Li, D and He, S and Podicheti, R and Stoiber, MH and Spanier, KI and Gilbert, D and Jansen, M and Rusch, DB and Pfrender, ME and Colbourne, JK and Frilander, MJ and Kvist, J and Decaestecker, E and De Schamphelaere, KAC and De Meester, L}, title = {Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {886-897}, pmid = {28746735}, issn = {1365-294X}, support = {R00 HG006698/HG/NHGRI NIH HHS/United States ; R24 GM078274/GM/NIGMS NIH HHS/United States ; }, abstract = {Natural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor largely limit our understanding of biological responses to environmental change. In particular, early response to unpredictable environmental change, critical to survival and fitness in later life stages, is largely uncharacterized. Here, we characterize the early transcriptional response of the keystone species Daphnia magna to twelve environmental perturbations, including biotic and abiotic stressors. We first perform a differential expression analysis aimed at identifying differential regulation of individual genes in response to stress. This preliminary analysis revealed that a few individual genes were responsive to environmental perturbations and they were modulated in a stressor and genotype-specific manner. Given the limited number of differentially regulated genes, we were unable to identify pathways involved in stress response. Hence, to gain a better understanding of the genetic and functional foundation of tolerance to multiple environmental stressors, we leveraged the correlative nature of networks and performed a weighted gene co-expression network analysis. We discovered that approximately one-third of the Daphnia genes, enriched for metabolism, cell signalling and general stress response, drives transcriptional early response to environmental stress and it is shared among genetic backgrounds. This initial response is followed by a genotype- and/or condition-specific transcriptional response with a strong genotype-by-environment interaction. Intriguingly, genotype- and condition-specific transcriptional response is found in genes not conserved beyond crustaceans, suggesting niche-specific adaptation.}, }
@article {pmid28723902, year = {2017}, author = {Igea, J and Miller, EF and Papadopulos, AST and Tanentzap, AJ}, title = {Seed size and its rate of evolution correlate with species diversification across angiosperms.}, journal = {PLoS biology}, volume = {15}, number = {7}, pages = {e2002792}, pmid = {28723902}, issn = {1545-7885}, mesh = {Adaptation, Biological ; Bayes Theorem ; Biodiversity ; *Biological Evolution ; Botany/methods ; Databases, Factual ; Genetic Speciation ; Genome Size ; Genome, Plant ; Magnoliopsida/classification/genetics/*growth &amp; development/physiology ; *Models, Biological ; *Phylogeny ; Reproductive Isolation ; Seeds/classification/genetics/*growth &amp; development/physiology ; Species Specificity ; Time Factors ; }, abstract = {Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, which can subsequently influence speciation and extinction. The rate at which seed mass changes across the angiosperm phylogeny may also be linked to diversification by increasing reproductive isolation and allowing access to novel ecological niches. However, the magnitude and direction of the association between seed mass and diversification has not been assessed across the angiosperm phylogeny. Here, we show that absolute seed size and the rate of change in seed size are both associated with variation in diversification rates. Based on the largest available angiosperm phylogenetic tree, we found that smaller-seeded plants had higher rates of diversification, possibly due to improved colonisation potential. The rate of phenotypic change in seed size was also strongly positively correlated with speciation rates, providing rare, large-scale evidence that rapid morphological change is associated with species divergence. Our study now reveals that variation in morphological traits and, importantly, the rate at which they evolve can contribute to explaining the extremely uneven distribution of diversity across the ToL.}, }
@article {pmid28681587, year = {2017}, author = {Zhang, AL and Sun, XY and Yin, Q and Zeng, JH and Zhang, Z and Li, JQ and Zhang, H}, title = {Functional characterization of the promoter of carbonyl reductase 1 gene in porcine endometrial cells.}, journal = {Journal of Zhejiang University. Science. B}, volume = {18}, number = {7}, pages = {626-634}, pmid = {28681587}, issn = {1862-1783}, mesh = {Animals ; Binding Sites ; Carbonyl Reductase (NADPH)/*metabolism ; Catalysis ; Chromatin Immunoprecipitation ; Cloning, Molecular ; Computational Biology ; Endometrium/*cytology/metabolism ; Epithelial Cells/metabolism ; Female ; Inflammation ; NF-kappa B/*metabolism ; Pregnancy ; *Promoter Regions, Genetic ; RNA, Small Interfering/metabolism ; Swine ; Transcription Factors/metabolism ; }, abstract = {Prostaglandins (PGs) play a critical role in porcine reproduction, of which prostaglandin E2 (PGE2) and prostaglandin F2α (PGF2α) exert antiluteolytic and luteolysis actions, respectively. As a rate-limiting enzyme, carbonyl reductase 1 (CBR1) catalyzes the conversion of PGE2 to PGF2α. A high ratio of PGE2:PGF2α is beneficial to the establishment and maintenance of porcine pregnancy. PG is essential for the establishment of pregnancy which resembles the proinflammatory response and nuclear factor κB (NF-κB) is involved in the process. Bioinformatic analysis has shown that NF-κB is a possible factor bound to two cis-regulatory elements in CBR1 promoter. In this study, we cloned the 2997 bp (-2875/+122) of the promoter, and constructed six 5'-deleted dual-luciferase reporter recombinant vectors. In endometrial cells, the region of P2 (-1640/+7) exhibited the greatest transcriptional activity at driving luciferase expression, but not significantly different from that of P1 (-2089/+7). The activity of P1, P2, and P3 (-1019/+7) was highly significantly higher than that of others (P<0.01), suggesting that two positive regulatory elements were likely present in the regions of -1640/-1019 and -1019/-647. The results also showed that the -1640/-647 region was indispensable for the promoter. The results of chromatin immunoprecipitation (ChIP) demonstrated that the NF-κB subunit p65 binds to one site around -1545/-1531. Using four reference genes, we found that the over-expression of p65 enhanced the expression of CBR1 (P<0.05) in porcine endometrial epithelial cells, while knockdown of the p65 did not down-regulate the CBR1 expression. These results indicated that NF-κB (p65) could bind to the special element of CBR1 gene promoter in porcine endometrial epithelial cells in vitro. The binding site of NF-κB was a positive regulator for the CBR1 gene promoter, but was not necessary for the basic expression.}, }
@article {pmid28654871, year = {2017}, author = {Mennis, J and Mason, M and Ambrus, A and Way, T and Henry, K}, title = {The spatial accuracy of geographic ecological momentary assessment (GEMA): Error and bias due to subject and environmental characteristics.}, journal = {Drug and alcohol dependence}, volume = {178}, number = {}, pages = {188-193}, doi = {10.1016/j.drugalcdep.2017.05.019}, pmid = {28654871}, issn = {1879-0046}, mesh = {Adolescent ; Bias ; Ecological Momentary Assessment/*standards ; *Environment ; Female ; Geographic Information Systems/standards ; Humans ; Male ; Residence Characteristics ; Substance-Related Disorders/diagnosis/*epidemiology/*psychology ; }, abstract = {BACKGROUND: Geographic ecological momentary assessment (GEMA) combines ecological momentary assessment (EMA) with global positioning systems (GPS) and geographic information systems (GIS). This study evaluates the spatial accuracy of GEMA location data and bias due to subject and environmental data characteristics.<br><br>METHODS: Using data for 72 subjects enrolled in a study of urban adolescent substance use, we compared the GPS-based location of EMA responses in which the subject indicated they were at home to the geocoded home address. We calculated the percentage of EMA locations within a sixteenth, eighth, quarter, and half miles from the home, and the percentage within the same tract and block group as the home. We investigated if the accuracy measures were associated with subject demographics, substance use, and emotional dysregulation, as well as environmental characteristics of the home neighborhood.<br><br>RESULTS: Half of all subjects had more than 88% of their EMA locations within a half mile, 72% within a quarter mile, 55% within an eighth mile, 50% within a sixteenth of a mile, 83% in the correct tract, and 71% in the correct block group. There were no significant associations with subject or environmental characteristics.<br><br>CONCLUSIONS: Results support the use of GEMA for analyzing subjects' exposures to urban environments. Researchers should be aware of the issue of spatial accuracy inherent in GEMA, and interpret results accordingly. Understanding spatial accuracy is particularly relevant for the development of 'ecological momentary interventions' (EMI), which may depend on accurate location information, though issues of privacy protection remain a concern.}, }
@article {pmid28647495, year = {2017}, author = {Gámez, M and López, I and Rodríguez, C and Varga, Z and Garay, J}, title = {Ecological monitoring in a discrete-time prey-predator model.}, journal = {Journal of theoretical biology}, volume = {429}, number = {}, pages = {52-60}, doi = {10.1016/j.jtbi.2017.06.025}, pmid = {28647495}, issn = {1095-8541}, mesh = {Animals ; Ecological Parameter Monitoring/*methods ; *Ecosystem ; Environmental Monitoring/methods ; *Models, Biological ; Population Dynamics ; *Predatory Behavior ; Time Factors ; }, abstract = {The paper is aimed at the methodological development of ecological monitoring in discrete-time dynamic models. In earlier papers, in the framework of continuous-time models, we have shown how a systems-theoretical methodology can be applied to the monitoring of the state process of a system of interacting populations, also estimating certain abiotic environmental changes such as pollution, climatic or seasonal changes. In practice, however, there may be good reasons to use discrete-time models. (For instance, there may be discrete cycles in the development of the populations, or observations can be made only at discrete time steps.) Therefore the present paper is devoted to the development of the monitoring methodology in the framework of discrete-time models of population ecology. By monitoring we mean that, observing only certain component(s) of the system, we reconstruct the whole state process. This may be necessary, e.g., when in a complex ecosystem the observation of the densities of certain species is impossible, or too expensive. For the first presentation of the offered methodology, we have chosen a discrete-time version of the classical Lotka-Volterra prey-predator model. This is a minimal but not trivial system where the methodology can still be presented. We also show how this methodology can be applied to estimate the effect of an abiotic environmental change, using a component of the population system as an environmental indicator. Although this approach is illustrated in a simplest possible case, it can be easily extended to larger ecosystems with several interacting populations and different types of abiotic environmental effects.}, }
@article {pmid28642608, year = {2017}, author = {Vizzini, S and Martínez-Crego, B and Andolina, C and Massa-Gallucci, A and Connell, SD and Gambi, MC}, title = {Ocean acidification as a driver of community simplification via the collapse of higher-order and rise of lower-order consumers.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4018}, pmid = {28642608}, issn = {2045-2322}, abstract = {Increasing oceanic uptake of CO2 is predicted to drive ecological change as both a resource (i.e. CO2 enrichment on primary producers) and stressor (i.e. lower pH on consumers). We use the natural ecological complexity of a CO2 vent (i.e. a seagrass system) to assess the potential validity of conceptual models developed from laboratory and mesocosm research. Our observations suggest that the stressor-effect of CO2 enrichment combined with its resource-effect drives simplified food web structure of lower trophic diversity and shorter length. The transfer of CO2 enrichment from plants to herbivores through consumption (apparent resource-effect) was not compensated by predation, because carnivores failed to contain herbivore outbreaks. Instead, these higher-order consumers collapsed (apparent stressor-effect on carnivores) suggesting limited trophic propagation to predator populations. The dominance of primary producers and their lower-order consumers along with the loss of carnivores reflects the duality of intensifying ocean acidification acting both as resource-effect (i.e. bottom-up control) and stressor-effect (i.e. top-down control) to simplify community and trophic structure and function. This shifting balance between the propagation of resource enrichment and its consumption across trophic levels provides new insights into how the trophic dynamics might stabilize against or propagate future environmental change.}, }
@article {pmid28584342, year = {2017}, author = {Hampton, SE and Jones, MB and Wasser, LA and Schildhauer, MP and Supp, SR and Brun, J and Hernandez, RR and Boettiger, C and Collins, SL and Gross, LJ and Fernández, DS and Budden, A and White, EP and Teal, TK and Labou, SG and Aukema, JE}, title = {Skills and Knowledge for Data-Intensive Environmental Research.}, journal = {Bioscience}, volume = {67}, number = {6}, pages = {546-557}, pmid = {28584342}, issn = {0006-3568}, abstract = {The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap.}, }
@article {pmid28562826, year = {2017}, author = {Mormul, RP and Mormul, TDS and Santos, GMB and Santana, ARA}, title = {Looking for attitudes related to amphibian species decline: how are peer-reviewed publications of education activities compared to ecological research?.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {89}, number = {1 Suppl 0}, pages = {491-496}, doi = {10.1590/0001-3765201720160463}, pmid = {28562826}, issn = {1678-2690}, mesh = {*Amphibians ; Animals ; *Bibliometrics ; Databases, Bibliographic ; Ecology/statistics &amp; numerical data ; Extinction, Biological ; Humans ; *Peer Review, Research/trends ; Periodicals as Topic ; }, abstract = {Biodiversity decline has been the focus of discussions in the last decade, especially on the amphibian species decline. After a scientometric analysis using international databases, we found that the number of peer-reviewed articles considering education practices related to the theme increased along with the number of ecological researches. However, the increase in ecological researches is much higher than the increase in publications of education practices. Studies suggest that conservation attitudes are important and that education practices are an important tool for improving human perceptions on this subject. In this sense, increase the publication of projects and programs results related to local education practices in international journals could help the dissemination of efficient methods for conservation, as well as facilitating access to information internationally, since species decline, especially for amphibians, is a global concern. Then, we suggest that educational practices, at least when related to conservation, should follow a more standardized protocol, and be published in international journals, as the efficiency of such practices should be evaluated and methods once published could help other nations to improve their ecological literacy.}, }
@article {pmid28552183, year = {2017}, author = {Padilla, O and Rosas, P and Moreno, W and Toulkeridis, T}, title = {Modeling of the ecological niches of the anopheles spp in Ecuador by the use of geo-informatic tools.}, journal = {Spatial and spatio-temporal epidemiology}, volume = {21}, number = {}, pages = {1-11}, doi = {10.1016/j.sste.2016.12.001}, pmid = {28552183}, issn = {1877-5853}, mesh = {Animals ; Anopheles/*growth &amp; development ; Ecology/*statistics &amp; numerical data ; *Ecosystem ; Ecuador ; Geographic Information Systems ; Geography ; *Insect Vectors ; Logistic Models ; Malaria/*transmission ; }, abstract = {Ecuador in the northwestern edge of South America is struggling by vector-borne diseases with an endemic-epidemic behavior leading to an enormous public health problem. Malaria, which has a cyclicality in its dynamics, is closely related to climatic, ecological and socio-economic phenomena. The main objective of this research has been to compare three different prediction species models, the so-called Maxent, logistic regression and multi criteria evaluation with fuzzy logic, in order to determine the model which best describes the ecological niche of the Anopheles spp species, which transmits malaria within Ecuador. After performing a detailed data collection and data processing, we applied the mentioned models and validated them with a statistical analysis in order to discover that the Maxent model has been the model that best defines the distribution of Anopheles spp within the territory. The determined sites, which are of high strategic value and important for the increasing national development, will now be able to initiate preventive countermeasures based on this study.}, }
@article {pmid28524860, year = {2017}, author = {Wang, S and Loreau, M and Arnoldi, JF and Fang, J and Rahman, KA and Tao, S and de Mazancourt, C}, title = {An invariability-area relationship sheds new light on the spatial scaling of ecological stability.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15211}, pmid = {28524860}, issn = {2041-1723}, mesh = {Animals ; Biomass ; Birds/*physiology ; Databases as Topic ; *Ecosystem ; Internationality ; *Models, Biological ; }, abstract = {The spatial scaling of stability is key to understanding ecological sustainability across scales and the sensitivity of ecosystems to habitat destruction. Here we propose the invariability-area relationship (IAR) as a novel approach to investigate the spatial scaling of stability. The shape and slope of IAR are largely determined by patterns of spatial synchrony across scales. When synchrony decays exponentially with distance, IARs exhibit three phases, characterized by steeper increases in invariability at both small and large scales. Such triphasic IARs are observed for primary productivity from plot to continental scales. When synchrony decays as a power law with distance, IARs are quasilinear on a log-log scale. Such quasilinear IARs are observed for North American bird biomass at both species and community levels. The IAR provides a quantitative tool to predict the effects of habitat loss on population and ecosystem stability and to detect regime shifts in spatial ecological systems, which are goals of relevance to conservation and policy.}, }
@article {pmid28505840, year = {2017}, author = {Wilsenach, J and Landi, P and Hui, C}, title = {Evolutionary fields can explain patterns of high-dimensional complexity in ecology.}, journal = {Physical review. E}, volume = {95}, number = {4-1}, pages = {042401}, doi = {10.1103/PhysRevE.95.042401}, pmid = {28505840}, issn = {2470-0053}, mesh = {Animals ; *Biological Evolution ; *Ecological and Environmental Phenomena ; England ; Foxes ; *Models, Biological ; Nonlinear Dynamics ; Predatory Behavior ; Rabbits ; }, abstract = {One of the properties that make ecological systems so unique is the range of complex behavioral patterns that can be exhibited by even the simplest communities with only a few species. Much of this complexity is commonly attributed to stochastic factors that have very high-degrees of freedom. Orthodox study of the evolution of these simple networks has generally been limited in its ability to explain complexity, since it restricts evolutionary adaptation to an inertia-free process with few degrees of freedom in which only gradual, moderately complex behaviors are possible. We propose a model inspired by particle-mediated field phenomena in classical physics in combination with fundamental concepts in adaptation, which suggests that small but high-dimensional chaotic dynamics near to the adaptive trait optimum could help explain complex properties shared by most ecological datasets, such as aperiodicity and pink, fractal noise spectra. By examining a simple predator-prey model and appealing to real ecological data, we show that this type of complexity could be easily confused for or confounded by stochasticity, especially when spurred on or amplified by stochastic factors that share variational and spectral properties with the underlying dynamics.}, }
@article {pmid28461482, year = {2017}, author = {Alroy, J}, title = {Effects of habitat disturbance on tropical forest biodiversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {23}, pages = {6056-6061}, pmid = {28461482}, issn = {1091-6490}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources/*methods/*trends ; Databases, Factual ; Ecology ; Ecosystem ; Extinction, Biological ; Forests ; Rainforest ; Trees ; Tropical Climate ; }, abstract = {It is widely expected that habitat destruction in the tropics will cause a mass extinction in coming years, but the potential magnitude of the loss is unclear. Existing literature has focused on estimating global extinction rates indirectly or on quantifying effects only at local and regional scales. This paper directly predicts global losses in 11 groups of organisms that would ensue from disturbance of all remaining tropical forest habitats. The results are based on applying a highly accurate method of estimating species richness to 875 ecological samples. About 41% of the tree and animal species in this dataset are absent from disturbed habitats, even though most samples do still represent forests of some kind. The individual figures are 30% for trees and 8-65% for 10 animal groups. Local communities are more robust to disturbance because losses are partially balanced out by gains resulting from homogenization.}, }
@article {pmid28458014, year = {2017}, author = {Cicconardi, F and Marcatili, P and Arthofer, W and Schlick-Steiner, BC and Steiner, FM}, title = {Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation.}, journal = {Molecular phylogenetics and evolution}, volume = {112}, number = {}, pages = {230-243}, doi = {10.1016/j.ympev.2017.04.023}, pmid = {28458014}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Drosophila/*genetics ; Evolution, Molecular ; Gene Ontology ; *Genetic Variation ; Genome, Mitochondrial ; Longevity ; Phylogeny ; *Selection, Genetic ; Species Specificity ; Stress, Physiological ; Temperature ; Transcriptome/genetics ; }, abstract = {The growing genomic information on non-model organisms eases exploring the evolutionary history of biodiversity. This is particularly true for Drosophila flies, in which the number of sequenced species doubled recently. Because of its outstanding diversity of species, Drosophila has become one of the most important systems to study adaptive radiation. In this study, we performed a genome-wide analysis of positive diversifying selection on more than 2000 single-copy orthologous groups in 25 species using a recent method of increased accuracy for detecting positive diversifying selection. Adopting this novel approach enabled us to find a consistent selection signal throughout the genus Drosophila, and a total of 1342 single-copy orthologous groups were identified with a putative signal of positive diversifying selection, corresponding to 1.9% of all loci. Specifically, in lineages leading to D. grimshawi, a strong putative signal of positive diversifying selection was found related to cell, morphological, neuronal, and sensorial development and function. A recurrent signal of positive diversifying selection was found on genes related to aging and lifespan, suggesting that selection had shaped lifespan diversity in Drosophila, including extreme longevity. Our study, one of the largest and most comprehensive ones on genome-wide positive diversifying selection to date, shows that positive diversifying selection has promoted species-specific differentiation among evolutionary lineages throughout the Drosophila radiation. Acting on the same biological processes via different routes, positive diversifying selection has promoted diversity of functions and adaptive divergence.}, }
@article {pmid28447371, year = {2017}, author = {Cavaliere, M and Feng, S and Soyer, OS and Jiménez, JI}, title = {Cooperation in microbial communities and their biotechnological applications.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {2949-2963}, pmid = {28447371}, issn = {1462-2920}, support = {BB/M017982/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M009769/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K003240/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Biotechnology ; Ecology ; Microbial Consortia/*physiology ; Microbial Interactions/*physiology ; *Models, Biological ; }, abstract = {Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross-feeding, which can be understood in the general framework of ecological and evolutionary (eco-evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of 'cheating' cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications.}, }
@article {pmid28444848, year = {2018}, author = {Parsons, MH and Apfelbach, R and Banks, PB and Cameron, EZ and Dickman, CR and Frank, ASK and Jones, ME and McGregor, IS and McLean, S and Müller-Schwarze, D and Sparrow, EE and Blumstein, DT}, title = {Biologically meaningful scents: a framework for understanding predator-prey research across disciplines.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {1}, pages = {98-114}, doi = {10.1111/brv.12334}, pmid = {28444848}, issn = {1469-185X}, abstract = {Fear of predation is a universal motivator. Because predators hunt using stealth and surprise, there is a widespread ability among prey to assess risk from chemical information - scents - in their environment. Consequently, scents often act as particularly strong modulators of memory and emotions. Recent advances in ecological research and analytical technology are leading to novel ways to use this chemical information to create effective attractants, repellents and anti-anxiolytic compounds for wildlife managers, conservation biologists and health practitioners. However, there is extensive variation in the design, results, and interpretation of studies of olfactory-based risk discrimination. To understand the highly variable literature in this area, we adopt a multi-disciplinary approach and synthesize the latest findings from neurobiology, chemical ecology, and ethology to propose a contemporary framework that accounts for such disparate factors as the time-limited stability of chemicals, highly canalized mechanisms that influence prey responses, and the context within which these scents are detected (e.g. availability of alternative resources, perceived shelter, and ambient physical parameters). This framework helps to account for the wide range of reported responses by prey to predator scents, and explains, paradoxically, how the same individual predator scent can be interpreted as either safe or dangerous to a prey animal depending on how, when and where the cue was deposited. We provide a hypothetical example to illustrate the most common factors that influence how a predator scent (from dingoes, Canis dingo) may both attract and repel the same target organism (kangaroos, Macropus spp.). This framework identifies the catalysts that enable dynamic scents, odours or odorants to be used as attractants as well as deterrents. Because effective scent tools often relate to traumatic memories (fear and/or anxiety) that cause future avoidance, this information may also guide the development of appeasement, enrichment and anti-anxiolytic compounds, and help explain the observed variation in post-traumatic-related behaviours (including post-traumatic stress disorder, PTSD) among diverse terrestrial taxa, including humans.}, }
@article {pmid28387705, year = {2017}, author = {Fox, MA and Brewer, LE and Martin, L}, title = {An Overview of Literature Topics Related to Current Concepts, Methods, Tools, and Applications for Cumulative Risk Assessment (2007-2016).}, journal = {International journal of environmental research and public health}, volume = {14}, number = {4}, pages = {}, pmid = {28387705}, issn = {1660-4601}, mesh = {Ecosystem ; Ecotoxicology/*methods ; Environmental Exposure/*adverse effects/statistics &amp; numerical data ; Genetic Markers ; Geographic Information Systems ; Health Status ; Humans ; Risk Assessment/*methods ; }, abstract = {Cumulative risk assessments (CRAs) address combined risks from exposures to multiple chemical and nonchemical stressors and may focus on vulnerable communities or populations. Significant contributions have been made to the development of concepts, methods, and applications for CRA over the past decade. Work in both human health and ecological cumulative risk has advanced in two different contexts. The first context is the effects of chemical mixtures that share common modes of action, or that cause common adverse outcomes. In this context two primary models are used for predicting mixture effects, dose addition or response addition. The second context is evaluating the combined effects of chemical and nonchemical (e.g., radiation, biological, nutritional, economic, psychological, habitat alteration, land-use change, global climate change, and natural disasters) stressors. CRA can be adapted to address risk in many contexts, and this adaptability is reflected in the range in disciplinary perspectives in the published literature. This article presents the results of a literature search and discusses a range of selected work with the intention to give a broad overview of relevant topics and provide a starting point for researchers interested in CRA applications.}, }
@article {pmid28369087, year = {2017}, author = {Pocock, MJ and Tweddle, JC and Savage, J and Robinson, LD and Roy, HE}, title = {The diversity and evolution of ecological and environmental citizen science.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0172579}, pmid = {28369087}, issn = {1932-6203}, mesh = {Data Collection ; Data Interpretation, Statistical ; *Ecology/statistics &amp; numerical data/trends ; Humans ; Internet ; Statistics as Topic ; *Volunteers ; }, abstract = {Citizen science-the involvement of volunteers in data collection, analysis and interpretation-simultaneously supports research and public engagement with science, and its profile is rapidly rising. Citizen science represents a diverse range of approaches, but until now this diversity has not been quantitatively explored. We conducted a systematic internet search and discovered 509 environmental and ecological citizen science projects. We scored each project for 32 attributes based on publicly obtainable information and used multiple factor analysis to summarise this variation to assess citizen science approaches. We found that projects varied according to their methodological approach from 'mass participation' (e.g. easy participation by anyone anywhere) to 'systematic monitoring' (e.g. trained volunteers repeatedly sampling at specific locations). They also varied in complexity from approaches that are 'simple' to those that are 'elaborate' (e.g. provide lots of support to gather rich, detailed datasets). There was a separate cluster of entirely computer-based projects but, in general, we found that the range of citizen science projects in ecology and the environment showed continuous variation and cannot be neatly categorised into distinct types of activity. While the diversity of projects begun in each time period (pre 1990, 1990-99, 2000-09 and 2010-13) has not increased, we found that projects tended to have become increasingly different from each other as time progressed (possibly due to changing opportunities, including technological innovation). Most projects were still active so consequently we found that the overall diversity of active projects (available for participation) increased as time progressed. Overall, understanding the landscape of citizen science in ecology and the environment (and its change over time) is valuable because it informs the comparative evaluation of the 'success' of different citizen science approaches. Comparative evaluation provides an evidence-base to inform the future development of citizen science activities.}, }
@article {pmid28337822, year = {2017}, author = {Berney, C and Ciuprina, A and Bender, S and Brodie, J and Edgcomb, V and Kim, E and Rajan, J and Parfrey, LW and Adl, S and Audic, S and Bass, D and Caron, DA and Cochrane, G and Czech, L and Dunthorn, M and Geisen, S and Glöckner, FO and Mahé, F and Quast, C and Kaye, JZ and Simpson, AGB and Stamatakis, A and Del Campo, J and Yilmaz, P and de Vargas, C}, title = {UniEuk: Time to Speak a Common Language in Protistology!.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {3}, pages = {407-411}, pmid = {28337822}, issn = {1550-7408}, mesh = {Animals ; Bacteria/classification ; Biodiversity ; *Classification ; Databases, Nucleic Acid ; Ecosystem ; Environment ; Eukaryota/*classification/cytology/genetics/physiology ; Eukaryotic Cells ; Fungi/classification ; Phylogeny ; }, abstract = {Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes.}, }
@article {pmid28296954, year = {2017}, author = {Tripathi, P and Behera, MD and Roy, PS}, title = {Optimized grid representation of plant species richness in India-Utility of an existing national database in integrated ecological analysis.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173774}, pmid = {28296954}, issn = {1932-6203}, mesh = {*Biodiversity ; *Databases, Factual ; *Ecology ; India ; Plants/*classification ; }, abstract = {Data on the distribution of plant species at spatial (grid) scales are required as input for integrative analysis along with related climate, environment, topography and soil data. Although the world's scientific community is increasingly generating data on plant species at various spatial grids and statistically interpolating and extrapolating the available information, data on plant diversity from the Asian continent are scant. Such data are unavailable for India, the mainland of which has part of three of the world's 36 biodiversity hotspots. Although sufficient field sampling is always impossible and impractical, it is essential to utilize fully any available database by adjudging the sampling sufficiency at a given scale. In this work, we used an exhaustive database of the plant species of the Indian mainland that was sufficient in terms of sampling vegetation types. We transformed the data, obtained the distribution at the 1° and 2° spatial grid levels and evaluated the sampling sufficiency at acceptable threshold limits (60% to 80%). The greatest species richness values recorded in the 0.04 ha quadrant, 1° grid and 2° grid were 59, 623 and 1244, respectively. Clench model was significantly (p value < 0.001) fitted using the plant species data at both the grid levels with a very high coefficient of determination (>0.95). At an acceptable threshold limit of 70%, almost all the grids at the 2° level and more than 80% of the grids at the 1° level were found to be sufficiently sampled. Sampling sufficiency was observed to be highly scale-dependent as a greater number of 2° grids attained asymptotic behaviour following the species-area curve. Grid-level sampling insufficiency was attributed to lower numbers of sampling quadrats in forests with poor approachability, which coincided with the world biodiversity hotspots', suggesting that additional sampling was required. We prescribe the use of the 1° and 2° spatial grids with sufficient sampling for any ecological analysis in conjunction with other data and thereby offer grid-level plant species richness data for the Indian mainland for the first time.}, }
@article {pmid28294342, year = {2017}, author = {Zeng, L and Zhang, N and Zhang, Q and Endress, PK and Huang, J and Ma, H}, title = {Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.}, journal = {The New phytologist}, volume = {214}, number = {3}, pages = {1338-1354}, doi = {10.1111/nph.14503}, pmid = {28294342}, issn = {1469-8137}, mesh = {Cell Nucleus/*genetics ; Codon/genetics ; *Databases, Genetic ; *Genes, Plant ; *Genetic Variation ; Magnoliopsida/*genetics ; *Phylogeny ; Polyploidy ; Sequence Analysis, RNA ; Time Factors ; Transcriptome/*genetics ; }, abstract = {Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots.}, }
@article {pmid28273342, year = {2017}, author = {Price, DC and Bhattacharya, D}, title = {Robust Dinoflagellata phylogeny inferred from public transcriptome databases.}, journal = {Journal of phycology}, volume = {53}, number = {3}, pages = {725-729}, doi = {10.1111/jpy.12529}, pmid = {28273342}, issn = {1529-8817}, mesh = {Databases, Nucleic Acid ; Dinoflagellida/*classification/*genetics ; *Phylogeny ; *Transcriptome ; }, abstract = {Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number. To address this issue, we used recently generated public sequencing data, including from the Moore Microbial Eukaryote Transcriptome Sequencing Project, to identify dinoflagellate-specific ortholog groups. These orthologs were combined to create a broadly sampled and highly resolved phylogeny of dinoflagellates. Our results emphasize the scope and utility of public sequencing databases in creating broad and robust phylogenies for large and complex taxonomic lineages, while also providing unique insights into the evolution of thecate dinoflagellates.}, }
@article {pmid28164331, year = {2017}, author = {Wilson, AW and Hosaka, K and Mueller, GM}, title = {Evolution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria.}, journal = {The New phytologist}, volume = {213}, number = {4}, pages = {1862-1873}, pmid = {28164331}, issn = {1469-8137}, mesh = {*Biodiversity ; *Biological Evolution ; Carbon Isotopes ; Databases as Topic ; Laccaria/*physiology ; *Models, Biological ; Mycorrhizae/*physiology ; Nitrogen Isotopes ; *Phylogeography ; Species Specificity ; }, abstract = {A systematic and evolutionary ecology study of the model ectomycorrhizal (ECM) genus Laccaria was performed using herbarium material and field collections from over 30 countries covering its known geographic range. A four-gene (nrITS, 28S, RPB2, EF1α) nucleotide sequence dataset consisting of 232 Laccaria specimens was analyzed phylogenetically. The resulting Global Laccaria dataset was used for molecular dating and estimating diversification rates in the genus. Stable isotope analysis of carbon and nitrogen was used to evaluate the origin of Laccaria's ECM ecology. In all, 116 Laccaria molecular species were identified, resulting in a near 50% increase in its known diversity, including the new species described herein: Laccaria ambigua. Molecular dating indicates that the most recent common ancestor to Laccaria existed in the early Paleocene (56-66 million yr ago), probably in Australasia. At this time, Laccaria split into two lineages: one represented by the new species L. ambigua, and the other reflecting a large shift in diversification that resulted in the remainder of Laccaria. L. ambigua shows a different isotopic profile than all other Laccaria species. Isotopes and diversification results suggest that the evolution of the ECM ecology was a key innovation in the evolution of Laccaria. Diversification shifts associated with Laccaria's dispersal to the northern hemisphere are attributed to adaptations to new ecological niches.}, }
@article {pmid28149178, year = {2017}, author = {El-Sheikh, MA and Thomas, J and Alfarhan, AH and Alatar, AA and Mayandy, S and Hennekens, SM and Schaminėe, JH and Mucina, L and Alansari, AM}, title = {SaudiVeg ecoinformatics: Aims, current status and perspectives.}, journal = {Saudi journal of biological sciences}, volume = {24}, number = {2}, pages = {389-398}, pmid = {28149178}, issn = {1319-562X}, abstract = {During the last decade many electronic databases of vegetation plots were established in many countries around the world. These databases contain valuable phytosociological information assisting both governmental and NGO (Non-governmental organizations) agencies to formulate strategies and on-ground plans to manage and protect nature resources. This paper provides an account on aims, current status and perspectives of building of a vegetation database for the Central Region (Najd) of Saudi Arabia - the founding element of the Saudi Vegetation Database (SVD). The data stored by the database are sample plots (vegetation relevés) collected according to the field techniques of the Braun-Blanquet approach (lists of taxa accompanied by semi-quantitative cover assessment), and are accompanied by general vegetation characteristics such as vegetation layering and cover, information on life-form of the recorded species, geographical coordinates, altitude, soil typology, topography and many more. More than 2900 vegetation-plot records (relevés) have so far been collected in the Najd region; of these more than 2000 have already been stored using the Turboveg database platform. These field records cover many habitats such as depressions, wadis (dry river beds), agricultural lands, sand dunes, sabkhas, and ruderal habitats. The ecological information collected in the database is currently the largest set of vegetation data collated into a database in the Middle East. These data are of great importance for biodiversity studies in Saudi Arabia, since the region is recording a loss of biodiversity at a fast rate due to environmental problems such as global warming and land-use changes. We envisage that this database would catalyze further data collection on vegetation of the entire Arabian Peninsula, and shall serve as one of the most important datasets for classification and mapping of the vegetation of the Kingdom of Saudi Arabia.}, }
@article {pmid28122127, year = {2017}, author = {Klimešová, J and Danihelka, J and Chrtek, J and de Bello, F and Herben, T}, title = {CLO-PLA: a database of clonal and bud-bank traits of the Central European flora.}, journal = {Ecology}, volume = {98}, number = {4}, pages = {1179}, doi = {10.1002/ecy.1745}, pmid = {28122127}, issn = {0012-9658}, mesh = {*Databases, Genetic ; Ecology ; Ecosystem ; Europe ; Phylogeny ; Plants/classification/*genetics ; }, abstract = {This dataset presents comprehensive and easy-to-use information on 29 functional traits of clonal growth, bud banks, and lifespan of members of the Central European flora. The source data were compiled from a number of published sources (see the reference file) and the authors' own observations or studies. In total, 2,909 species are included (2,745 herbs and 164 woody species), out of which 1,532 (i.e., 52.7% of total) are classified as possessing clonal growth organs (1,480, i.e., 53.9%, if woody plants are excluded). This provides a unique, and largely unexplored, set of traits of clonal growth that can be used in studies on comparative plant ecology, plant evolution, community assembly, and ecosystem functioning across the large flora of Central Europe. It can be directly imported into a number of programs and packages that perform trait-based and phylogenetic analyses aimed to answer a variety of open and pressing ecological questions.}, }
@article {pmid28094805, year = {2017}, author = {Byrne, SL and Erthmann, PØ and Agerbirk, N and Bak, S and Hauser, TP and Nagy, I and Paina, C and Asp, T}, title = {The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40728}, pmid = {28094805}, issn = {2045-2322}, mesh = {Barbarea/chemistry/classification/*genetics/metabolism ; Computational Biology/methods ; Disease Resistance/genetics ; Genetic Variation ; *Genome, Plant ; *Genomics/methods ; Glucosinolates/metabolism ; Metabolome ; Metabolomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Plant Proteins/genetics/metabolism ; Quantitative Trait Loci ; Quantitative Trait, Heritable ; Whole Genome Sequencing ; }, abstract = {The genus Barbarea has emerged as a model for evolution and ecology of plant defense compounds, due to its unusual glucosinolate profile and production of saponins, unique to the Brassicaceae. One species, B. vulgaris, includes two 'types', G-type and P-type that differ in trichome density, and their glucosinolate and saponin profiles. A key difference is the stereochemistry of hydroxylation of their common phenethylglucosinolate backbone, leading to epimeric glucobarbarins. Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. B. vulgaris is resistant to the diamondback moth, and may be exploited for &quot;dead-end&quot; trap cropping where glucosinolates stimulate oviposition and saponins deter larvae to the extent that they die. The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding.}, }
@article {pmid28086860, year = {2017}, author = {Brockmöller, T and Ling, Z and Li, D and Gaquerel, E and Baldwin, IT and Xu, S}, title = {Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {79}, pmid = {28086860}, issn = {1471-2164}, mesh = {Computational Biology/*methods ; *Databases, Genetic ; Gene Expression Profiling ; Gene Expression Regulation ; Genomics/*methods ; *Metabolome ; Metabolomics/*methods ; Phylogeny ; Tobacco/classification/*genetics/*metabolism ; *Transcriptome ; }, abstract = {BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now.<br><br>DESCRIPTION: We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites.<br><br>CONCLUSION: The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/ .}, }
@article {pmid28004348, year = {2017}, author = {Demirkesen, AC and Evrendilek, F}, title = {Compositing climate change vulnerability of a Mediterranean region using spatiotemporally dynamic proxies for ecological and socioeconomic impacts and stabilities.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {1}, pages = {29}, pmid = {28004348}, issn = {1573-2959}, mesh = {*Climate Change ; Ecology ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Mediterranean Region ; Temperature ; Turkey ; }, abstract = {The study presents a new methodology to quantify spatiotemporal dynamics of climate change vulnerability at a regional scale adopting a new conceptual model of vulnerability as a function of climate change impacts, ecological stability, and socioeconomic stability. Spatiotemporal trends of equally weighted proxy variables for the three vulnerability components were generated to develop a composite climate change vulnerability index (CCVI) for a Mediterranean region of Turkey combining Landsat time series data, digital elevation model (DEM)-derived data, ordinary kriging, and geographical information system. Climate change impact was based on spatiotemporal trends of August land surface temperature (LST) between 1987 and 2016. Ecological stability was based on DEM, slope, aspect, and spatiotemporal trends of normalized difference vegetation index (NDVI), while socioeconomic stability was quantified as a function of spatiotemporal trends of land cover, population density, per capita gross domestic product, and illiteracy. The zones ranked on the five classes of no-to-extreme vulnerability were identified where highly and moderately vulnerable lands covered 0.02% (12 km2) and 11.8% (6374 km2) of the study region, respectively, mostly occurring in the interior central part. The adoption of this composite CCVI approach is expected to lead to spatiotemporally dynamic policy recommendations towards sustainability and tailor preventive and mitigative measures to locally specific characteristics of coupled ecological-socioeconomic systems.}, }
@article {pmid27992952, year = {2017}, author = {Ryan, EM and Ogle, K and Peltier, D and Walker, AP and De Kauwe, MG and Medlyn, BE and Williams, DG and Parton, W and Asao, S and Guenet, B and Harper, AB and Lu, X and Luus, KA and Zaehle, S and Shu, S and Werner, C and Xia, J and Pendall, E}, title = {Gross primary production responses to warming, elevated CO2 , and irrigation: quantifying the drivers of ecosystem physiology in a semiarid grassland.}, journal = {Global change biology}, volume = {23}, number = {8}, pages = {3092-3106}, doi = {10.1111/gcb.13602}, pmid = {27992952}, issn = {1365-2486}, mesh = {*Carbon Cycle ; Carbon Dioxide ; Climate ; *Ecosystem ; *Grassland ; Wyoming ; }, abstract = {Determining whether the terrestrial biosphere will be a source or sink of carbon (C) under a future climate of elevated CO2 (eCO2) and warming requires accurate quantification of gross primary production (GPP), the largest flux of C in the global C cycle. We evaluated 6 years (2007-2012) of flux-derived GPP data from the Prairie Heating and CO2 Enrichment (PHACE) experiment, situated in a grassland in Wyoming, USA. The GPP data were used to calibrate a light response model whose basic formulation has been successfully used in a variety of ecosystems. The model was extended by modeling maximum photosynthetic rate (Amax) and light-use efficiency (Q) as functions of soil water, air temperature, vapor pressure deficit, vegetation greenness, and nitrogen at current and antecedent (past) timescales. The model fits the observed GPP well (R2 = 0.79), which was confirmed by other model performance checks that compared different variants of the model (e.g. with and without antecedent effects). Stimulation of cumulative 6-year GPP by warming (29%, P = 0.02) and eCO2 (26%, P = 0.07) was primarily driven by enhanced C uptake during spring (129%, P = 0.001) and fall (124%, P = 0.001), respectively, which was consistent across years. Antecedent air temperature (Tairant) and vapor pressure deficit (VPDant) effects on Amax (over the past 3-4 days and 1-3 days, respectively) were the most significant predictors of temporal variability in GPP among most treatments. The importance of VPDant suggests that atmospheric drought is important for predicting GPP under current and future climate; we highlight the need for experimental studies to identify the mechanisms underlying such antecedent effects. Finally, posterior estimates of cumulative GPP under control and eCO2 treatments were tested as a benchmark against 12 terrestrial biosphere models (TBMs). The narrow uncertainties of these data-driven GPP estimates suggest that they could be useful semi-independent data streams for validating TBMs.}, }
@article {pmid27984661, year = {2017}, author = {Gibb, H and Dunn, RR and Sanders, NJ and Grossman, BF and Photakis, M and Abril, S and Agosti, D and Andersen, AN and Angulo, E and Armbrecht, I and Arnan, X and Baccaro, FB and Bishop, TR and Boulay, R and Brühl, C and Castracani, C and Cerda, X and Del Toro, I and Delsinne, T and Diaz, M and Donoso, DA and Ellison, AM and Enriquez, ML and Fayle, TM and Feener, DH and Fisher, BL and Fisher, RN and Fitzpatrick, MC and Gómez, C and Gotelli, NJ and Gove, A and Grasso, DA and Groc, S and Guenard, B and Gunawardene, N and Heterick, B and Hoffmann, B and Janda, M and Jenkins, C and Kaspari, M and Klimes, P and Lach, L and Laeger, T and Lattke, J and Leponce, M and Lessard, JP and Longino, J and Lucky, A and Luke, SH and Majer, J and McGlynn, TP and Menke, S and Mezger, D and Mori, A and Moses, J and Munyai, TC and Pacheco, R and Paknia, O and Pearce-Duvet, J and Pfeiffer, M and Philpott, SM and Resasco, J and Retana, J and Silva, RR and Sorger, MD and Souza, J and Suarez, A and Tista, M and Vasconcelos, HL and Vonshak, M and Weiser, MD and Yates, M and Parr, CL}, title = {A global database of ant species abundances.}, journal = {Ecology}, volume = {98}, number = {3}, pages = {883-884}, doi = {10.1002/ecy.1682}, pmid = {27984661}, issn = {0012-9658}, mesh = {Animals ; Ants/classification/*physiology ; *Databases, Factual ; *Ecology ; Ecosystem ; }, abstract = {What forces structure ecological assemblages? A key limitation to general insights about assemblage structure is the availability of data that are collected at a small spatial grain (local assemblages) and a large spatial extent (global coverage). Here, we present published and unpublished data from 51 ,388 ant abundance and occurrence records of more than 2,693 species and 7,953 morphospecies from local assemblages collected at 4,212 locations around the world. Ants were selected because they are diverse and abundant globally, comprise a large fraction of animal biomass in most terrestrial communities, and are key contributors to a range of ecosystem functions. Data were collected between 1949 and 2014, and include, for each geo-referenced sampling site, both the identity of the ants collected and details of sampling design, habitat type, and degree of disturbance. The aim of compiling this data set was to provide comprehensive species abundance data in order to test relationships between assemblage structure and environmental and biogeographic factors. Data were collected using a variety of standardized methods, such as pitfall and Winkler traps, and will be valuable for studies investigating large-scale forces structuring local assemblages. Understanding such relationships is particularly critical under current rates of global change. We encourage authors holding additional data on systematically collected ant assemblages, especially those in dry and cold, and remote areas, to contact us and contribute their data to this growing data set.}, }
@article {pmid27976627, year = {2016}, author = {Wayland, MT and Chubb, JC}, title = {A new R package and web application for detecting bilateral asymmetry in parasitic infections.}, journal = {Folia parasitologica}, volume = {63}, number = {}, pages = {}, doi = {10.14411/fp.2016.039}, pmid = {27976627}, issn = {0015-5683}, mesh = {Animals ; Data Interpretation, Statistical ; Fish Diseases/*parasitology/pathology ; Metacercariae/physiology ; Perches/parasitology ; *Software ; Trematoda/*physiology ; Trematode Infections/*parasitology/*pathology ; }, abstract = {When parasites invade paired structures of their host non-randomly, the resulting asymmetry may have both pathological and ecological significance. To facilitate the detection and visualisation of asymmetric infections we have developed a free software tool, Analysis of Symmetry of Parasitic Infections (ASPI). This tool has been implemented as an R package (https://cran.r-project.org/package=aspi) and a web application (https://wayland.shinyapps.io/aspi). ASPI can detect both consistent bias towards one side, and inconsistent bias in which the left side is favoured in some hosts and the right in others. Application of ASPI is demonstrated using previously unpublished data on the distribution of metacercariae of species of Diplostomum von Nordmann, 1832 in the eyes of ruffe Gymnocephalus cernua (Linnaeus). Invasion of the lenses appeared to be random, with the proportion of metacercariae in the left and right lenses showing the pattern expected by chance. However, analysis of counts of metacercariae from the humors, choroid and retina revealed asymmetry between eyes in 38% of host fish.}, }
@article {pmid27940071, year = {2017}, author = {Šumberová, K and Ducháček, M}, title = {Analysis of plant soil seed banks and seed dispersal vectors: Its potential and limits for forensic investigations.}, journal = {Forensic science international}, volume = {270}, number = {}, pages = {121-128}, doi = {10.1016/j.forsciint.2016.11.030}, pmid = {27940071}, issn = {1872-6283}, mesh = {Botany ; Databases as Topic ; Ecosystem ; Europe ; Forensic Sciences ; Geography ; *Seed Bank ; *Seed Dispersal ; *Seeds ; *Soil ; }, abstract = {Plant seeds exhibit many species-specific traits, thus potentially being especially helpful for forensic investigations. Seeds of a broad range of plant species occur in soil seed banks of various habitats and may become attached in large quantities to moving objects. Although plant seeds are now routinely used as trace evidence in forensic practice, only scant information has been published on this topic in the scientific literature. Thus, the standard methods remain unknown to specialists in such botanical subjects as plant ecology and plant geography. These specialists, if made aware of the forensic uses of seeds, could help in development of new, more sophisticated approaches. We aim to bridge the gap between forensic analysts and botanists. Therefore, we explore the available literature and compare it with our own experiences to reveal both the potential and limits of soil seed bank and seed dispersal analysis in forensic investigations. We demonstrate that habitat-specific and thus relatively rare species are of the greatest forensic value. Overall species composition, in terms of species presence/absence and relative abundance can also provide important information. In particular, the ecological profiles of seeds found on any moving object can help us identify the types of environments through which the object had travelled. We discuss the applicability of this approach to various European environments, with the ability to compare seed samples with georeferenced vegetation databases being particularly promising for forensic investigations. We also explore the forensic limitations of soil seed bank and seed dispersal vector analyses.}, }
@article {pmid27932852, year = {2016}, author = {Watson, RA and Mills, R and Buckley, CL and Kouvaris, K and Jackson, A and Powers, ST and Cox, C and Tudge, S and Davies, A and Kounios, L and Power, D}, title = {Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.}, journal = {Evolutionary biology}, volume = {43}, number = {4}, pages = {553-581}, pmid = {27932852}, issn = {0071-3260}, abstract = {The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term &quot;evolutionary connectionism&quot; to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.}, }
@article {pmid27925167, year = {2017}, author = {Harnos, A and Lang, Z and Petrás, D and Bush, SE and Szabó, K and Rózsa, L}, title = {Size matters for lice on birds: Coevolutionary allometry of host and parasite body size.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {2}, pages = {421-431}, doi = {10.1111/evo.13147}, pmid = {27925167}, issn = {1558-5646}, mesh = {Amblycera/*physiology ; Animals ; *Biological Evolution ; Bird Diseases/parasitology ; Birds/*parasitology ; *Body Size ; Female ; *Host-Parasite Interactions ; Ischnocera/*physiology ; Lice Infestations/parasitology/veterinary ; Male ; }, abstract = {Body size is one of the most fundamental characteristics of all organisms. It influences physiology, morphology, behavior, and even interspecific interactions such as those between parasites and their hosts. Host body size influences the magnitude and variability of parasite size according to Harrison's rule (HR: positive relationship between host and parasite body sizes) and Poulin's Increasing Variance Hypothesis (PIVH: positive relationship between host body size and the variability of parasite body size). We analyzed parasite-host body size allometry for 581 species of avian lice (∼15% of known diversity) and their hosts. We applied phylogenetic generalized least squares (PGLS) methods to account for phylogenetic nonindependence controlling for host and parasite phylogenies separately and variance heterogeneity. We tested HR and PIVH for the major families of avian lice (Ricinidae, Menoponidae, Philopteridae), and for distinct ecological guilds within Philopteridae. Our data indicate that most families and guilds of avian lice follow both HR and PIVH; however, ricinids did not follow PIVH and the &quot;body lice&quot; guild of philopterid lice did not follow HR or PIVH. We discuss mathematical and ecological factors that may be responsible for these patterns, and we discuss the potential pervasiveness of these relationships among all parasites on Earth.}, }
@article {pmid27919075, year = {2016}, author = {Gossner, MM and Lewinsohn, TM and Kahl, T and Grassein, F and Boch, S and Prati, D and Birkhofer, K and Renner, SC and Sikorski, J and Wubet, T and Arndt, H and Baumgartner, V and Blaser, S and Blüthgen, N and Börschig, C and Buscot, F and Diekötter, T and Jorge, LR and Jung, K and Keyel, AC and Klein, AM and Klemmer, S and Krauss, J and Lange, M and Müller, J and Overmann, J and Pašalić, E and Penone, C and Perović, DJ and Purschke, O and Schall, P and Socher, SA and Sonnemann, I and Tschapka, M and Tscharntke, T and Türke, M and Venter, PC and Weiner, CN and Werner, M and Wolters, V and Wurst, S and Westphal, C and Fischer, M and Weisser, WW and Allan, E}, title = {Land-use intensification causes multitrophic homogenization of grassland communities.}, journal = {Nature}, volume = {540}, number = {7632}, pages = {266-269}, pmid = {27919075}, issn = {1476-4687}, mesh = {*Agriculture ; Animals ; Arthropods ; *Biodiversity ; Birds ; Bryopsida ; Chiroptera ; Conservation of Natural Resources ; Datasets as Topic ; Food Chain ; Fungi ; Germany ; *Grassland ; *Human Activities ; Lichens ; Plants ; Soil Microbiology ; Species Specificity ; }, abstract = {Land-use intensification is a major driver of biodiversity loss. Alongside reductions in local species diversity, biotic homogenization at larger spatial scales is of great concern for conservation. Biotic homogenization means a decrease in β-diversity (the compositional dissimilarity between sites). Most studies have investigated losses in local (α)-diversity and neglected biodiversity loss at larger spatial scales. Studies addressing β-diversity have focused on single or a few organism groups (for example, ref. 4), and it is thus unknown whether land-use intensification homogenizes communities at different trophic levels, above- and belowground. Here we show that even moderate increases in local land-use intensity (LUI) cause biotic homogenization across microbial, plant and animal groups, both above- and belowground, and that this is largely independent of changes in α-diversity. We analysed a unique grassland biodiversity dataset, with abundances of more than 4,000 species belonging to 12 trophic groups. LUI, and, in particular, high mowing intensity, had consistent effects on β-diversity across groups, causing a homogenization of soil microbial, fungal pathogen, plant and arthropod communities. These effects were nonlinear and the strongest declines in β-diversity occurred in the transition from extensively managed to intermediate intensity grassland. LUI tended to reduce local α-diversity in aboveground groups, whereas the α-diversity increased in belowground groups. Correlations between the β-diversity of different groups, particularly between plants and their consumers, became weaker at high LUI. This suggests a loss of specialist species and is further evidence for biotic homogenization. The consistently negative effects of LUI on landscape-scale biodiversity underscore the high value of extensively managed grasslands for conserving multitrophic biodiversity and ecosystem service provision. Indeed, biotic homogenization rather than local diversity loss could prove to be the most substantial consequence of land-use intensification.}, }
@article {pmid27915182, year = {2017}, author = {Chicas, SD and Omine, K and Ford, JB and Sugimura, K and Yoshida, K}, title = {Using spatial metrics and surveys for the assessment of trans-boundary deforestation in protected areas of the Maya Mountain Massif: Belize-Guatemala border.}, journal = {Journal of environmental management}, volume = {187}, number = {}, pages = {320-329}, doi = {10.1016/j.jenvman.2016.11.063}, pmid = {27915182}, issn = {1095-8630}, mesh = {Belize ; *Conservation of Natural Resources ; Ecology ; *Environmental Monitoring ; Forestry/*statistics &amp; numerical data ; *Geographic Information Systems ; Guatemala ; Humans ; }, abstract = {Understanding the trans-boundary deforestation history and patterns in protected areas along the Belize-Guatemala border is of regional and global importance. To assess deforestation history and patterns in our study area along a section of the Belize-Guatemala border, we incorporated multi-temporal deforestation rate analysis and spatial metrics with survey results. This multi-faceted approach provides spatial analysis with relevant insights from local stakeholders to better understand historic deforestation dynamics, spatial characteristics and human perspectives regarding the underlying causes thereof. During the study period 1991-2014, forest cover declined in Belize's protected areas: Vaca Forest Reserve 97.88%-87.62%, Chiquibul National Park 99.36%-92.12%, Caracol Archeological Reserve 99.47%-78.10% and Colombia River Forest Reserve 89.22%-78.38% respectively. A comparison of deforestation rates and spatial metrics indices indicated that between time periods 1991-1995 and 2012-2014 deforestation and fragmentation increased in protected areas. The major underlying causes, drivers, impacts, and barriers to bi-national collaboration and solutions of deforestation along the Belize-Guatemala border were identified by community leaders and stakeholders. The Mann-Whitney U test identified significant differences between leaders and stakeholders regarding the ranking of challenges faced by management organizations in the Maya Mountain Massif, except for the lack of assessment and quantification of deforestation (LD, SH: 18.67, 23.25, U = 148, p > 0.05). The survey results indicated that failure to integrate buffer communities, coordinate among managing organizations and establish strong bi-national collaboration has resulted in continued ecological and environmental degradation. The information provided by this research should aid managing organizations in their continued aim to implement effective deforestation mitigation strategies.}, }
@article {pmid27912008, year = {2016}, author = {Senior, AM and Grueber, CE and Kamiya, T and Lagisz, M and O'Dwyer, K and Santos, ES and Nakagawa, S}, title = {Heterogeneity in ecological and evolutionary meta-analyses: its magnitude and implications.}, journal = {Ecology}, volume = {97}, number = {12}, pages = {3293-3299}, doi = {10.1002/ecy.1591}, pmid = {27912008}, issn = {0012-9658}, mesh = {Bias ; *Biological Evolution ; Data Interpretation, Statistical ; Ecology/*methods ; *Meta-Analysis as Topic ; Models, Statistical ; Research Design ; }, abstract = {Meta-analysis is the gold standard for synthesis in ecology and evolution. Together with estimating overall effect magnitudes, meta-analyses estimate differences between effect sizes via heterogeneity statistics. It is widely hypothesized that heterogeneity will be present in ecological/evolutionary meta-analyses due to the system-specific nature of biological phenomena. Despite driving recommended best practices, the generality of heterogeneity in ecological data has never been systematically reviewed. We reviewed 700 studies, finding 325 that used formal meta-analysis, of which total heterogeneity was reported in fewer than 40%. We used second-order meta-analysis to collate heterogeneity statistics from 86 studies. Our analysis revealed that the median and mean heterogeneity, expressed as I2 , are 84.67% and 91.69%, respectively. These estimates are well above &quot;high&quot; heterogeneity (i.e., 75%), based on widely adopted benchmarks. We encourage reporting heterogeneity in the forms of I2 and the estimated variance components (e.g., τ2) as standard practice. These statistics provide vital insights in to the degree to which effect sizes vary, and provide the statistical support for the exploration of predictors of effect-size magnitude. Along with standard meta-regression techniques that fit moderator variables, multi-level models now allow partitioning of heterogeneity among correlated (e.g., phylogenetic) structures that exist within data.}, }
@article {pmid27905442, year = {2016}, author = {Crowther, TW and Todd-Brown, KE and Rowe, CW and Wieder, WR and Carey, JC and Machmuller, MB and Snoek, BL and Fang, S and Zhou, G and Allison, SD and Blair, JM and Bridgham, SD and Burton, AJ and Carrillo, Y and Reich, PB and Clark, JS and Classen, AT and Dijkstra, FA and Elberling, B and Emmett, BA and Estiarte, M and Frey, SD and Guo, J and Harte, J and Jiang, L and Johnson, BR and Kröel-Dulay, G and Larsen, KS and Laudon, H and Lavallee, JM and Luo, Y and Lupascu, M and Ma, LN and Marhan, S and Michelsen, A and Mohan, J and Niu, S and Pendall, E and Peñuelas, J and Pfeifer-Meister, L and Poll, C and Reinsch, S and Reynolds, LL and Schmidt, IK and Sistla, S and Sokol, NW and Templer, PH and Treseder, KK and Welker, JM and Bradford, MA}, title = {Quantifying global soil carbon losses in response to warming.}, journal = {Nature}, volume = {540}, number = {7631}, pages = {104-108}, pmid = {27905442}, issn = {1476-4687}, mesh = {Atmosphere/*chemistry ; Carbon/*analysis ; *Carbon Cycle ; Databases, Factual ; Ecosystem ; Feedback ; *Geography ; *Global Warming ; Models, Statistical ; Reproducibility of Results ; Soil/*chemistry ; Temperature ; }, abstract = {The majority of the Earth's terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming. Despite evidence that warming enhances carbon fluxes to and from the soil, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia. We find that the effects of warming are contingent on the size of the initial soil carbon stock, with considerable losses occurring in high-latitude areas. By extrapolating this empirical relationship to the global scale, we provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections. Our empirical relationship suggests that global soil carbon stocks in the upper soil horizons will fall by 30 ± 30 petagrams of carbon to 203 ± 161 petagrams of carbon under one degree of warming, depending on the rate at which the effects of warming are realized. Under the conservative assumption that the response of soil carbon to warming occurs within a year, a business-as-usual climate scenario would drive the loss of 55 ± 50 petagrams of carbon from the upper soil horizons by 2050. This value is around 12-17 per cent of the expected anthropogenic emissions over this period. Despite the considerable uncertainty in our estimates, the direction of the global soil carbon response is consistent across all scenarios. This provides strong empirical support for the idea that rising temperatures will stimulate the net loss of soil carbon to the atmosphere, driving a positive land carbon-climate feedback that could accelerate climate change.}, }
@article {pmid27895628, year = {2016}, author = {Morris, MM and Haggerty, JM and Papudeshi, BN and Vega, AA and Edwards, MS and Dinsdale, EA}, title = {Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1800}, pmid = {27895628}, issn = {1664-302X}, abstract = {Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with macroalgae. Pelagic and biofilm-associated microbes interact with macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for Macrocystis pyrifera. Here we investigate the influence of microbes from coastal environments on recruitment of giant kelp, M. pyrifera. Through repeated laboratory experiments, we tested the effects of altered pelagic microbial abundance on the settlement and development of the microscopic propagules of M. pyrifera during recruitment. M. pyrifera zoospores were reared in laboratory microcosms exposed to environmental microbial communities from seawater during the complete haploid stages of the kelp recruitment cycle, including zoospore release, followed by zoospore settlement, to gametophyte germination and development. We altered the microbial abundance states differentially in three independent experiments with repeated trials, where microbes were (a) present or absent in seawater, (b) altered in community composition, and (c) altered in abundance. Within the third experiment, we also tested the effect of nearshore versus offshore microbial communities on the macroalgal propagules. Distinct pelagic microbial communities were collected from two southern California temperate environments reflecting contrasting intensity of human influence, the nearshore Point Loma kelp forest and the offshore Santa Catalina Island kelp forest. The Point Loma kelp forest is a high impacted coastal region adjacent to the populous San Diego Bay; whereas the kelp forest at Catalina Island is a low impacted region of the Channel Islands, 40 km offshore the southern California coast, and is adjacent to a marine protected area. Kelp gametophytes reared with nearshore Point Loma microbes showed lower survival, growth, and deteriorated morphology compared to gametophytes with the offshore Catalina Island microbial community, and these effects were magnified under high microbial abundances. Reducing abundance of Point Loma microbes restored M. pyrifera propagule success. Yet an intermediate microbial abundance was optimal for kelp propagules reared with Catalina Island microbes, suggesting that microbes also have a beneficial influence on kelp. Our study shows that pelagic microbes from nearshore and offshore environments are differentially influencing kelp propagule success, which has significant implications for kelp recruitment and kelp forest ecosystem health.}, }
@article {pmid27887731, year = {2017}, author = {Khodami, S and Surif, M and W O, WM and Daryanabard, R}, title = {Assessment of heavy metal pollution in surface sediments of the Bayan Lepas area, Penang, Malaysia.}, journal = {Marine pollution bulletin}, volume = {114}, number = {1}, pages = {615-622}, doi = {10.1016/j.marpolbul.2016.09.038}, pmid = {27887731}, issn = {1879-3363}, mesh = {Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geologic Sediments/*chemistry ; Malaysia ; Metals, Heavy/*analysis ; Models, Theoretical ; Risk Assessment ; Rivers/chemistry ; Seasons ; Seawater/chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {This study aimed to evaluate the spatial and temporal distribution of heavy metals (Cd, Cr, Cu, Co, Fe, Pb, Ni, V, and Zn) in the sediments of Bayan Lepas Free Industrial Zone of Penang, Malaysia. Ten sampling stations were selected and sediment samples were collected during low tide (2012-2013). Metals were analyzed and the spatial distribution of metals were evaluated based on GIS mapping. According to interim sediment quality guidelines (ISQG), metal contents ranged from below low level to above high level at different stations. Based on the geoaccumulation index (Igeo) of sediment, sampling stations were categorized from unpolluted to strongly polluted. The enrichment factor (EF) of metals in the sediment varied between no enrichment to extremely high enrichment. The potential ecological risk index (RI) indicated Bayan Lepas FIZ was at low risk.}, }
@article {pmid27885171, year = {2016}, author = {Poyatos, R and Granda, V and Molowny-Horas, R and Mencuccini, M and Steppe, K and Martínez-Vilalta, J}, title = {SAPFLUXNET: towards a global database of sap flow measurements.}, journal = {Tree physiology}, volume = {36}, number = {12}, pages = {1449-1455}, doi = {10.1093/treephys/tpw110}, pmid = {27885171}, issn = {1758-4469}, mesh = {*Databases, Factual ; Droughts ; Ecosystem ; *Plant Transpiration ; Water/metabolism ; }, abstract = {Plant transpiration is the main evaporative flux from terrestrial ecosystems; it controls land surface energy balance, determines catchment hydrological responses and influences regional and global climate. Transpiration regulation by plants is a key (and still not completely understood) process that underlies vegetation drought responses and land evaporative fluxes under global change scenarios. Thermometric methods of sap flow measurement have now been widely used to quantify whole-plant and stand transpiration in forests, shrublands and orchards around the world. A large body of research has applied sap flow methods to analyse seasonal and diurnal patterns of transpiration and to quantify their responses to hydroclimatic variability, but syntheses of sap flow data at regional to global scales are extremely rare. Here we present the SAPFLUXNET initiative, aimed at building the first global database of plant-level sap flow measurements. A preliminary metadata survey launched in December 2015 showed an encouraging response by the sap flow community, with sap flow data sets from field studies representing >160 species and >120 globally distributed sites. The main goal of SAPFLUXNET is to analyse the ecological factors driving plant- and stand-level transpiration. SAPFLUXNET will open promising research avenues at an unprecedented global scope, namely: (i) exploring the spatio-temporal variability of plant transpiration and its relationship with plant and stand attributes, (ii) summarizing physiological regulation of transpiration by means of few water-use traits, usable for land surface models, (iii) improving our understanding of the coordination between gas exchange and plant-level traits (e.g., hydraulics) and (iv) analysing the ecological factors controlling stand transpiration and evapotranspiration partitioning. Finally, SAPFLUXNET can provide a benchmark to test models of physiological controls of transpiration, contributing to improve the accuracy of individual water stress responses, a key element to obtain robust predictions of vegetation responses to climate change.}, }
@article {pmid27859171, year = {2016}, author = {Wang, Y and Pederson, N and Ellison, AM and Buckley, HL and Case, BS and Liang, E and Julio Camarero, J}, title = {Increased stem density and competition may diminish the positive effects of warming at alpine treeline.}, journal = {Ecology}, volume = {97}, number = {7}, pages = {1668-1679}, doi = {10.1890/15-1264.1}, pmid = {27859171}, issn = {0012-9658}, mesh = {Abies/*physiology ; Environmental Monitoring ; *Forests ; *Global Warming ; Plant Stems/*physiology ; Trees/physiology ; }, abstract = {The most widespread response to global warming among alpine treeline ecotones is not an upward shift, but an increase in tree density. However, the impact of increasing density on interactions among trees at treeline is not well understood. Here, we test if treeline densification induced by climatic warming leads to increasing intraspecific competition. We mapped and measured the size and age of Smith fir trees growing in two treelines located in the southeastern Tibetan Plateau. We used spatial point-pattern and codispersion analyses to describe the spatial association and covariation among seedlings, juveniles, and adults grouped in 30-yr age classes from the 1860s to the present. Effects of competition on tree height and regeneration were inferred from bivariate mark-correlations. Since the 1950s, a rapid densification occurred at both sites in response to climatic warming. Competition between adults and juveniles or seedlings at small scales intensified as density increased. Encroachment negatively affected height growth and further reduced recruitment around mature trees. We infer that tree recruitment at the studied treelines was more cold-limited prior to 1950 and shifted to a less temperature-constrained regime in response to climatic warming. Therefore, the ongoing densification and encroachment of alpine treelines could alter the way climate drives their transitions toward subalpine forests.}, }
@article {pmid27851814, year = {2016}, author = {Coetzer, W and Moodley, D and Gerber, A}, title = {Eliciting and Representing High-Level Knowledge Requirements to Discover Ecological Knowledge in Flower-Visiting Data.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166559}, pmid = {27851814}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Behavior, Animal ; Biodiversity ; *Ecosystem ; Flowers/*physiology ; Insecta/*physiology ; *Knowledge ; Pollen/physiology ; Probability ; Reproducibility of Results ; }, abstract = {Observations of individual organisms (data) can be combined with expert ecological knowledge of species, especially causal knowledge, to model and extract from flower-visiting data useful information about behavioral interactions between insect and plant organisms, such as nectar foraging and pollen transfer. We describe and evaluate a method to elicit and represent such expert causal knowledge of behavioral ecology, and discuss the potential for wider application of this method to the design of knowledge-based systems for knowledge discovery in biodiversity and ecosystem informatics.}, }
@article {pmid27851756, year = {2016}, author = {Iwanowicz, DD and Vandergast, AG and Cornman, RS and Adams, CR and Kohn, JR and Fisher, RN and Brehme, CS}, title = {Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165366}, pmid = {27851756}, issn = {1932-6203}, mesh = {Animals ; California ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; *Diet ; *Endangered Species ; Extinction, Biological ; Feces/*chemistry ; Herbivory/*physiology ; Rodentia/*genetics ; Seasons ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Understanding the diet of an endangered species illuminates the animal's ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4-14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.}, }
@article {pmid27802151, year = {2016}, author = {Clemente, CJ and Cooper, CE and Withers, PC and Freakley, C and Singh, S and Terrill, P}, title = {The private life of echidnas: using accelerometry and GPS to examine field biomechanics and assess the ecological impact of a widespread, semi-fossorial monotreme.}, journal = {The Journal of experimental biology}, volume = {219}, number = {Pt 20}, pages = {3271-3283}, doi = {10.1242/jeb.143867}, pmid = {27802151}, issn = {1477-9145}, mesh = {*Accelerometry ; Animals ; Biomechanical Phenomena ; Body Weight ; Echidna/*physiology ; *Ecosystem ; *Geographic Information Systems ; Seasons ; Species Specificity ; Walking/physiology ; }, abstract = {The short-beaked echidna (Tachyglossus aculeatus) is a monotreme and therefore provides a unique combination of phylogenetic history, morphological differentiation and ecological specialisation for a mammal. The echidna has a unique appendicular skeleton, a highly specialised myrmecophagous lifestyle and a mode of locomotion that is neither typically mammalian nor reptilian, but has aspects of both lineages. We therefore were interested in the interactions of locomotor biomechanics, ecology and movements for wild, free-living short-beaked echidnas. To assess locomotion in its complex natural environment, we attached both GPS and accelerometer loggers to the back of echidnas in both spring and summer. We found that the locomotor biomechanics of echidnas is unique, with lower stride length and stride frequency than reported for similar-sized mammals. Speed modulation is primarily accomplished through changes in stride frequency, with a mean of 1.39 Hz and a maximum of 2.31 Hz. Daily activity period was linked to ambient air temperature, which restricted daytime activity during the hotter summer months. Echidnas had longer activity periods and longer digging bouts in spring compared with summer. In summer, echidnas had higher walking speeds than in spring, perhaps because of the shorter time suitable for activity. Echidnas spent, on average, 12% of their time digging, which indicates their potential to excavate up to 204 m3 of soil a year. This information highlights the important contribution towards ecosystem health, via bioturbation, of this widespread Australian monotreme.}, }
@article {pmid27798064, year = {2017}, author = {Lucas, R and Groeneveld, J and Harms, H and Johst, K and Frank, K and Kleinsteuber, S}, title = {A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {1}, pages = {}, doi = {10.1093/femsec/fiw209}, pmid = {27798064}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Data Interpretation, Statistical ; Databases, Genetic ; Ecology ; Ecosystem ; }, abstract = {In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application.}, }
@article {pmid27793827, year = {2017}, author = {Hermans, SM and Buckley, HL and Case, BS and Curran-Cournane, F and Taylor, M and Lear, G}, title = {Bacteria as Emerging Indicators of Soil Condition.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {1}, pages = {}, pmid = {27793827}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Carbon/metabolism ; Climate ; Ecosystem ; Hydrogen-Ion Concentration ; Microbial Consortia/*genetics/physiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition.<br><br>IMPORTANCE: The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.}, }
@article {pmid27776492, year = {2016}, author = {Kasumovic, MM and Chen, Z and Wilkins, MR}, title = {Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {827}, pmid = {27776492}, issn = {1471-2164}, mesh = {Animals ; *Behavior, Animal ; Biological Evolution ; Cluster Analysis ; Computational Biology/methods ; Female ; *Gene Expression ; Gene Expression Profiling ; Gene Ontology ; Gryllidae/*anatomy &amp; histology/*physiology ; Male ; Molecular Sequence Annotation ; Neurons/*metabolism ; Phenotype ; Quantitative Trait, Heritable ; Sex Factors ; }, abstract = {BACKGROUND: Ecological and evolutionary model organisms have provided extensive insight into the ecological triggers, adaptive benefits, and evolution of life-history driven developmental plasticity. Despite this, we still have a poor understanding of the underlying genetic changes that occur during shifts towards different developmental trajectories. The goal of this study is to determine whether we can identify underlying gene expression patterns that can describe the different life-history trajectories individuals follow in response to social cues of competition. To do this, we use the Australian black field cricket (Teleogryllus commodus), a species with sex-specific developmental trajectories moderated by the density and quality of calls heard during immaturity. In this study, we manipulated the social information males and females could hear by rearing individuals in either calling or silent treatments. We next used RNA-Seq to develop a reference transcriptome to study changes in brain gene expression at two points prior to sexual maturation.<br><br>RESULTS: We show accelerated development in both sexes when exposed to calling; changes were also seen in growth, lifespan, and reproductive effort. Functional relationships between genes and phenotypes were apparent from ontological enrichment analysis. We demonstrate that increased investment towards traits such as growth and reproductive effort were often associated with the expression of a greater number of genes with similar effect, thus providing a suite of candidate genes for future research in this and other invertebrate organisms.<br><br>CONCLUSIONS: Our results provide interesting insight into the genomic underpinnings of developmental plasticity and highlight the potential of a genomic exploration of other evolutionary theories such as condition dependence and sex-specific developmental strategies.}, }
@article {pmid27642032, year = {2016}, author = {Schlaich, AE and Klaassen, RH and Bouten, W and Bretagnolle, V and Koks, BJ and Villers, A and Both, C}, title = {How individual Montagu's Harriers cope with Moreau's Paradox during the Sahelian winter.}, journal = {The Journal of animal ecology}, volume = {85}, number = {6}, pages = {1491-1501}, doi = {10.1111/1365-2656.12583}, pmid = {27642032}, issn = {1365-2656}, mesh = {*Animal Migration ; Animals ; *Climate Change ; *Ecosystem ; Falconiformes/*physiology ; Female ; *Food Chain ; Geographic Information Systems ; Grasshoppers/physiology ; Male ; Seasons ; Senegal ; }, abstract = {Hundreds of millions of Afro-Palaearctic migrants winter in the Sahel, a semi-arid belt south of the Sahara desert, where they experience deteriorating ecological conditions during their overwintering stay and have to prepare for spring migration when conditions are worst. This well-known phenomenon was first described by R.E. Moreau and is known ever since as Moreau's Paradox. However, empirical evidence of the deteriorating seasonal ecological conditions is limited and little is known on how birds respond. Montagu's Harriers Circus pygargus spend 6 months of the year in their wintering areas in the Sahel. Within the wintering season, birds move gradually to the south, visiting several distinct sites to which they are site-faithful in consecutive years. At the last wintering site, birds find themselves at the southern edge of the Sahelian zone and have no other options than facing deteriorating conditions. We tracked 36 Montagu's Harriers with GPS trackers to study their habitat use and behaviour during winter and collected data on the abundance of their main prey, grasshoppers, in Senegal. Since grasshopper abundance was positively related to vegetation greenness (measured as normalized difference vegetation index, NDVI), we used NDVI values as a proxy for prey abundance in areas where no field data were collected. Prey abundance (grasshopper counts and vegetation greenness) at wintering sites of Montagu's Harriers decreased during the wintering period. Montagu's Harriers responded to decreasing food availability by increasing their flight time during the second half of the winter. Individuals increased flight time more in areas with stronger declines in NDVI values, suggesting that lower food abundance required more intense foraging to achieve energy requirements. The apparent consequence was that Montagu's Harriers departed later in spring when their final wintering site had lower NDVI values and presumably lower food abundance and consequently arrived later at their breeding site. Our results confirmed the suggestions Moreau made 40 years ago: the late wintering period might be a bottleneck during the annual cycle with possible carry-over effects to the breeding season. Ongoing climate change with less rainfall in the Sahel region paired with increased human pressure on natural and agricultural habitats resulting in degradation and desertification is likely to make this period more demanding, which may negatively impact populations of migratory birds using the Sahel.}, }
@article {pmid27667388, year = {2017}, author = {Yang, X and Zhang, Z and Gu, T and Dong, M and Peng, Q and Bai, L and Li, Y}, title = {Quantitative proteomics reveals ecological fitness cost of multi-herbicide resistant barnyardgrass (Echinochloa crus-galli L.).}, journal = {Journal of proteomics}, volume = {150}, number = {}, pages = {160-169}, doi = {10.1016/j.jprot.2016.09.009}, pmid = {27667388}, issn = {1876-7737}, mesh = {Echinochloa/*drug effects/genetics/growth &amp; development/*metabolism ; Ecology ; *Environment ; Gene Ontology ; Genetic Fitness/drug effects ; *Herbicide Resistance/genetics ; Herbicides/pharmacology ; Photosynthesis/drug effects/genetics ; Proteomics/*methods ; }, abstract = {Barnyardgrass (Echinochloa crus-galli) is one of the top 15 herbicide-resistant weeds around the world that interferes with rice growth, resulting in major losses of rice yield. Thus, multi-herbicide resistance in barnyardgrass presents a major threat, with the underlying mechanisms that contribute to resistance requiring elucidation. In an attempt to characterize this multi-herbicide resistance at the proteomic level, comparative analysis of resistant and susceptible barnyardgrasses was performed using iTRAQ, both with and without quinclorac, bispyribac-sodium and penoxsulam herbicidal treatment. A total of 1342 protein species were identified from 2248 unique peptides by searching the UniProt database and conducting data analysis. Approximately 904 protein species with 4774 Gene Ontology (GO) terms were grouped into the categories of biological process, cellular component and molecular function. Among these, 688 protein species were annotated into 1583 KEGG pathways, with 980 protein species relating to metabolism and 93 relating to environmental information processing. A total of 292 protein species showed more than a 1.2-fold change in abundance in the resistant biotype relative to the susceptible biotype. Furthermore, herbicide treatment resulted in 157 protein species that showed more than a 1.2-fold change in the resistant biotype. Moreover, physiological analyses demonstrated an ecological fitness cost in the resistant biotype.<br><br>SIGNIFICANCE: While some studies have shown a fitness cost to be associated with an altered ecological interaction, our understanding of the fitness costs associated with herbicide resistance are limited. Herein, physiological and proteomic analysis demonstrates herbicide resistance associated ecological fitness cost and potential mechanisms of herbicide-resistance in resistant biotypes of E. crus-galli. The results presented herein have revealed differences in ecological adaptation between resistant and susceptible biotypes in E. crus-galli and provide a fundamental basis enabling the development of new strategies for weed control. Lastly, this is the first large-scale proteomics study to examine herbicide stress responses in different barnyardgrass biotypes.}, }
@article {pmid27765035, year = {2016}, author = {Hardisty, AR and Bacall, F and Beard, N and Balcázar-Vargas, MP and Balech, B and Barcza, Z and Bourlat, SJ and De Giovanni, R and de Jong, Y and De Leo, F and Dobor, L and Donvito, G and Fellows, D and Guerra, AF and Ferreira, N and Fetyukova, Y and Fosso, B and Giddy, J and Goble, C and Güntsch, A and Haines, R and Ernst, VH and Hettling, H and Hidy, D and Horváth, F and Ittzés, D and Ittzés, P and Jones, A and Kottmann, R and Kulawik, R and Leidenberger, S and Lyytikäinen-Saarenmaa, P and Mathew, C and Morrison, N and Nenadic, A and de la Hidalga, AN and Obst, M and Oostermeijer, G and Paymal, E and Pesole, G and Pinto, S and Poigné, A and Fernandez, FQ and Santamaria, M and Saarenmaa, H and Sipos, G and Sylla, KH and Tähtinen, M and Vicario, S and Vos, RA and Williams, AR and Yilmaz, P}, title = {BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.}, journal = {BMC ecology}, volume = {16}, number = {1}, pages = {49}, pmid = {27765035}, issn = {1472-6785}, mesh = {*Biodiversity ; Ecology/instrumentation/*methods ; Internet ; Models, Biological ; Software ; Workflow ; }, abstract = {BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as &quot;Web services&quot;) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust &quot;in silico&quot; science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.<br><br>RESULTS: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.<br><br>CONCLUSIONS: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.}, }
@article {pmid27747959, year = {2016}, author = {Grossmann, L and Beisser, D and Bock, C and Chatzinotas, A and Jensen, M and Preisfeld, A and Psenner, R and Rahmann, S and Wodniok, S and Boenigk, J}, title = {Trade-off between taxon diversity and functional diversity in European lake ecosystems.}, journal = {Molecular ecology}, volume = {25}, number = {23}, pages = {5876-5888}, doi = {10.1111/mec.13878}, pmid = {27747959}, issn = {1365-294X}, mesh = {*Biodiversity ; Chlorophyta/classification ; Ciliophora/classification ; Diatoms/classification ; *Ecosystem ; Germany ; Italy ; *Lakes ; Romania ; Spain ; Transcriptome ; }, abstract = {Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater data set which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a.s.l) to 3110 m a.s.l. The dominant taxa were Chlorophyta and streptophytic algae, Ciliophora, Bacillariophyta and Chrysophyta. Metatranscriptomics provided insights into differences in community composition and into functional diversity via the relative share of taxa to the overall read abundance of distinct functional genes on the ecosystem level. The dominant metabolic pathways in terms of the fraction of expressed sequences in the cDNA libraries were affiliated with primary metabolism, specifically oxidative phosphorylation, photosynthesis and the TCA cycle. Our analyses indicate that community composition is a good first proxy for the analysis of ecosystem functions. However, differential gene regulation modifies the relative importance of taxa in distinct pathways. Whereas taxon composition varies considerably between lakes, the relative importance of distinct metabolic pathways is much more stable, indicating that ecosystem functioning is buffered against shifts in community composition through a functional redundancy of taxa.}, }
@article {pmid27729074, year = {2016}, author = {Ulicsni, V and Svanberg, I and Molnár, Z}, title = {Folk knowledge of invertebrates in Central Europe - folk taxonomy, nomenclature, medicinal and other uses, folklore, and nature conservation.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {12}, number = {1}, pages = {47}, pmid = {27729074}, issn = {1746-4269}, mesh = {Animals ; *Conservation of Natural Resources ; Europe ; *Folklore ; Humans ; Invertebrates ; *Knowledge ; *Medicine, Traditional ; Terminology as Topic ; }, abstract = {BACKGROUND: There is scarce information about European folk knowledge of wild invertebrate fauna. We have documented such folk knowledge in three regions, in Romania, Slovakia and Croatia. We provide a list of folk taxa, and discuss folk biological classification and nomenclature, salient features, uses, related proverbs and sayings, and conservation.<br><br>METHODS: We collected data among Hungarian-speaking people practising small-scale, traditional agriculture. We studied &quot;all&quot; invertebrate species (species groups) potentially occurring in the vicinity of the settlements. We used photos, held semi-structured interviews, and conducted picture sorting.<br><br>RESULTS: We documented 208 invertebrate folk taxa. Many species were known which have, to our knowledge, no economic significance. 36 % of the species were known to at least half of the informants. Knowledge reliability was high, although informants were sometimes prone to exaggeration. 93 % of folk taxa had their own individual names, and 90 % of the taxa were embedded in the folk taxonomy. Twenty four species were of direct use to humans (4 medicinal, 5 consumed, 11 as bait, 2 as playthings). Completely new was the discovery that the honey stomachs of black-coloured carpenter bees (Xylocopa violacea, X. valga) were consumed. 30 taxa were associated with a proverb or used for weather forecasting, or predicting harvests. Conscious ideas about conserving invertebrates only occurred with a few taxa, but informants would generally refrain from harming firebugs (Pyrrhocoris apterus), field crickets (Gryllus campestris) and most butterflies. We did not find any mythical creatures among invertebrate folk taxa. Almost every invertebrate species was regarded as basically harmful. Where possible, they were destroyed or at least regarded as worth eradicating. However, we could find no evidence to suggest any invertebrate species had suffered population loss as a result of conscious destruction. Sometimes knowledge pertaining to the taxa could have more general relevance, and be regarded as folk wisdom concerning the functioning of nature as a whole.<br><br>CONCLUSIONS: The high number of known invertebrate folk taxa suggests that it would be worth conducting further investigations in other areas of Europe.}, }
@article {pmid27716053, year = {2016}, author = {Peterson, BF and Scharf, ME}, title = {Metatranscriptome analysis reveals bacterial symbiont contributions to lower termite physiology and potential immune functions.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {772}, pmid = {27716053}, issn = {1471-2164}, mesh = {Amidohydrolases/genetics/metabolism ; Animals ; Antibiosis ; Bacteria/*genetics ; Computational Biology/methods ; Fungi/physiology ; Gene Expression Profiling ; Genes, rRNA ; Glutathione Transferase/metabolism ; Isoptera/*immunology/metabolism/*microbiology ; *Metagenome ; *Metagenomics/methods ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Reproducibility of Results ; *Symbiosis ; *Transcriptome ; }, abstract = {BACKGROUND: Symbioses throughout the animal kingdom are known to extend physiological and ecological capabilities to hosts. Insect-microbe associations are extremely common and are often related to novel niche exploitation, fitness advantages, and even speciation events. These phenomena include expansions in host diet, detoxification of insecticides and toxins, and increased defense against pathogens. However, dissecting the contributions of individual groups of symbionts at the molecular level is often underexplored due to methodological and analytical limitations. Termites are one of the best studied systems for physiological collaborations between host and symbiota; however, most work in lower termites (those with bacterial and protist symbionts) focuses on the eukaryotic members of this symbiotic consortium. Here we present a metatranscriptomic analysis which provides novel insights into bacterial contributions to the holobiont of the eastern subterranean termite, Reticulitermes flavipes, in the presence and absence of a fungal pathogen.<br><br>RESULTS: Using a customized ribodepletion strategy, a metatranscriptome assembly was obtained representing the host termite as well as bacterial and protist symbiota. Sequence data provide new insights into biosynthesis, catabolism, and transport of major organic molecules and ions by the gut consortium, and corroborate previous findings suggesting that bacteria play direct roles in nitrogen fixation, amino acid biosynthesis, and lignocellulose digestion. With regard to fungal pathogen challenge, a total of 563 differentially expressed candidate host and symbiont contigs were identified (162 up- and 401 downregulated; α/FDR = 0.05) including an upregulated bacterial amidohydrolase.<br><br>CONCLUSIONS: This study presents the most complete bacterial metatranscriptome from a lower termite and provides a framework on which to build a more complete model of termite-symbiont interactions including, but not limited to, digestion and pathogen defense.}, }
@article {pmid27708022, year = {2016}, author = {Greenville, AC and Emery, NJ}, title = {Gathering lots of data on a small budget.}, journal = {Science (New York, N.Y.)}, volume = {353}, number = {6306}, pages = {1360-1361}, doi = {10.1126/science.aag3057}, pmid = {27708022}, issn = {1095-9203}, mesh = {Animals ; Budgets ; Data Collection/economics/*instrumentation ; Environmental Monitoring/economics/*instrumentation ; Geographic Information Systems/*instrumentation ; Microcomputers/*economics ; Remote Sensing Technology/economics/*instrumentation ; Software ; }, }
@article {pmid27706173, year = {2016}, author = {Harris, LW and Davies, TJ}, title = {A Complete Fossil-Calibrated Phylogeny of Seed Plant Families as a Tool for Comparative Analyses: Testing the 'Time for Speciation' Hypothesis.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0162907}, pmid = {27706173}, issn = {1932-6203}, mesh = {Bayes Theorem ; Biological Evolution ; DNA, Plant/chemistry/metabolism ; Databases, Genetic ; *Fossils ; Linear Models ; Models, Theoretical ; Phylogeny ; Plants/*classification/genetics ; Seeds/genetics ; }, abstract = {Explaining the uneven distribution of species richness across the branches of the tree of life has been a major challenge for evolutionary biologists. Advances in phylogenetic reconstruction, allowing the generation of large, well-sampled, phylogenetic trees have provided an opportunity to contrast competing hypotheses. Here, we present a new time-calibrated phylogeny of seed plant families using Bayesian methods and 26 fossil calibrations. While there are various published phylogenetic trees for plants which have a greater density of species sampling, we are still a long way from generating a complete phylogeny for all ~300,000+ plants. Our phylogeny samples all seed plant families and is a useful tool for comparative analyses. We use this new phylogenetic hypothesis to contrast two alternative explanations for differences in species richness among higher taxa: time for speciation versus ecological limits. We calculated net diversification rate for each clade in the phylogeny and assessed the relationship between clade age and species richness. We then fit models of speciation and extinction to individual branches in the tree to identify major rate-shifts. Our data suggest that the majority of lineages are diversifying very slowly while a few lineages, distributed throughout the tree, are diversifying rapidly. Diversification is unrelated to clade age, no matter the age range of the clades being examined, contrary to both the assumption of an unbounded lineage increase through time, and the paradigm of fixed ecological limits. These findings are consistent with the idea that ecology plays a role in diversification, but rather than imposing a fixed limit, it may have variable effects on per lineage diversification rates through time.}, }
@article {pmid27694967, year = {2016}, author = {Zhou, X and Zhao, M and Zhou, L and Yang, G and Huang, L and Yan, C and Huang, Q and Ye, L and Zhang, X and Guo, L and Ke, X and Guo, J}, title = {Regionalization of Habitat Suitability of Masson's Pine based on geographic information system and Fuzzy Matter-Element Model.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34716}, pmid = {27694967}, issn = {2045-2322}, mesh = {China ; Ecology ; *Ecosystem ; Fuzzy Logic ; *Geographic Information Systems ; Geography ; *Models, Theoretical ; Pinus/*growth &amp; development ; }, abstract = {Pine needles have been widely used in the development of anti-hypertensive and anti-hyperlipidemic agents and health food. However, the widespread distribution of this tree poses great obstacles to the quality control and efficacy evaluation. To facilitate the effective and rational exploitation of Masson's pine (Pinus massoniana Lamb), as well as ensure effective development of Masson's pine needles as a medicinal agent, we investigated the spatial distribution of habitat suitability and evaluated the optimal ranges of ecological factors of P. massoniana with 280 samples collected from 12 provinces in China through the evaluation of four constituents known to be effective medicinally. The results of habitat suitability evaluation were also verified by Root Mean Square Error (RMSE). Finally, five ecological factors were chosen in the establishment of a habitat suitability evaluation system. The most suitable areas for P. massoniana growth were mainly concentrated in the middle and lower reaches of the Yangtze River basin, such as Sichuan, Guizhou, and Jiangxi provinces, while the best quality needles were from Guizhou, Sichuan, and the junction area of Chongqing, Hunan, and Hubei provinces. This information revealed that suitable areas for effective constituent accumulation of Masson's pine needles accounted for only 7.41% of its distribution area.}, }
@article {pmid27693307, year = {2016}, author = {Maldonado-Gómez, MX and Martínez, I and Bottacini, F and O'Callaghan, A and Ventura, M and van Sinderen, D and Hillmann, B and Vangay, P and Knights, D and Hutkins, RW and Walter, J}, title = {Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.}, journal = {Cell host &amp; microbe}, volume = {20}, number = {4}, pages = {515-526}, doi = {10.1016/j.chom.2016.09.001}, pmid = {27693307}, issn = {1934-6069}, mesh = {Administration, Oral ; Bifidobacterium longum/*growth &amp; development ; *Carrier State ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Probiotics/*administration &amp; dosage ; Time Factors ; }, abstract = {Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution.}, }
@article {pmid29932619, year = {2016}, author = {Zhang, Q and Zeng, FL and Zhang, DF and Xie, CX and Chen, SL}, title = {[Ecology suitability regions and ecological characteristics of Panax notoginseng (Burk.) F.H. Chen based on maximum entropy model].}, journal = {Yao xue xue bao = Acta pharmaceutica Sinica}, volume = {51}, number = {10}, pages = {1629-1637}, pmid = {29932619}, issn = {0513-4870}, mesh = {Altitude ; Biodiversity ; China ; *Climate ; *Ecology ; Entropy ; Geographic Information Systems ; Models, Theoretical ; Panax notoginseng/*growth &amp; development ; Soil ; Temperature ; }, abstract = {The ecology suitability and ecological characteristics of Panax notoginseng (Burk.) F. H. Chen were studied to provide a reference for its artificial introduction and cultivation. The maximum entropy model (MaxEnt) and geographic information system (GIS) were used to investigate the global ecology suitability regions for Panax notoginseng (Burk.) F. H. Chen based on its 67 distribution points collected from global biodiversity information facility (GBIF), Chinese virtual herbarium(CVH) and the related references. The results showed that the possible ecological suitable regions of Panax notoginseng (Burk.) F. H. Chen were located in Yunnan, Guangxi, Guangdong, Guizhou, Hainan, Sichuan, Fujian and Chongqing provinces. The areas with ecological similarity higher than 60% were about 89 571.3 square kilometers in total, mainly distributing in Yunnan and Guangxi provinces and small portion was located in Guangdong and Guizhou provinces. The areas with ecological similarity between 40% and 60% were about 155 172 square kilometers, mainly in Yunnan,Guangxi, Guangdong, Guizhou, Hainan, Sichuan provinces. The distribution areas were about 329 952.8 square kilometers with ecological similarity between 20% and 40%, mainly in Yunnan, Guangxi, Guangdong, Guizhou, Hainan, Sichuan, Fujian and Chongqing. The climate factors mainly affecting the distribution of Panax notoginseng (Burk.) F. H. Chen were precipitation of warmest quarter, SD of temperature seasonality, altitude, isothermality, coefficient of variation of precipitation seasonality, mean temperature of monthly, precipitation of driest month, reference bulk density of soil and soil texture.}, }
@article {pmid27672114, year = {2016}, author = {Shen, XX and Zhou, X and Kominek, J and Kurtzman, CP and Hittinger, CT and Rokas, A}, title = {Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {12}, pages = {3927-3939}, pmid = {27672114}, issn = {2160-1836}, support = {R21 AI105619/AI/NIAID NIH HHS/United States ; }, mesh = {Ascomycota/*classification/*genetics ; Computational Biology/methods ; Genetic Markers ; *Genome, Fungal ; *Genomics/methods ; *Phylogeny ; Workflow ; }, abstract = {Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.}, }
@article {pmid27668852, year = {2017}, author = {Mo, W and Wang, Y and Zhang, Y and Zhuang, D}, title = {Impacts of road network expansion on landscape ecological risk in a megacity, China: A case study of Beijing.}, journal = {The Science of the total environment}, volume = {574}, number = {}, pages = {1000-1011}, doi = {10.1016/j.scitotenv.2016.09.048}, pmid = {27668852}, issn = {1879-1026}, mesh = {Beijing ; Cities ; *Conservation of Natural Resources ; Ecology ; *Ecosystem ; Geographic Information Systems ; Risk Assessment ; *Transportation ; }, abstract = {Road networks affect the spatial structure of urban landscapes, and with continuous expansion, it will also exert more widespread influences on the regional ecological environment. With the support of geographic information system (GIS) technology, based on the application of various spatial analysis methods, this study analyzed the spatiotemporal changes of road networks and landscape ecological risk in the research area of Beijing to explore the impacts of road network expansion on ecological risk in the urban landscape. The results showed the following: 1) In the dynamic processes of change in the overall landscape pattern, the changing differences in landscape indices of various landscape types were obvious and were primarily related to land-use type. 2) For the changes in a time series, the expansion of the road kernel area was consistent with the extension of the sub-low-risk area in the urban center, but some differences were observed during different stages of development. 3) For the spatial position, the expanding changes in the road kernel area were consistent with the grade changes of the urban central ecological risk, primarily because both had a certain spatial correlation with the expressways. 4) The influence of road network expansion on the ecological risk in the study area had obvious spatial differences, which may be closely associated with the distribution of ecosystem types.}, }
@article {pmid27654921, year = {2016}, author = {Roux, S and Brum, JR and Dutilh, BE and Sunagawa, S and Duhaime, MB and Loy, A and Poulos, BT and Solonenko, N and Lara, E and Poulain, J and Pesant, S and Kandels-Lewis, S and Dimier, C and Picheral, M and Searson, S and Cruaud, C and Alberti, A and Duarte, CM and Gasol, JM and Vaqué, D and ,  and Bork, P and Acinas, SG and Wincker, P and Sullivan, MB}, title = {Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.}, journal = {Nature}, volume = {537}, number = {7622}, pages = {689-693}, pmid = {27654921}, issn = {1476-4687}, mesh = {DNA, Viral/analysis ; Datasets as Topic ; Ecology ; *Ecosystem ; Expeditions ; Genes, Viral ; *Genome, Viral ; Geographic Mapping ; Metagenome ; *Metagenomics ; Nitrogen Cycle ; Oceans and Seas ; Seawater/*virology ; Sulfur/metabolism ; Viruses/*genetics/*isolation &amp; purification/metabolism ; }, abstract = {Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.}, }
@article {pmid27645228, year = {2016}, author = {Devictor, V and Bensaude-Vincent, B}, title = {From ecological records to big data: the invention of global biodiversity.}, journal = {History and philosophy of the life sciences}, volume = {38}, number = {4}, pages = {13}, doi = {10.1007/s40656-016-0113-2}, pmid = {27645228}, issn = {0391-9714}, mesh = {*Biodiversity ; Conservation of Natural Resources/*history ; Data Collection ; Databases, Factual/*history ; Ecology/*history ; History, 20th Century ; History, 21st Century ; }, abstract = {This paper is a critical assessment of the epistemological impact of the systematic quantification of nature with the accumulation of big datasets on the practice and orientation of ecological science. We examine the contents of big databases and argue that it is not just accumulated information; records are translated into digital data in a process that changes their meanings. In order to better understand what is at stake in the 'datafication' process, we explore the context for the emergence and quantification of biodiversity in the 1980s, along with the concept of the global environment. In tracing the origin and development of the global biodiversity information facility (GBIF) we describe big data biodiversity projects as a techno-political construction dedicated to monitoring a new object: the global diversity. We argue that, biodiversity big data became a powerful driver behind the invention of the concept of the global environment, and a way to embed ecological science in the political agenda.}, }
@article {pmid27621130, year = {2017}, author = {Lopes-Lima, M and Froufe, E and Do, VT and Ghamizi, M and Mock, KE and Kebapçı, Ü and Klishko, O and Kovitvadhi, S and Kovitvadhi, U and Paulo, OS and Pfeiffer, JM and Raley, M and Riccardi, N and Şereflişan, H and Sousa, R and Teixeira, A and Varandas, S and Wu, X and Zanatta, DT and Zieritz, A and Bogan, AE}, title = {Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes.}, journal = {Molecular phylogenetics and evolution}, volume = {106}, number = {}, pages = {174-191}, doi = {10.1016/j.ympev.2016.08.021}, pmid = {27621130}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Bivalvia/*classification/genetics ; Cytochromes c/classification/genetics/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Likelihood Functions ; Phylogeny ; RNA, Ribosomal, 28S/classification/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032bp (COI+28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.}, }
@article {pmid27614455, year = {2016}, author = {Joffard, N and Buatois, B and Schatz, B}, title = {Integrative taxonomy of the fly orchid group: insights from chemical ecology.}, journal = {Die Naturwissenschaften}, volume = {103}, number = {9-10}, pages = {77}, pmid = {27614455}, issn = {1432-1904}, mesh = {Classification/*methods ; Datasets as Topic ; Flowers/*chemistry ; Gas Chromatography-Mass Spectrometry ; Hydrocarbons/*analysis/chemistry ; Orchidaceae/*chemistry/*classification ; Species Specificity ; }, abstract = {Several authors have recently stressed the need to develop an integrative approach in taxonomy, but studies applying such an approach to Mediterranean orchids are scarce. In sexually deceptive orchids from the taxonomically difficult genus Ophrys, pollination is specific and performed by male insects attracted to the flowers by sex pheromone-mimicking floral scents. Floral compounds are therefore of primary importance for reproductive isolation and species delimitations in this genus. In the fly orchid group, molecular, morphological, and ecological characters have been extensively studied, but a comprehensive survey of floral scents is still lacking. In the present study, the blends of floral compounds of its three members, Ophrys insectifera, Ophrys aymoninii, and Ophrys subinsectifera, were extracted and analyzed by gas chromatography-mass spectrometry. A total of 107 compounds were found, with a majority of saturated and unsaturated hydrocarbons. Significant differentiation, both qualitative and quantitative, was found among the three taxa. This result, pooled with those from the literature, forms a comprehensive and congruent dataset that allows us to elucidate the taxonomic rank of the three members of the fly orchid group.}, }
@article {pmid27614083, year = {2017}, author = {Yoshida, K and Makino, T and Kitano, J}, title = {Accumulation of Deleterious Mutations on the Neo-Y Chromosome of Japan Sea Stickleback (Gasterosteus nipponicus).}, journal = {The Journal of heredity}, volume = {108}, number = {1}, pages = {63-68}, doi = {10.1093/jhered/esw054}, pmid = {27614083}, issn = {1465-7333}, mesh = {Animals ; Female ; Gene Ontology ; Male ; Open Reading Frames ; Polymorphism, Single Nucleotide ; *Sequence Deletion ; Smegmamorpha/*genetics ; *Y Chromosome ; }, abstract = {Degeneration of Y chromosomes is a common evolutionary path of XY sex chromosome systems. Recent genomic studies in flies and plants have revealed that even young neo-sex chromosomes with the age of a few million years show signs of Y degeneration, such as the accumulation of nonsense and frameshift mutations. However, it remains unclear whether neo-Y chromosomes also show rapid degeneration in fishes, which often have homomorphic sex chromosomes. Here, we investigated whether a neo-Y chromosome of Japan Sea stickleback (Gasterosteus nipponicus), which was formed by a Y-autosome fusion within the last 2 million years, accumulates deleterious mutations. Our previous genomic analyses did not detect excess nonsense and frameshift mutations on the Japan Sea stickleback neo-Y. In the present study, we found that the nonrecombining region of the neo-Y near the fusion end has accumulated nonsynonymous mutations altering amino acids of evolutionarily highly conserved residues. Enrichment of gene ontology terms related to protein phosphorylation and cellular protein modification process was found in the genes with potentially deleterious mutations on the neo-Y. These results suggest that the neo-Y of the Japan Sea stickleback has already accumulated mutations that may impair protein functions.}, }
@article {pmid27549737, year = {2016}, author = {Mark, K and Cornejo, C and Keller, C and Flück, D and Scheidegger, C}, title = {Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.}, journal = {Genome}, volume = {59}, number = {9}, pages = {685-704}, doi = {10.1139/gen-2015-0189}, pmid = {27549737}, issn = {1480-3321}, mesh = {Biodiversity ; Biological Evolution ; Computational Biology ; Consensus Sequence ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; *High-Throughput Nucleotide Sequencing/instrumentation/methods ; Lichens/*classification/*genetics ; Molecular Typing/instrumentation/methods ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database-currently the most complete database for lichen-forming fungi-can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).}, }
@article {pmid27494607, year = {2016}, author = {Han, JC and Huang, Y and Li, Z and Zhao, C and Cheng, G and Huang, P}, title = {Groundwater level prediction using a SOM-aided stepwise cluster inference model.}, journal = {Journal of environmental management}, volume = {182}, number = {}, pages = {308-321}, doi = {10.1016/j.jenvman.2016.07.069}, pmid = {27494607}, issn = {1095-8630}, mesh = {*Agriculture ; China ; Droughts ; Environmental Monitoring ; Geographic Information Systems ; *Groundwater ; Humans ; *Models, Theoretical ; *Water Supply ; }, abstract = {Accurate groundwater level (GWL) prediction can contribute to sustaining reliable water supply to domestic, agricultural and industrial uses as well as ecological services, especially in arid and semi-arid areas. In this paper, a regional GWL modeling framework was first presented through coupling both spatial and temporal clustering techniques. Specifically, the self-organizing map (SOM) was applied to identify spatially homogeneous clusters of GWL piezometers, while GWL time series forecasting was performed through developing a stepwise cluster multisite inference model with various predictors including climate conditions, well extractions, surface runoffs, reservoir operations and GWL measurements at previous steps. The proposed modeling approach was then demonstrated by a case of an arid irrigation district in the western Hexi Corridor, northwest China. Spatial clustering analysis identified 6 regionally representative central piezometers out of 30, for which sensitivity and uncertainty analysis were carried out regarding GWL predictions. As the stepwise cluster tree provided uncertain predictions, we added an AR(1) error model to the mean prediction to forecast GWL 1 month ahead. Model performance indicators suggest that the modeling system is a useful tool to aid decision-making for informed groundwater resource management in arid areas, and would have a great potential to extend its applications to more areas or regions in the future.}, }
@article {pmid27442252, year = {2016}, author = {Bohlen, J and Šlechtová, V and Šlechta, V and Šlechtová, V and Sember, A and Ráb, P}, title = {A Ploidy Difference Represents an Impassable Barrier for Hybridisation in Animals. Is There an Exception among Botiid Loaches (Teleostei: Botiidae)?.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159311}, pmid = {27442252}, issn = {1932-6203}, mesh = {Animals ; China ; Chromosomes/genetics ; Cypriniformes/anatomy &amp; histology/*genetics ; Cytochromes b/genetics ; Databases, Genetic ; Geography ; *Hybridization, Genetic ; Karyotyping ; Phylogeny ; Pigmentation/genetics ; *Ploidies ; Rivers ; Sequence Analysis, DNA ; }, abstract = {One of the most efficient mechanisms to keep animal lineages separate is a difference in ploidy level (number of whole genome copies), since hybrid offspring from parents with different ploidy level are functionally sterile. In the freshwater fish family Botiidae, ploidy difference has been held responsible for the separation of its two subfamilies, the evolutionary tetraploid Botiinae and the diploid Leptobotiinae. Diploid and tetraploid species coexist in the upper Yangtze, the Pearl River and the Red River basins in China. Interestingly, the species 'Botia' zebra from the Pearl River basin combines a number of morphological characters that otherwise are found in the diploid genus Leptobotia with morphological characters of the tetraploid genus Sinibotia, therefore the aim of the present study is to test weather 'B.' zebra is the result of a hybridisation event between species from different subfamilies with different ploidy level. A closer morphological examination indeed demonstrates a high similarity of 'B.' zebra to two co-occurring species, the diploid Leptobotia guilinensis and the tetraploid Sinibotia pulchra. These two species thus could have been the potential parental species in case of a hybrid origin of 'B.' zebra. The morphologic analysis further reveals that 'B.' zebra bears even the diagnostic characters of the genera Leptobotia (Leptobotiinae) and Sinibotia (Botiinae). In contrast, a comparison of six allozyme loci between 'B.' zebra, L. guilinensis and S. pulchra showed only similarities between 'B.' zebra and S. pulchra, not between 'B.' zebra and L. guilinensis. Six specimens of 'B.' zebra that were cytogenetically analysed were tetraploid with 4n = 100. The composition of the karyotype (18% metacentric, 18% submetacentric, 36% subtelocentric and 28% acrocentric chromosomes) differs from those of L. guilinensis (12%, 24%, 20% and 44%) and S. pulchra (20%, 26%, 28% and 26%), and cannot be obtained by any combination of genomes from L. guilinensis and S. pulchra. Phylogenetic reconstructions based on sequence data of the mitochondrial cytochrome b gene and the nuclear RAG-1 gene invariably places 'Botia' zebra as sister species to S. pulchra, while L. guilinensis is only distantly related. The presented combination of genetic data demonstrates that 'B.' zebra is not the result of a hybridisation, but a species of tetraploid genus Sinibotia with a striking morphological evolution towards an enormous similarity with a co-occurring, but not directly related species. The complete lack of knowledge of the ecology of these species, their main predators or their ecological interactions hampers any conclusion regarding the evolutionary advantage of such adaptation.}, }
@article {pmid27420028, year = {2017}, author = {Bolduc, B and Youens-Clark, K and Roux, S and Hurwitz, BL and Sullivan, MB}, title = {iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {7-14}, pmid = {27420028}, issn = {1751-7370}, mesh = {*Databases, Genetic ; Environmental Microbiology ; Internet ; Metagenome ; Open Reading Frames ; Software ; Viruses/classification/genetics/*isolation &amp; purification ; }, abstract = {Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as 'Apps') for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.}, }
@article {pmid27411240, year = {2016}, author = {Hunsicker, ME and Kappel, CV and Selkoe, KA and Halpern, BS and Scarborough, C and Mease, L and Amrhein, A}, title = {Characterizing driver-response relationships in marine pelagic ecosystems for improved ocean management.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {26}, number = {3}, pages = {651-663}, pmid = {27411240}, issn = {1051-0761}, mesh = {Animals ; Biomass ; Databases, Factual ; *Ecosystem ; Marine Biology/*methods ; *Models, Biological ; *Oceans and Seas ; Population Density ; }, abstract = {Scientists and resource managers often use methods and tools that assume ecosystem components respond linearly to environmental drivers and human stressors. However, a growing body of literature demonstrates that many relationships are-non-linear, where small changes in a driver prompt a disproportionately large ecological response. We aim to provide a comprehensive assessment of the relationships between drivers and ecosystem components to identify where and when non-linearities are likely to occur. We focused our analyses on one of the best-studied marine systems, pelagic ecosystems, which allowed us to apply robust statistical techniques on a large pool of previously published studies. In this synthesis, we (1) conduct a wide literature review on single driver-response relationships in pelagic systems, (2) use statistical models to identify the degree of non-linearity in these relationships, and (3) assess whether general patterns exist in the strengths and shapes of non-linear relationships across drivers. Overall we found that non-linearities are common in pelagic ecosystems, comprising at least 52% of all driver-response relation- ships. This is likely an underestimate, as papers with higher quality data and analytical approaches reported non-linear relationships at a higher frequency (on average 11% more). Consequently, in the absence of evidence for a linear relationship, it is safer to assume a relationship is non-linear. Strong non-linearities can lead to greater ecological and socioeconomic consequences if they are unknown (and/or unanticipated), but if known they may provide clear thresholds to inform management targets. In pelagic systems, strongly non-linear relationships are often driven by climate and trophodynamic variables but are also associated with local stressors, such as overfishing and pollution, that can be more easily controlled by managers. Even when marine resource managers cannot influence ecosystem change, they can use information about threshold responses to guide how other stressors are managed and to adapt to new ocean conditions. As methods to detect and reduce uncertainty around threshold values improve, managers will be able to better understand and account for ubiquitous non-linear relationships.}, }
@article {pmid27392936, year = {2017}, author = {Huang, YJ and Erb-Downward, JR and Dickson, RP and Curtis, JL and Huffnagle, GB and Han, MK}, title = {Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {179}, number = {}, pages = {71-83}, pmid = {27392936}, issn = {1878-1810}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 HL007749/HL/NHLBI NIH HHS/United States ; K23 HL105572/HL/NHLBI NIH HHS/United States ; L30 HL120241/HL/NHLBI NIH HHS/United States ; I01 CX000911/CX/CSRD VA/United States ; U01 HL098961/HL/NHLBI NIH HHS/United States ; K23 HL130641/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammation/pathology ; Lung/microbiology/pathology ; *Microbiota ; Pulmonary Disease, Chronic Obstructive/*microbiology ; }, abstract = {In the past several years, advances in sequencing platforms and bioinformatics have transformed our understanding of the relationship between microbial ecology and human health. Both the normal and diseased lung are host to hundreds of bacterial genera, blurring the lines between &quot;colonization&quot; and &quot;infection&quot;. However, whereas in health the respiratory microbiome is determined primarily by the dynamic balance of immigration and elimination, in chronic disease conditions become much more favorable for the reproduction of resident bacteria. Recent studies demonstrate that the microbiota of the chronic obstructive pulmonary disease (COPD) lung differ from the healthy lung although significant intrasubject and intersubject heterogeneity are still present with variation impacted by factors such as disease stage and inhaled medications. Changes in the relative abundance of specific bacterial taxa during COPD exacerbations have also been noted although further longitudinal analyses are needed to ascertain the malleability and resilience of this ecological system and its role in the occurrence and frequency of exacerbations. Whether patients with a &quot;frequent exacerbator&quot; phenotype possess specific or greater alterations in their airway microbiome that predispose them to recurrent exacerbations as compared with nonfrequent exacerbators needs to be determined. Although recent data suggest that the presence of bacteria has the potential to influence the host immune response, a key challenge in the next few years will be to continue to move beyond descriptive studies to define the clinical relevance of differences in lung microbiota associated with COPD.}, }
@article {pmid27392085, year = {2017}, author = {Llorens-Marès, T and Liu, Z and Allen, LZ and Rusch, DB and Craig, MT and Dupont, CL and Bryant, DA and Casamayor, EO}, title = {Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {201-211}, pmid = {27392085}, issn = {1751-7370}, mesh = {Bacterial Proteins/metabolism ; Bacteriochlorophylls/metabolism ; Chlorobium/classification/genetics/isolation &amp; purification/*metabolism ; Ecosystem ; *Gene Transfer, Horizontal ; Lakes/*microbiology ; Metagenomics ; Photosynthesis ; RNA, Ribosomal, 16S/genetics ; Spain ; Sulfur/*metabolism ; }, abstract = {A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273T. Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273T synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB.}, }
@article {pmid27391016, year = {2016}, author = {Kirby, KR and Gray, RD and Greenhill, SJ and Jordan, FM and Gomes-Ng, S and Bibiko, HJ and Blasi, DE and Botero, CA and Bowern, C and Ember, CR and Leehr, D and Low, BS and McCarter, J and Divale, W and Gavin, MC}, title = {D-PLACE: A Global Database of Cultural, Linguistic and Environmental Diversity.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0158391}, pmid = {27391016}, issn = {1932-6203}, mesh = {*Cultural Diversity ; *Databases, Factual ; Female ; Humans ; *Language ; Male ; }, abstract = {From the foods we eat and the houses we construct, to our religious practices and political organization, to who we can marry and the types of games we teach our children, the diversity of cultural practices in the world is astounding. Yet, our ability to visualize and understand this diversity is limited by the ways it has been documented and shared: on a culture-by-culture basis, in locally-told stories or difficult-to-access repositories. In this paper we introduce D-PLACE, the Database of Places, Language, Culture, and Environment. This expandable and open-access database (accessible at https://d-place.org) brings together a dispersed corpus of information on the geography, language, culture, and environment of over 1400 human societies. We aim to enable researchers to investigate the extent to which patterns in cultural diversity are shaped by different forces, including shared history, demographics, migration/diffusion, cultural innovations, and environmental and ecological conditions. We detail how D-PLACE helps to overcome four common barriers to understanding these forces: i) location of relevant cultural data, (ii) linking data from distinct sources using diverse ethnonyms, (iii) variable time and place foci for data, and (iv) spatial and historical dependencies among cultural groups that present challenges for analysis. D-PLACE facilitates the visualisation of relationships among cultural groups and between people and their environments, with results downloadable as tables, on a map, or on a linguistic tree. We also describe how D-PLACE can be used for exploratory, predictive, and evolutionary analyses of cultural diversity by a range of users, from members of the worldwide public interested in contrasting their own cultural practices with those of other societies, to researchers using large-scale computational phylogenetic analyses to study cultural evolution. In summary, we hope that D-PLACE will enable new lines of investigation into the major drivers of cultural change and global patterns of cultural diversity.}, }
@article {pmid27362222, year = {2016}, author = {Thackeray, SJ and Henrys, PA and Hemming, D and Bell, JR and Botham, MS and Burthe, S and Helaouet, P and Johns, DG and Jones, ID and Leech, DI and Mackay, EB and Massimino, D and Atkinson, S and Bacon, PJ and Brereton, TM and Carvalho, L and Clutton-Brock, TH and Duck, C and Edwards, M and Elliott, JM and Hall, SJ and Harrington, R and Pearce-Higgins, JW and Høye, TT and Kruuk, LE and Pemberton, JM and Sparks, TH and Thompson, PM and White, I and Winfield, IJ and Wanless, S}, title = {Phenological sensitivity to climate across taxa and trophic levels.}, journal = {Nature}, volume = {535}, number = {7611}, pages = {241-245}, doi = {10.1038/nature18608}, pmid = {27362222}, issn = {1476-4687}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Aquatic Organisms ; Climate ; Climate Change/*statistics &amp; numerical data ; Datasets as Topic ; *Ecosystem ; Forecasting ; Rain ; Seasons ; Species Specificity ; Temperature ; Time Factors ; United Kingdom ; }, abstract = {Differences in phenological responses to climate change among species can desynchronise ecological interactions and thereby threaten ecosystem function. To assess these threats, we must quantify the relative impact of climate change on species at different trophic levels. Here, we apply a Climate Sensitivity Profile approach to 10,003 terrestrial and aquatic phenological data sets, spatially matched to temperature and precipitation data, to quantify variation in climate sensitivity. The direction, magnitude and timing of climate sensitivity varied markedly among organisms within taxonomic and trophic groups. Despite this variability, we detected systematic variation in the direction and magnitude of phenological climate sensitivity. Secondary consumers showed consistently lower climate sensitivity than other groups. We used mid-century climate change projections to estimate that the timing of phenological events could change more for primary consumers than for species in other trophic levels (6.2 versus 2.5-2.9 days earlier on average), with substantial taxonomic variation (1.1-14.8 days earlier on average).}, }
@article {pmid27336696, year = {2016}, author = {Wang, J and Xue, DX and Zhang, BD and Li, YL and Liu, BJ and Liu, JX}, title = {Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus).}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157809}, pmid = {27336696}, issn = {1932-6203}, mesh = {Animals ; Bass/*genetics ; Cluster Analysis ; Computational Biology/methods ; Gene Ontology ; *Genetic Variation ; *Genetics, Population ; *Genome-Wide Association Study ; *Genotype ; Molecular Sequence Annotation ; *Polymorphism, Single Nucleotide ; }, abstract = {Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.}, }
@article {pmid27336462, year = {2016}, author = {Clare, EL and Chain, FJ and Littlefair, JE and Cristescu, ME}, title = {The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data.}, journal = {Genome}, volume = {59}, number = {11}, pages = {981-990}, doi = {10.1139/gen-2015-0184}, pmid = {27336462}, issn = {1480-3321}, mesh = {*Biodiversity ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; Ecology ; *Ecosystem ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {The combination of DNA barcoding and high-throughput (next-generation) sequencing (metabarcoding) provides many promises but also serious challenges. Generating a reliable comparable estimate of biodiversity remains a central challenge to the application of the technology. Many approaches have been used to turn millions of sequences into distinct taxonomic units. However, the extent to which these methods impact the outcome of simple ecological analyses is not well understood. Here we performed a simple analysis of dietary overlap by skinks and shrews on Ile Aux Aigrettes, Mauritius. We used a combination of filtering thresholds and clustering algorithms on a COI metabarcoding dataset and demonstrate that all bioinformatics parameters will have interacting effects on molecular operational taxonomic unit (MOTU) recovery rates. These effects generated estimates covering two orders of magnitude. However, the effect on a simple ecological analysis was not large and, despite the wide variation in estimates of niche overlap, the same ecological conclusion was drawn in most cases. We advise that a conservative clustering programme coupled with larger sequence divergences to define a cluster, the removal of singletons, rigorous length filtering, and stringent match criteria for Molecular Identifier tags are preferable to avoid MOTU inflation and that the same parameters be used in all comparative analyses.}, }
@article {pmid27243207, year = {2016}, author = {Foote, AD and Vijay, N and Ávila-Arcos, MC and Baird, RW and Durban, JW and Fumagalli, M and Gibbs, RA and Hanson, MB and Korneliussen, TS and Martin, MD and Robertson, KM and Sousa, VC and Vieira, FG and Vinař, T and Wade, P and Worley, KC and Excoffier, L and Morin, PA and Gilbert, MT and Wolf, JB}, title = {Genome-culture coevolution promotes rapid divergence of killer whale ecotypes.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11693}, pmid = {27243207}, issn = {2041-1723}, mesh = {Adaptation, Biological/genetics ; Animals ; Biopsy ; *Ecotype ; *Evolution, Molecular ; Female ; Gene-Environment Interaction ; Genetic Drift ; *Genetic Speciation ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome ; Genomics/methods ; Male ; Phylogeny ; Reproductive Isolation ; Selection, Genetic/*genetics ; Skin ; Sympatry/genetics ; Whale, Killer/*physiology ; }, abstract = {Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.}, }
@article {pmid29737714, year = {2016}, author = {Li, J}, title = {[Dilemma of null hypothesis in ecological hypothesis's experiment test.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {27}, number = {6}, pages = {2031-2038}, doi = {10.13287/j.1001-9332.201606.025}, pmid = {29737714}, issn = {1001-9332}, mesh = {Data Interpretation, Statistical ; Ecology/*methods ; *Models, Statistical ; Research Design ; }, abstract = {Experimental test is one of the major test methods of ecological hypothesis, though there are many arguments due to null hypothesis. Quinn and Dunham (1983) analyzed the hypothesis deduction model from Platt (1964) and thus stated that there is no null hypothesis in ecology that can be strictly tested by experiments. Fisher's falsificationism and Neyman-Pearson (N-P)'s non-decisivity inhibit statistical null hypothesis from being strictly tested. Moreover, since the null hypothesis H0(α=1, β=0) and alternative hypothesis H1'(α'=1, β'=0) in ecological progresses are diffe-rent from classic physics, the ecological null hypothesis can neither be strictly tested experimentally. These dilemmas of null hypothesis could be relieved via the reduction of P value, careful selection of null hypothesis, non-centralization of non-null hypothesis, and two-tailed test. However, the statistical null hypothesis significance testing (NHST) should not to be equivalent to the causality logistical test in ecological hypothesis. Hence, the findings and conclusions about methodological studies and experimental tests based on NHST are not always logically reliable.}, }
@article {pmid27229931, year = {2016}, author = {Phuong, MA and Mahardika, GN and Alfaro, ME}, title = {Dietary breadth is positively correlated with venom complexity in cone snails.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {401}, pmid = {27229931}, issn = {1471-2164}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {*Animal Feed ; Animals ; Cluster Analysis ; Computational Biology/methods ; *Conus Snail/genetics/metabolism ; Gene Expression ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Peptides/genetics ; Phylogeny ; Transcriptome ; *Venoms/chemistry ; }, abstract = {BACKGROUND: Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data from past studies in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist.<br><br>RESULTS: We discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90 % of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity.<br><br>CONCLUSIONS: The poor performance of prey taxonomic class in predicting venom components suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also show that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.}, }
@article {pmid27224050, year = {2016}, author = {Gove, B and Williams, LJ and Beresford, AE and Roddis, P and Campbell, C and Teuten, E and Langston, RH and Bradbury, RB}, title = {Reconciling Biodiversity Conservation and Widespread Deployment of Renewable Energy Technologies in the UK.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0150956}, pmid = {27224050}, issn = {1932-6203}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; Ecology ; *Renewable Energy ; Solar Energy ; United Kingdom ; Water Movements ; Wind ; }, abstract = {Renewable energy will potentially make an important contribution towards the dual aims of meeting carbon emission reduction targets and future energy demand. However, some technologies have considerable potential to impact on the biodiversity of the environments in which they are placed. In this study, an assessment was undertaken of the realistic deployment potential of a range of renewable energy technologies in the UK, considering constraints imposed by biodiversity conservation priorities. We focused on those energy sources that have the potential to make important energy contributions but which might conflict with biodiversity conservation objectives. These included field-scale solar, bioenergy crops, wind energy (both onshore and offshore), wave and tidal stream energy. The spatially-explicit analysis considered the potential opportunity available for each technology, at various levels of ecological risk. The resultant maps highlight the energy resource available, physical and policy constraints to deployment, and ecological sensitivity (based on the distribution of protected areas and sensitive species). If the technologies are restricted to areas which currently appear not to have significant ecological constraints, the total potential energy output from these energy sources was estimated to be in the region of 5,547 TWh/yr. This would be sufficient to meet projected energy demand in the UK, and help to achieve carbon reduction targets. However, we highlight two important caveats. First, further ecological monitoring and surveillance is required to improve understanding of wildlife distributions and therefore potential impacts of utilising these energy sources. This is likely to reduce the total energy available, especially at sea. Second, some of the technologies under investigation are currently not deployed commercially. Consequently this potential energy will only be available if continued effort is put into developing these energy sources/technologies, to enable realisation of their full potential.}, }
@article {pmid27221127, year = {2016}, author = {Mandic, S and Williams, J and Moore, A and Hopkins, D and Flaherty, C and Wilson, G and García Bengoechea, E and Spence, JC}, title = {Built Environment and Active Transport to School (BEATS) Study: protocol for a cross-sectional study.}, journal = {BMJ open}, volume = {6}, number = {5}, pages = {e011196}, pmid = {27221127}, issn = {2044-6055}, mesh = {Accelerometry ; Adolescent ; Anthropometry ; *Bicycling ; Body Weight ; Cross-Sectional Studies ; *Environment Design ; Faculty ; Female ; Focus Groups ; Geographic Information Systems ; Geographic Mapping ; Humans ; Interviews as Topic ; Male ; New Zealand ; Parents/psychology ; Perception ; Research Design ; Residence Characteristics ; Safety ; Schools/organization &amp; administration ; Students/psychology ; Surveys and Questionnaires ; Transportation/*methods ; *Walking ; }, abstract = {INTRODUCTION: Active transport to school (ATS) is a convenient way to increase physical activity and undertake an environmentally sustainable travel practice. The Built Environment and Active Transport to School (BEATS) Study examines ATS in adolescents in Dunedin, New Zealand, using ecological models for active transport that account for individual, social, environmental and policy factors. The study objectives are to: (1) understand the reasons behind adolescents and their parents' choice of transport mode to school; (2) examine the interaction between the transport choices, built environment, physical activity and weight status in adolescents; and (3) identify policies that promote or hinder ATS in adolescents.<br><br>METHODS AND ANALYSIS: The study will use a mixed-method approach incorporating both quantitative (surveys, anthropometry, accelerometers, Geographic Information System (GIS) analysis, mapping) and qualitative methods (focus groups, interviews) to gather data from students, parents, teachers and school principals. The core data will include accelerometer-measured physical activity, anthropometry, GIS measures of the built environment and the use of maps indicating route to school (students)/work (parents) and perceived safe/unsafe areas along the route. To provide comprehensive data for understanding how to change the infrastructure to support ATS, the study will also examine complementary variables such as individual, family and social factors, including student and parental perceptions of walking and cycling to school, parental perceptions of different modes of transport to school, perceptions of the neighbourhood environment, route to school (students)/work (parents), perceptions of driving, use of information communication technology, reasons for choosing a particular school and student and parental physical activity habits, screen time and weight status. The study has achieved a 100% school recruitment rate (12 secondary schools).<br><br>ETHICS AND DISSEMINATION: The study has been approved by the University of Otago Ethics Committee. The results will be actively disseminated through reports and presentations to stakeholders, symposiums and scientific publications.}, }
@article {pmid27196065, year = {2016}, author = {Díez, B and Nylander, JA and Ininbergs, K and Dupont, CL and Allen, AE and Yooseph, S and Rusch, DB and Bergman, B}, title = {Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155757}, pmid = {27196065}, issn = {1932-6203}, mesh = {Biological Evolution ; Chlorophyll/chemistry ; Chlorophyll A ; Cyanobacteria/*genetics ; Ecosystem ; Genome, Bacterial ; Indian Ocean ; Likelihood Functions ; *Metagenome ; Metagenomics ; Phycobilisomes/genetics ; Phylogeny ; Prochlorococcus/*genetics ; Seawater/microbiology ; Synechococcus/*genetics ; Temperature ; }, abstract = {Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.}, }
@article {pmid27194808, year = {2016}, author = {Song, H and Yu, ZL and Sun, LN and Xue, DX and Zhang, T and Wang, HY}, title = {Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {7}, pages = {2181-2193}, pmid = {27194808}, issn = {2160-1836}, mesh = {Animals ; Apoptosis ; Digestive System/growth &amp; development/metabolism ; Gastropoda/*genetics/growth &amp; development ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; *Gene Library ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Immune System/growth &amp; development/metabolism ; Larva/*genetics/growth &amp; development ; Molecular Sequence Annotation ; Nervous System/growth &amp; development/metabolism ; Shellfish ; *Transcriptome ; }, abstract = {During the life cycle of shellfish, larval development, especially metamorphosis, has a vital influence on the dynamics, distribution, and recruitment of natural populations, as well as seed breeding. Rapana venosa, a carnivorous gastropod, is an important commercial shellfish in China, and is an ecological invader in the United States, Argentina, and France. However, information about the mechanism of its early development is still limited, because research in this area has long suffered from a lack of genomic resources. In this study, 15 digital gene expression (DGE) libraries from five developmental stages of R. venosa were constructed and sequenced on the IIIumina Hi-Sequation 2500 platform. Bioinformaticsanalysis identified numerous differentially and specifically expressed genes, which revealed that genes associated with growth, nervous system, digestive system, immune system, and apoptosis participate in important developmental processes. The functional analysis of differentially expressed genes was further implemented by gene ontology, and Kyoto encyclopedia of genes and genomes enrichment. DGE profiling provided a general picture of the transcriptomic activities during the early development of R. venosa, which may provide interesting hints for further study. Our data represent the first comparative transcriptomic information available for the early development of R. venosa, which is a prerequisite for a better understanding of the physiological traits controlling development.}, }
@article {pmid27177237, year = {2016}, author = {Holden, PA and Gardea-Torresdey, JL and Klaessig, F and Turco, RF and Mortimer, M and Hund-Rinke, K and Cohen Hubal, EA and Avery, D and Barceló, D and Behra, R and Cohen, Y and Deydier-Stephan, L and Ferguson, PL and Fernandes, TF and Herr Harthorn, B and Henderson, WM and Hoke, RA and Hristozov, D and Johnston, JM and Kane, AB and Kapustka, L and Keller, AA and Lenihan, HS and Lovell, W and Murphy, CJ and Nisbet, RM and Petersen, EJ and Salinas, ER and Scheringer, M and Sharma, M and Speed, DE and Sultan, Y and Westerhoff, P and White, JC and Wiesner, MR and Wong, EM and Xing, B and Steele Horan, M and Godwin, HA and Nel, AE}, title = {Considerations of Environmentally Relevant Test Conditions for Improved Evaluation of Ecological Hazards of Engineered Nanomaterials.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {12}, pages = {6124-6145}, pmid = {27177237}, issn = {1520-5851}, support = {9999-NIST/ImNIST/Intramural NIST DOC/United States ; P42 ES013660/ES/NIEHS NIH HHS/United States ; }, mesh = {*Ecology ; Ecosystem ; Ecotoxicology ; Environment ; Humans ; *Nanostructures ; }, abstract = {Engineered nanomaterials (ENMs) are increasingly entering the environment with uncertain consequences including potential ecological effects. Various research communities view differently whether ecotoxicological testing of ENMs should be conducted using environmentally relevant concentrations-where observing outcomes is difficult-versus higher ENM doses, where responses are observable. What exposure conditions are typically used in assessing ENM hazards to populations? What conditions are used to test ecosystem-scale hazards? What is known regarding actual ENMs in the environment, via measurements or modeling simulations? How should exposure conditions, ENM transformation, dose, and body burden be used in interpreting biological and computational findings for assessing risks? These questions were addressed in the context of this critical review. As a result, three main recommendations emerged. First, researchers should improve ecotoxicology of ENMs by choosing test end points, duration, and study conditions-including ENM test concentrations-that align with realistic exposure scenarios. Second, testing should proceed via tiers with iterative feedback that informs experiments at other levels of biological organization. Finally, environmental realism in ENM hazard assessments should involve greater coordination among ENM quantitative analysts, exposure modelers, and ecotoxicologists, across government, industry, and academia.}, }
@article {pmid27164179, year = {2016}, author = {Orsini, L and Gilbert, D and Podicheti, R and Jansen, M and Brown, JB and Solari, OS and Spanier, KI and Colbourne, JK and Rusch, DB and Decaestecker, E and Asselman, J and De Schamphelaere, KA and Ebert, D and Haag, CR and Kvist, J and Laforsch, C and Petrusek, A and Beckerman, AP and Little, TJ and Chaturvedi, A and Pfrender, ME and De Meester, L and Frilander, MJ}, title = {Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160030}, pmid = {27164179}, issn = {2052-4463}, support = {R24 GM078274/GM/NIGMS NIH HHS/United States ; R24-GM078274/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Daphnia/*genetics ; Databases, Genetic ; Gene-Environment Interaction ; *Genome ; RNA/genetics ; *Transcriptome ; }, abstract = {The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.}, }
@article {pmid27163938, year = {2016}, author = {Chaudhary, VB and Rúa, MA and Antoninka, A and Bever, JD and Cannon, J and Craig, A and Duchicela, J and Frame, A and Gardes, M and Gehring, C and Ha, M and Hart, M and Hopkins, J and Ji, B and Johnson, NC and Kaonongbua, W and Karst, J and Koide, RT and Lamit, LJ and Meadow, J and Milligan, BG and Moore, JC and Pendergast, TH and Piculell, B and Ramsby, B and Simard, S and Shrestha, S and Umbanhowar, J and Viechtbauer, W and Walters, L and Wilson, GW and Zee, PC and Hoeksema, JD}, title = {MycoDB, a global database of plant response to mycorrhizal fungi.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160028}, pmid = {27163938}, issn = {2052-4463}, mesh = {Biomass ; *Databases, Factual ; *Mycorrhizae ; Phylogeny ; *Plants/microbiology ; *Symbiosis ; }, abstract = {Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.}, }
@article {pmid27145698, year = {2016}, author = {Wang, C and Tang, Y and Chen, J}, title = {Plant phenological synchrony increases under rapid within-spring warming.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25460}, pmid = {27145698}, issn = {2045-2322}, mesh = {Analysis of Variance ; Arctic Regions ; Climate Change ; Datasets as Topic ; Ecology ; Europe ; Flowers/*physiology ; *Models, Statistical ; Plant Development/*physiology ; Plant Leaves/*physiology ; Seasons ; *Spatio-Temporal Analysis ; Temperature ; }, abstract = {Phenological synchrony influences many ecological processes. Recent climate change has altered the synchrony of phenology, but little is known about the underlying mechanisms. Here using in situ phenological records from Europe, we found that the standard deviation (SD, as a measure of synchrony) of first leafing day (FLD) and the SD of first flowering day (FFD) among local plants were significantly smaller in the years and/or in the regions with a more rapid within-spring warming speed (WWS, the linear slope of the daily mean temperature against the days during spring, in (o)C/day) with correlation coefficients of -0.75 and -0.48 for FLD and -0.55 and -0.23 for FFD. We further found that the SDs of temperature sensitivity of local plants were smaller under the rapid WWS conditions with correlation coefficients of -0.46 and -0.33 for FLD and FFD respectively. This study provides the first evidence that the within-season rate of change of the temperature but not the magnitude determines plant phenological synchrony. It implies that temporally, the asymmetric seasonal climatic warming may decrease the synchrony via increasing WWS, especially in arctic regions; spatially, plants in coastal and low latitude areas with low WWS would have more diverse spring phenological traits.}, }
@article {pmid27144499, year = {2016}, author = {Del Signore, A and Hendriks, AJ and Lenders, HJ and Leuven, RS and Breure, AM}, title = {Development and application of the SSD approach in scientific case studies for ecological risk assessment.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {9}, pages = {2149-2161}, doi = {10.1002/etc.3474}, pmid = {27144499}, issn = {1552-8618}, mesh = {Animals ; Databases, Factual ; Ecosystem ; Ecotoxicology/*methods/*statistics &amp; numerical data ; Environmental Pollutants/*toxicity ; *Research Design ; Risk Assessment ; Species Specificity ; }, abstract = {Species sensitivity distributions (SSDs) are used in ecological risk assessment for extrapolation of the results of toxicity tests with single species to a toxicity threshold considered protective of ecosystem structure and functioning. The attention to and importance of the SSD approach has increased in scientific and regulatory communities since the 1990s. Discussion and criticism have been triggered on the concept of the approach as well as its technical aspects (e.g., distribution type, number of toxicity endpoints). Various questions remain unanswered, especially with regard to different endpoints, statistical methods, and protectiveness of threshold levels, for example. In the present literature review (covering the period 2002-2013), case studies are explored in which the SSD approach was applied, as well as how endpoint types, species choice, and data availability affect SSDs. How statistical methods may be used to construct reliable SSDs and whether the lower 5th percentile hazard concentrations (HC5s) from a generic SSD can be protective for a specific local community are also investigated. It is shown that estimated protective concentrations were determined by taxonomic groups rather than the statistical method used to construct the distribution. Based on comparisons between semifield and laboratory-based SSDs, the output from a laboratory SSD was protective of semifield communities in the majority of studies. Environ Toxicol Chem 2016;35:2149-2161. © 2016 SETAC.}, }
@article {pmid27088604, year = {2016}, author = {Lien, S and Koop, BF and Sandve, SR and Miller, JR and Kent, MP and Nome, T and Hvidsten, TR and Leong, JS and Minkley, DR and Zimin, A and Grammes, F and Grove, H and Gjuvsland, A and Walenz, B and Hermansen, RA and von Schalburg, K and Rondeau, EB and Di Genova, A and Samy, JK and Olav Vik, J and Vigeland, MD and Caler, L and Grimholt, U and Jentoft, S and Våge, DI and de Jong, P and Moen, T and Baranski, M and Palti, Y and Smith, DR and Yorke, JA and Nederbragt, AJ and Tooming-Klunderud, A and Jakobsen, KS and Jiang, X and Fan, D and Hu, Y and Liberles, DA and Vidal, R and Iturra, P and Jones, SJ and Jonassen, I and Maass, A and Omholt, SW and Davidson, WS}, title = {The Atlantic salmon genome provides insights into rediploidization.}, journal = {Nature}, volume = {533}, number = {7602}, pages = {200-205}, pmid = {27088604}, issn = {1476-4687}, mesh = {Animals ; DNA Transposable Elements/genetics ; *Diploidy ; *Evolution, Molecular ; Female ; Gene Duplication/*genetics ; Genes, Duplicate/*genetics ; Genome/*genetics ; Genomics ; Male ; Models, Genetic ; Mutagenesis/genetics ; Phylogeny ; Reference Standards ; Salmo salar/classification/*genetics ; Sequence Homology ; }, abstract = {The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.}, }
@article {pmid27082742, year = {2016}, author = {Schulze, J and Frank, K and Priess, JA and Meyer, MA}, title = {Assessing Regional-Scale Impacts of Short Rotation Coppices on Ecosystem Services by Modeling Land-Use Decisions.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153862}, pmid = {27082742}, issn = {1932-6203}, mesh = {Agriculture/*methods ; Biodiversity ; Biofuels/supply &amp; distribution ; Biomass ; Computer Simulation ; Conservation of Natural Resources/*economics ; Decision Support Techniques ; Ecology ; Ecosystem ; Germany ; Models, Economic ; Regression Analysis ; Soil ; Spatial Analysis ; }, abstract = {Meeting the world's growing energy demand through bioenergy production involves extensive land-use change which could have severe environmental and social impacts. Second generation bioenergy feedstocks offer a possible solution to this problem. They have the potential to reduce land-use conflicts between food and bioenergy production as they can be grown on low quality land not suitable for food production. However, a comprehensive impact assessment that considers multiple ecosystem services (ESS) and biodiversity is needed to identify the environmentally best feedstock option, as trade-offs are inherent. In this study, we simulate the spatial distribution of short rotation coppices (SRCs) in the landscape of the Mulde watershed in Central Germany by modeling profit-maximizing farmers under different economic and policy-driven scenarios using a spatially explicit economic simulation model. This allows to derive general insights and a mechanistic understanding of regional-scale impacts on multiple ESS in the absence of large-scale implementation. The modeled distribution of SRCs, required to meet the regional demand of combined heat and power (CHP) plants for solid biomass, had little or no effect on the provided ESS. In the policy-driven scenario, placing SRCs on low or high quality soils to provide ecological focus areas, as required within the Common Agricultural Policy in the EU, had little effect on ESS. Only a substantial increase in the SRC production area, beyond the regional demand of CHP plants, had a relevant effect, namely a negative impact on food production as well as a positive impact on biodiversity and regulating ESS. Beneficial impacts occurred for single ESS. However, the number of sites with balanced ESS supply hardly increased due to larger shares of SRCs in the landscape. Regression analyses showed that the occurrence of sites with balanced ESS supply was more strongly driven by biophysical factors than by the SRC share in the landscape. This indicates that SRCs negligibly affect trade-offs between individual ESS. Coupling spatially explicit economic simulation models with environmental and ESS assessment models can contribute to a comprehensive impact assessment of bioenergy feedstocks that have not yet been planted.}, }
@article {pmid27050459, year = {2016}, author = {Rodriguez, KA and Li, K and Nevo, E and Buffenstein, R}, title = {Mechanisms regulating proteostasis are involved in sympatric speciation of the blind mole rat, Spalax galili.}, journal = {Autophagy}, volume = {12}, number = {4}, pages = {703-704}, doi = {10.1080/15548627.2016.1143592}, pmid = {27050459}, issn = {1554-8635}, support = {K99 AG049940/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Gene Expression Regulation ; Gene Ontology ; *Genetic Speciation ; *Homeostasis ; Proteins/*metabolism ; Proteolysis ; Spalax/*metabolism ; *Sympatry ; }, abstract = {Genome-wide analysis demonstrates extensive genomic adaptive complexes involved in sympatric speciation between blind mole rats (Spalax galili) in abutting populations living in basalt and chalk soils. Among the gene ontology (GO) enrichment, musculature and metabolism stood out in basalt dwellers while nutrition and neurogenetics were highlighted in chalk residents. Measurements of mechanisms regulating protein homeostasis inspired by these GO terms suggest that at the proteomic level there is also a habitat/soil-type driven divergence with the basalt residents exhibiting higher proteasome activity whereas elevated levels of markers of autophagy are evident in the chalk inhabitants.}, }
@article {pmid27044302, year = {2016}, author = {Crawford, DL and Oleksiak, MF}, title = {Ecological population genomics in the marine environment.}, journal = {Briefings in functional genomics}, volume = {15}, number = {5}, pages = {342-351}, doi = {10.1093/bfgp/elw008}, pmid = {27044302}, issn = {2041-2657}, mesh = {Animals ; Computational Biology/*methods ; *Environment ; *Genetic Variation ; *Genetics, Population ; Genomics/*methods ; *Marine Biology ; Sequence Analysis, DNA ; }, abstract = {Marine species live in a wide diversity of environments and yet, because of their pelagic life stages, are thought to be well-connected: they have high migration rates that inhibit significant population structure. Recent innovations in sequencing technologies now provide information on nucleotide polymorphisms at thousands to tens of thousands of loci based on whole genomes, reduced representative portions of genomes (0.1-1%) or a majority of expressed mRNAs. Data from these genomic approaches are used to define and quantify single-nucleotide polymorphisms (SNPs). These SNP data tend to agree with data from older technologies (allozymes or microsatellites), which support well-connected populations with few genetic differences among populations. However, these studies also find few percentages of SNPs (1-5%) that readily distinguish genetic differences among populations on relatively small geographic scales. The magnitudes of the genetic differences (FST values) suggest that hundreds of loci with significant differences are due to positive selective pressures. Thus, these data suggest that natural selection is effectively altering allele frequencies at 100s of loci in marine populations. In this manuscript, we provide examples of these studies, the strengths and weaknesses of different genomic approaches as well as important technical aspects associated with genomic approaches.}, }
@article {pmid27037819, year = {2016}, author = {Buckley, HL and Case, BS and Zimmerman, JK and Thompson, J and Myers, JA and Ellison, AM}, title = {Using codispersion analysis to quantify and understand spatial patterns in species-environment relationships.}, journal = {The New phytologist}, volume = {211}, number = {2}, pages = {735-749}, doi = {10.1111/nph.13934}, pmid = {27037819}, issn = {1469-8137}, mesh = {Computer Simulation ; *Ecosystem ; Models, Theoretical ; Species Specificity ; }, abstract = {The analysis of spatial patterns in species-environment relationships can provide new insights into the niche requirements and potential co-occurrence of species, but species abundance and environmental data are routinely collected at different spatial scales. Here, we investigate the use of codispersion analysis to measure and assess the scale, directionality and significance of complex relationships between plants and their environment in large forest plots. We applied codispersion analysis to both simulated and field data on spatially located tree species basal area and environmental variables. The significance of the observed bivariate spatial associations between the basal area of key species and underlying environmental variables was tested using three null models. Codispersion analysis reliably detected directionality (anisotropy) in bivariate species-environment relationships and identified relevant scales of effects. Null model-based significance tests applied to codispersion analyses of forest plot data enabled us to infer the extent to which environmental conditions, tree sizes and/or tree spatial positions underpinned the observed basal area-environment relationships, or whether relationships were a result of other unmeasured factors. Codispersion analysis, combined with appropriate null models, can be used to infer hypothesized ecological processes from spatial patterns, allowing us to start disentangling the possible drivers of plant species-environment relationships.}, }
@article {pmid27029554, year = {2016}, author = {Speth, DR and In 't Zandt, MH and Guerrero-Cruz, S and Dutilh, BE and Jetten, MS}, title = {Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11172}, pmid = {27029554}, issn = {2041-1723}, mesh = {Ammonium Compounds/analysis ; Bacteria/classification/*genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Denitrification ; *Genome, Bacterial ; Metagenomics ; Nitrites/metabolism ; Phylogeny ; Sewage/chemistry/microbiology ; *Waste Water ; Water Purification/*methods ; }, abstract = {Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date.}, }
@article {pmid26991208, year = {2016}, author = {Pardo, A and García, FM and Valladares, F and Pulido, F}, title = {Simulated herbivory does not constrain phenotypic plasticity to shade through ontogeny in a relict tree.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {18}, number = {4}, pages = {618-626}, doi = {10.1111/plb.12447}, pmid = {26991208}, issn = {1438-8677}, mesh = {*Biological Ontologies ; Ecology ; *Herbivory ; Light ; Models, Biological ; Phenotype ; Plant Leaves/physiology/radiation effects ; Plant Roots/physiology/radiation effects ; Plant Shoots/physiology/radiation effects ; Seedlings/physiology/radiation effects ; Stress, Physiological ; Trees/*physiology/radiation effects ; }, abstract = {Ecological limits to phenotypic plasticity (PP), induced by simultaneous biotic and abiotic factors, can prevent organisms from exhibiting optimal plasticity, and in turn lead to decreased fitness. Herbivory is an important biotic stressor and may limit plant functional responses to challenging environmental conditions such as shading. In this study we investigated whether plant functional responses and PP to shade are constrained by herbivory, and whether such constraints are due to direct effects based on resource limitation by considering ontogeny. We used as a model system the relict tree Prunus lusitanica and implemented an indoor experiment to quantify the response of saplings of different ages to shade and herbivory. We measured five functional traits and quantitatively calculated PP. Results showed that herbivory did not constrain functional responses or PP to shade except for shoot:root ratio (SR), which, despite showing a high PP in damaged saplings, decreased under shade instead of increasing. Damaged saplings of older age did not exhibit reduced constraints on functional responses to shade and generally presented a lower PP than damaged saplings of younger age. Our findings suggest that herbivory-mediated constraints on plant plasticity to shade may not be as widespread as previously thought. Nonetheless, the negative effect of herbivory on SR plastic expression to shade could be detrimental for plant fitness. Finally, our results suggest a secondary role of direct effects (resource-based) on P. lusitanica plasticity limitation. Further studies should quantify plant resources in order to gain a better understanding of this seldom-explored subject.}, }
@article {pmid26981637, year = {2016}, author = {Li, X and Niu, X and Wang, B and Gao, P and Liu, Y}, title = {Driving Forces of Dynamic Changes in Soil Erosion in the Dahei Mountain Ecological Restoration Area of Northern China Based on GIS and RS.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0142331}, pmid = {26981637}, issn = {1932-6203}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; *Geographic Information Systems ; *Remote Sensing Technology ; *Soil ; }, abstract = {Dynamic change in soil erosion is an important focus of regional ecological restoration research. Here, the dynamic changes of soil erosion and its driving forces in the Dahei Mountain ecological restoration area of northern China were analyzed by LANDSAT TM remote sensing captured via geographic information system (GIS) technologies during three typical periods in 2004, 2008 and 2013. The results showed the following: (1) a decrease in intensive erosion and moderate erosion areas, as well as an increase in light erosion areas, was observed during two periods: one from 2004 to 2008 and the other from 2008 to 2013. (2) Between 2004 and 2008, the variation in the range of slight erosion was the largest (24.28%), followed by light erosion and intensive erosion; between 2008 and 2013, the variation in the range of intensive erosion area was the largest (9.89%), followed by slight erosion and moderate erosion. (3) Socioeconomic impact, accompanied by natural environmental factors, was the main driving force underlying the change in soil erosion within the ecological restoration area. In particular, the socioeconomic factors of per capita forest area and land reclamation rate, as well as the natural environmental factor of terrain slope, significantly influenced soil erosion changes within the ecological restoration area.}, }
@article {pmid26970666, year = {2016}, author = {Juggins, S and Kelly, M and Allott, T and Kelly-Quinn, M and Monteith, D}, title = {A Water Framework Directive-compatible metric for assessing acidification in UK and Irish rivers using diatoms.}, journal = {The Science of the total environment}, volume = {568}, number = {}, pages = {671-678}, doi = {10.1016/j.scitotenv.2016.02.163}, pmid = {26970666}, issn = {1879-1026}, mesh = {Calcium/analysis ; Conservation of Water Resources/legislation &amp; jurisprudence/*methods ; Databases, Factual ; Diatoms/*classification/isolation &amp; purification ; Environmental Monitoring/legislation &amp; jurisprudence/*methods ; Hydrogen-Ion Concentration ; Ireland ; Models, Theoretical ; Predictive Value of Tests ; Reference Values ; Rivers/*chemistry ; United Kingdom ; Water Pollutants, Chemical/*analysis ; }, abstract = {Freshwater acidification continues to be a major problem affecting large areas of Europe, and while there is evidence for chemical recovery, similar evidence for biological recovery of freshwaters is sparse. The need for a methodology to identify waterbodies impacted acidification and to assess the extent of biological recovery is relevant to the EU Water Framework Directive, which requires methods to quantify differences in biology between impacted and unimpacted or reference sites. This study presents a new WFD-compliant metric based on diatoms (Diatom Acidification Metric: DAM) for assessing the acidification status of rivers. A database of 558 benthic diatom samples and associated water chemistry data was assembled. Diatom taxa were assigned to one of 5 indicator classes on the basis of their pH optimum, assessed using Gaussian logistic regression, and these indicator values used to calculate a DAM score for each site using weighted averaging. Reference sites were selected on the basis of their acid neutralising capacity (ANC) and calcium concentration, and a regression model developed to predict expected DAM for each site using pH and total organic carbon (TOC) concentration. Site-specific DAM scores were used to calculate ecological quality ratios ranging from ≥1, where the diatom assemblage showed no impact, to (theoretically) 0, when the diatom assemblage was indicative of major anthropogenic activities. The boundary between 'high' and 'good' status was defined as the 25th percentile of Ecological Quality Ratios (EQRs) of all reference sites. The boundary between 'good' and 'moderate' status was set at the point at which nutrient-sensitive and nutrient-tolerant taxa were present in equal relative abundance. The methodology was evaluated using long-term data from 11 sites from the UK Uplands Waters Monitoring Network and is shown to perform well in discriminating naturally acid from acidified sites.}, }
@article {pmid26967526, year = {2016}, author = {Daume, S and Galaz, V}, title = {&quot;Anyone Know What Species This Is?&quot; - Twitter Conversations as Embryonic Citizen Science Communities.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151387}, pmid = {26967526}, issn = {1932-6203}, mesh = {*Classification ; *Communication ; Quality Control ; *Residence Characteristics ; Science/*methods ; *Social Media ; Time Factors ; }, abstract = {Social media like blogs, micro-blogs or social networks are increasingly being investigated and employed to detect and predict trends for not only social and physical phenomena, but also to capture environmental information. Here we argue that opportunistic biodiversity observations published through Twitter represent one promising and until now unexplored example of such data mining. As we elaborate, it can contribute to real-time information to traditional ecological monitoring programmes including those sourced via citizen science activities. Using Twitter data collected for a generic assessment of social media data in ecological monitoring we investigated a sample of what we denote biodiversity observations with species determination requests (N = 191). These entail images posted as messages on the micro-blog service Twitter. As we show, these frequently trigger conversations leading to taxonomic determinations of those observations. All analysed Tweets were posted with species determination requests, which generated replies for 64% of Tweets, 86% of those contained at least one suggested determination, of which 76% were assessed as correct. All posted observations included or linked to images with the overall image quality categorised as satisfactory or better for 81% of the sample and leading to taxonomic determinations at the species level in 71% of provided determinations. We claim that the original message authors and conversation participants can be viewed as implicit or embryonic citizen science communities which have to offer valuable contributions both as an opportunistic data source in ecological monitoring as well as potential active contributors to citizen science programmes.}, }
@article {pmid26950402, year = {2016}, author = {Jun, YW and Park, H and Lee, YK and Kaang, BK and Lee, JA and Jang, DJ}, title = {D-AKAP1a is a signal-anchored protein in the mitochondrial outer membrane.}, journal = {FEBS letters}, volume = {590}, number = {7}, pages = {954-961}, doi = {10.1002/1873-3468.12123}, pmid = {26950402}, issn = {1873-3468}, mesh = {A Kinase Anchor Proteins/chemistry/genetics/*metabolism ; Amino Acid Substitution ; Animals ; Biomarkers/metabolism ; Computational Biology ; Cyclic AMP/*metabolism ; Endoplasmic Reticulum ; Golgi Apparatus/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; HEK293 Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mice ; Microscopy, Confocal ; Microscopy, Fluorescence ; Mitochondrial Membranes/*metabolism ; *Models, Molecular ; Mutation ; Protein Structure, Tertiary ; Protein Transport ; Recombinant Fusion Proteins/chemistry/metabolism ; *Second Messenger Systems ; }, abstract = {Dual A-kinase anchoring protein 1a (D-AKAP1a, AKAP1) regulates cAMP signaling in mitochondria. However, it is not clear how D-AKAP1a is associated with mitochondria. In this study, we show that D-AKAP1a is a transmembrane protein in the mitochondrial outer membrane (MOM). We revealed that the N-terminus of D-AKAP1a is exposed to the intermembrane space of mitochondria and that its C-terminus is located on the cytoplasmic side of the MOM. Moderate hydrophobicity and the positively charged flanking residues of the transmembrane domain of D-AKAP1a were important for targeting. Taken together, D-AKAP1a can be classified as a signal-anchored protein in the MOM. Our topological study provides valuable information about the molecular and cellular mechanisms of mitochondrial targeting of AKAP1.}, }
@article {pmid26909419, year = {2015}, author = {Kendall, BE}, title = {Some directions in ecological theory.}, journal = {Ecology}, volume = {96}, number = {12}, pages = {3117-3125}, pmid = {26909419}, issn = {0012-9658}, mesh = {Animals ; Biomass ; Causality ; Conservation of Natural Resources/*methods ; Data Interpretation, Statistical ; Ecology/education/*methods ; Ecosystem ; Extinction, Biological ; Humans ; *Models, Theoretical ; }, abstract = {The role of theory within ecology has changed dramatically in recent decades. Once primarily a source of qualitative conceptual framing, ecological theories and models are now often used to develop quantitative explanations of empirical patterns and to project future dynamics of specific ecological systems. In this essay, I recount my own experience of this transformation, in which accelerating computing power and the widespread incorporation of stochastic processes into ecological theory combined to create some novel integration of mathematical and statistical models. This stronger integration drives theory towards incorporating more biological realism, and I explore ways in which we can grapple with that realism to generate new general theoretical insights. This enhanced realism, in turn, may lead to frameworks for projecting ecological responses to anthropogenic change, which is, arguably, the central challenge for 21st-century ecology. In an era of big data and synthesis, ecologists are increasingly seeking to infer causality from observational data; but conventional biometry provides few tools for this project. This is a realm where theorists can and should play an important role, and I close by pointing towards some analytical and philosophical approaches developed in our sister discipline of economics that address this very problem. While I make no grand prognostications about the likely discoveries of ecological theory over the coming century, you will find in this essay a scattering of more or less far-fetched ideas that I, at least, think are interesting and (possibly) fruitful directions for our field.}, }
@article {pmid26897477, year = {2017}, author = {Bennett, KB}, title = {Ecological interface design and system safety: One facet of Rasmussen's legacy.}, journal = {Applied ergonomics}, volume = {59}, number = {Pt B}, pages = {625-636}, doi = {10.1016/j.apergo.2015.08.001}, pmid = {26897477}, issn = {1872-9126}, mesh = {Decision Making ; *Decision Support Techniques ; *Ecology ; Humans ; Safety Management/*methods ; *Systems Analysis ; *User-Computer Interface ; }, abstract = {The focus of this manuscript is on cognitive systems engineering/ecological interface design (CSE/EID) and the role that this framework may play in improving system safety. First, the decision making and problem solving literatures are reviewed with an eye towards informational needs that are required to support these activities. The utility of two of Rasmussen's analytical tools (i.e., the abstraction and aggregation hierarchies) in conducting work domain analyses to identify associated information (i.e., categories and relationships) is discussed. The importance of designing ecological displays and interfaces that span the informational categories in the abstraction hierarchy is described and concrete examples are provided. The potential role that ecological interfaces can play in providing effective decision making (i.e., preventing accidents) and problem solving (i.e., dealing with accidents) support, thereby improving the safety of our socio-technical systems, is explored.}, }
@article {pmid26886349, year = {2016}, author = {Ujiié, Y and Ishitani, Y}, title = {Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148847}, pmid = {26886349}, issn = {1932-6203}, mesh = {Bayes Theorem ; *Biological Evolution ; Confidence Intervals ; DNA, Ribosomal/genetics ; Databases, Genetic ; Foraminifera/*genetics ; Genetic Variation ; Geography ; *Oceans and Seas ; Phylogeny ; Time Factors ; *Tropical Climate ; }, abstract = {Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world's oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.}, }
@article {pmid26881995, year = {2016}, author = {Hu, XG and Liu, H and Jin, Y and Sun, YQ and Li, Y and Zhao, W and El-Kassaby, YA and Wang, XR and Mao, JF}, title = {De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148985}, pmid = {26881995}, issn = {1932-6203}, mesh = {Adaptation, Physiological/genetics ; Alkyl and Aryl Transferases/genetics/*metabolism ; Coniferophyta/classification/genetics ; Databases, Genetic ; Gene Expression Profiling ; *Genes, Plant ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Stress, Physiological ; *Transcriptome ; }, abstract = {Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.}, }
@article {pmid26876925, year = {2016}, author = {Adamík, P and Emmenegger, T and Briedis, M and Gustafsson, L and Henshaw, I and Krist, M and Laaksonen, T and Liechti, F and Procházka, P and Salewski, V and Hahn, S}, title = {Barrier crossing in small avian migrants: individual tracking reveals prolonged nocturnal flights into the day as a common migratory strategy.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21560}, pmid = {26876925}, issn = {2045-2322}, mesh = {Africa, Northern ; Animal Migration/*physiology ; Animals ; Breeding ; Flight, Animal/*physiology ; Geographic Information Systems ; Mediterranean Sea ; Songbirds/*physiology ; }, abstract = {Over decades it has been unclear how individual migratory songbirds cross large ecological barriers such as seas or deserts. By deploying light-level geolocators on four songbird species weighing only about 12 g, we found that these otherwise mainly nocturnal migrants seem to regularly extend their nocturnal flights into the day when crossing the Sahara Desert and the Mediterranean Sea. The proportion of the proposed diurnally flying birds gradually declined over the day with similar landing patterns in autumn and spring. The prolonged flights were slightly more frequent in spring than in autumn, suggesting tighter migratory schedules when returning to breeding sites. Often we found several patterns for barrier crossing for the same individual in autumn compared to the spring journey. As only a small proportion of the birds flew strictly during the night and even some individuals might have flown non-stop, we suggest that prolonged endurance flights are not an exception even in small migratory species. We emphasise an individual's ability to perform both diurnal and nocturnal migration when facing the challenge of crossing a large ecological barrier to successfully complete a migratory journey.}, }
@article {pmid26875912, year = {2016}, author = {Breen, M and Villeneuve, DL and Ankley, GT and Bencic, D and Breen, MS and Watanabe, KH and Lloyd, AL and Conolly, RB}, title = {Computational model of the fathead minnow hypothalamic-pituitary-gonadal axis: Incorporating protein synthesis in improving predictability of responses to endocrine active chemicals.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {183-184}, number = {}, pages = {36-45}, doi = {10.1016/j.cbpc.2016.02.002}, pmid = {26875912}, issn = {1532-0456}, mesh = {Animals ; Aromatase/chemistry/genetics/*metabolism ; Aromatase Inhibitors/administration &amp; dosage/toxicity ; Computational Biology ; Cyprinidae/blood/growth &amp; development/*physiology ; Dose-Response Relationship, Drug ; Endocrine Disruptors/administration &amp; dosage/*toxicity ; Estradiol/blood ; Fadrozole/administration &amp; dosage/toxicity ; Female ; Fish Proteins/agonists/antagonists &amp; inhibitors/genetics/metabolism ; Gene Expression Regulation, Developmental/*drug effects ; Hypothalamo-Hypophyseal System/*drug effects/metabolism ; Male ; *Models, Biological ; Ovary/*drug effects/enzymology/metabolism ; RNA, Messenger/metabolism ; Random Allocation ; Reproducibility of Results ; Testis/drug effects/metabolism ; Toxicity Tests/methods ; Water Pollutants, Chemical/administration &amp; dosage/toxicity ; }, abstract = {There is international concern about chemicals that alter endocrine system function in humans and/or wildlife and subsequently cause adverse effects. We previously developed a mechanistic computational model of the hypothalamic-pituitary-gonadal (HPG) axis in female fathead minnows exposed to a model aromatase inhibitor, fadrozole (FAD), to predict dose-response and time-course behaviors for apical reproductive endpoints. Initial efforts to develop a computational model describing adaptive responses to endocrine stress providing good fits to empirical plasma 17β-estradiol (E2) data in exposed fish were only partially successful, which suggests that additional regulatory biology processes need to be considered. In this study, we addressed short-comings of the previous model by incorporating additional details concerning CYP19A (aromatase) protein synthesis. Predictions based on the revised model were evaluated using plasma E2 concentrations and ovarian cytochrome P450 (CYP) 19A aromatase mRNA data from two fathead minnow time-course experiments with FAD, as well as from a third 4-day study. The extended model provides better fits to measured E2 time-course concentrations, and the model accurately predicts CYP19A mRNA fold changes and plasma E2 dose-response from the 4-d concentration-response study. This study suggests that aromatase protein synthesis is an important process in the biological system to model the effects of FAD exposure.}, }
@article {pmid26834710, year = {2015}, author = {Melendrez, MC and Becraft, ED and Wood, JM and Olsen, MT and Bryant, DA and Heidelberg, JF and Rusch, DB and Cohan, FM and Ward, DM}, title = {Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1540}, pmid = {26834710}, issn = {1664-302X}, abstract = {Recent studies of bacterial speciation have claimed to support the biological species concept-that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B') of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B' lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.}, }
@article {pmid26822217, year = {2016}, author = {Barać, N and Škrivanj, S and Bukumirić, Z and Živojinović, D and Manojlović, D and Barać, M and Petrović, R and Ćorac, A}, title = {Distribution and mobility of heavy elements in floodplain agricultural soils along the Ibar River (Southern Serbia and Northern Kosovo). Chemometric investigation of pollutant sources and ecological risk assessment.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {9}, pages = {9000-9011}, pmid = {26822217}, issn = {1614-7499}, mesh = {Agriculture ; Ecology ; *Environmental Monitoring ; Industry ; Kosovo ; Metals, Heavy/*analysis ; Risk Assessment ; Rivers/chemistry ; Serbia ; Soil/chemistry ; Soil Pollutants/*analysis ; }, abstract = {This work investigates the influence of a high-magnitude flood event on heavy elements (HEs) pollution and mobility in the agricultural soils along Ibar River in Southern Serbia and Northern Kosovo. The study area was one of the most important Pb/Zn industrial regions in Europe. Soil samples (n = 50) collected before and after the floods in May 2014 were subjected to the sequential extraction procedure proposed by the Community Bureau of Reference (BCR). The results indicated that the floods significantly increased not only the pseudo total concentrations of HEs in the soil but also their mobile and potentially bioavailable amounts. Moreover, higher concentrations (both pseudo total and potentially bioavailable) were found in the agricultural soils closer to the industrial hotspots. Principal component analysis and hierarchical cluster analysis successfully grouped the analyzed elements according to their anthropogenic or natural origin. The floods significantly increased the potential ecological risk of HEs associated with Pb/Zn industrial activities in the study area. The potential ecological risk of Cd after the floods was highest and should be of special concern.}, }
@article {pmid26814420, year = {2016}, author = {Salguero-Gómez, R and Jones, OR and Archer, CR and Bein, C and de Buhr, H and Farack, C and Gottschalk, F and Hartmann, A and Henning, A and Hoppe, G and Römer, G and Ruoff, T and Sommer, V and Wille, J and Voigt, J and Zeh, S and Vieregg, D and Buckley, YM and Che-Castaldo, J and Hodgson, D and Scheuerlein, A and Caswell, H and Vaupel, JW}, title = {COMADRE: a global data base of animal demography.}, journal = {The Journal of animal ecology}, volume = {85}, number = {2}, pages = {371-384}, pmid = {26814420}, issn = {1365-2656}, mesh = {Animals ; *Databases, Factual ; *Demography ; Ecology/*methods ; *Models, Biological ; }, abstract = {UNLABELLED: The open-data scientific philosophy is being widely adopted and proving to promote considerable progress in ecology and evolution. Open-data global data bases now exist on animal migration, species distribution, conservation status, etc. However, a gap exists for data on population dynamics spanning the rich diversity of the animal kingdom world-wide. This information is fundamental to our understanding of the conditions that have shaped variation in animal life histories and their relationships with the environment, as well as the determinants of invasion and extinction. Matrix population models (MPMs) are among the most widely used demographic tools by animal ecologists. MPMs project population dynamics based on the reproduction, survival and development of individuals in a population over their life cycle. The outputs from MPMs have direct biological interpretations, facilitating comparisons among animal species as different as Caenorhabditis elegans, Loxodonta africana and Homo sapiens. Thousands of animal demographic records exist in the form of MPMs, but they are dispersed throughout the literature, rendering comparative analyses difficult. Here, we introduce the COMADRE Animal Matrix Database, an open-data online repository, which in its version 1.0.0 contains data on 345 species world-wide, from 402 studies with a total of 1625 population projection matrices. COMADRE also contains ancillary information (e.g. ecoregion, taxonomy, biogeography, etc.) that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs. We provide R code to some of these examples.<br><br>SYNTHESIS: We introduce the COMADRE Animal Matrix Database, a resource for animal demography. Its open-data nature, together with its ancillary information, will facilitate comparative analysis, as will the growing availability of databases focusing on other aspects of the rich animal diversity, and tools to query and combine them. Through future frequent updates of COMADRE, and its integration with other online resources, we encourage animal ecologists to tackle global ecological and evolutionary questions with unprecedented sample size.}, }
@article {pmid26805925, year = {2017}, author = {Xu, XH and Lv, ZQ and Zhou, XY and Jiang, N}, title = {Drought prediction and sustainable development of the ecological environment.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {35}, pages = {26974-26982}, doi = {10.1007/s11356-015-6011-4}, pmid = {26805925}, issn = {1614-7499}, mesh = {China ; Conservation of Natural Resources/*methods ; *Droughts ; Geographic Information Systems ; *Models, Theoretical ; Prognosis ; *Rain ; Seasons ; }, abstract = {In the 1990s ecological early warning research began with the aim of elucidating the effect of drought in dry regions of the world. Drought has been a prevalent natural disaster, ravaging the Yun'nan province of China for over 5 years since 2009. Due to the extensive range, depth and devastating losses, the drought has reached a once-in-a-century severity. Yun'nan province suffered particularly badly from the drought, which took its toll on both the ecological environment and the sustainable economic development of the province. We chose to study Pu'er city in Yun'nun province for this research, and analysed the drought traits of Pu'er city utilizing geographic information technology. We applied the Mann-Kendall test for trend, linear tendency estimation and percentage of precipitation anomalies, as well as using combinations of monthly data searches of meteorological reports from 1980-2010. The results showed that except for a small rise in spring precipitation, the overall rainfall of Pu'er city showed a decreasing trend. The results of this study can provide an adequate and reliable theoretical basis and technological methods for use in government decision making, and promote research into early warning ecology.}, }
@article {pmid26803258, year = {2016}, author = {D'Antonio, A and Monz, C}, title = {The influence of visitor use levels on visitor spatial behavior in off-trail areas of dispersed recreation use.}, journal = {Journal of environmental management}, volume = {170}, number = {}, pages = {79-87}, doi = {10.1016/j.jenvman.2016.01.011}, pmid = {26803258}, issn = {1095-8630}, mesh = {California ; Conservation of Natural Resources/*methods ; *Geographic Information Systems ; Humans ; *Recreation ; *Spatial Behavior ; Wyoming ; }, abstract = {A variety of social and ecological factors influence the level and extent of ecological change that occurs in a park or protected area. Understanding these factors and how they are interrelated can help managers prevent undesirable ecological impacts, especially in areas without formal trails and visitor sites. This study examines the relationship between levels of visitor use and spatial patterns of visitor behavior at a variety of backcountry recreation destinations. Current assumptions in both the literature and simulation modeling efforts assume that visitor behavior either does not change with use level or that visitors are more likely to disperse at high levels of visitor use. Using visitor counts and GPS tracks of visitor behavior in locations where visitors could disperse off-trail, we found that visitors' spatial behavior does vary with visitor use level in some recreation settings, however the patterns of visitor behavior observed in this study are sometimes contrary to current generalizations. When visitor behavior does vary with use level, visitors are dispersing more at low levels of visitor use not when use level is high. Overall, these findings suggest that in certain situations the amount of visitor use at a recreation destination may be a less important driver of ecological change than visitor behavior.}, }
@article {pmid26704455, year = {2016}, author = {Mislan, KAS and Heer, JM and White, EP}, title = {Elevating The Status of Code in Ecology.}, journal = {Trends in ecology &amp; evolution}, volume = {31}, number = {1}, pages = {4-7}, doi = {10.1016/j.tree.2015.11.006}, pmid = {26704455}, issn = {1872-8383}, mesh = {*Access to Information ; *Ecology ; *Periodicals as Topic ; Programming Languages ; Research Report ; *Software ; }, abstract = {Code is increasingly central to ecological research but often remains unpublished and insufficiently recognized. Making code available allows analyses to be more easily reproduced and can facilitate research by other scientists. We evaluate journal handling of code, discuss barriers to its publication, and suggest approaches for promoting and archiving code.}, }
@article {pmid26700811, year = {2016}, author = {Díaz, S and Kattge, J and Cornelissen, JH and Wright, IJ and Lavorel, S and Dray, S and Reu, B and Kleyer, M and Wirth, C and Prentice, IC and Garnier, E and Bönisch, G and Westoby, M and Poorter, H and Reich, PB and Moles, AT and Dickie, J and Gillison, AN and Zanne, AE and Chave, J and Wright, SJ and Sheremet'ev, SN and Jactel, H and Baraloto, C and Cerabolini, B and Pierce, S and Shipley, B and Kirkup, D and Casanoves, F and Joswig, JS and Günther, A and Falczuk, V and Rüger, N and Mahecha, MD and Gorné, LD}, title = {The global spectrum of plant form and function.}, journal = {Nature}, volume = {529}, number = {7585}, pages = {167-171}, pmid = {26700811}, issn = {1476-4687}, mesh = {Biodiversity ; Databases, Factual ; Genetic Variation ; Internationality ; Models, Biological ; Nitrogen/analysis ; Organ Size ; *Phenotype ; Plant Development ; Plant Leaves/anatomy &amp; histology ; *Plant Physiological Phenomena ; Plant Stems/anatomy &amp; histology ; Plants/*anatomy &amp; histology/classification ; Reproduction ; Seeds/anatomy &amp; histology ; Selection, Genetic ; Species Specificity ; }, abstract = {Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today's terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Three-quarters of trait variation is captured in a two-dimensional global spectrum of plant form and function. One major dimension within this plane reflects the size of whole plants and their parts; the other represents the leaf economics spectrum, which balances leaf construction costs against growth potential. The global plant trait spectrum provides a backdrop for elucidating constraints on evolution, for functionally qualifying species and ecosystems, and for improving models that predict future vegetation based on continuous variation in plant form and function.}, }
@article {pmid26675011, year = {2016}, author = {Romero-Ramirez, A and Bonifácio, P and Labrune, C and Sardá, R and Amouroux, JM and Bellan, G and Duchêne, JC and Hermand, R and Karakassis, I and Dounas, C and Grémare, A}, title = {Long-term (1998-2010) large-scale comparison of the ecological quality status of gulf of lions (NW Mediterranean) benthic habitats.}, journal = {Marine pollution bulletin}, volume = {102}, number = {1}, pages = {102-113}, doi = {10.1016/j.marpolbul.2015.11.052}, pmid = {26675011}, issn = {1879-3363}, mesh = {Animals ; Aquatic Organisms/*physiology ; *Biodiversity ; Databases, Factual ; Ecology ; *Ecosystem ; Environmental Monitoring/methods ; Geologic Sediments/chemistry ; Mediterranean Sea ; *Water Quality ; }, abstract = {A comprehensive Mediterranean data set has been used to address 3 questions associated with the use of sensitivity/tolerance based biotic indices to infer the Ecological Quality status (EcoQs) of benthic habitats. Our results showed: (1) a significant effect of the reference database on derived sensitivity/tolerance measure (ES500.05) as well as associated Benthic Quality Index values and derived EcoQs; (2) a lack of correlation neither between BQI and AZTI Marine Biotic Index values nor between BQI and Multivariate-AZTI Marine Biotic Index values; (3) a lack of correlation between the values of the Benthic Habitat Quality Index (index derived from Sediment Profile Imagery) and those of either of the 3 tested biotic indices; and (4) a general agreement between the 3 tested biotic indices in describing the lack of global trend for the EcoQs of the Gulf of Lions despite the occurrence of significant changes in benthic macrofauna composition between 1998 and 2010.}, }
@article {pmid26645667, year = {2015}, author = {Pauli, M and Chakarov, N and Rupp, O and Kalinowski, J and Goesmann, A and Sorenson, MD and Krüger, O and Hoffman, JI}, title = {De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1038}, pmid = {26645667}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Animals ; *Computational Biology/methods ; Gene Expression Regulation ; Genetic Markers ; *Genomics/methods ; Haemosporida/*genetics ; High-Throughput Nucleotide Sequencing ; Melanins/metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Polymorphism, Genetic ; Raptors/*genetics/metabolism/*parasitology ; Reproducibility of Results ; Sequence Alignment ; *Transcriptome ; }, abstract = {BACKGROUND: Studies of non-model species are important for understanding the molecular processes underpinning phenotypic variation under natural ecological conditions. The common buzzard (Buteo buteo; Aves: Accipitriformes) is a widespread and common Eurasian raptor with three distinct plumage morphs that differ in several fitness-related traits, including parasite infestation. To provide a genomic resource for plumage polymorphic birds in general and to search for candidate genes relating to fitness, we generated a transcriptome from a single dead buzzard specimen plus easily accessible, minimally invasive samples from live chicks.<br><br>RESULTS: We not only de novo assembled a near-complete buzzard transcriptome, but also obtained a significant fraction of the transcriptome of its malaria-like parasite, Leucocytozoon buteonis. By identifying melanogenesis-related transcripts that are differentially expressed in light ventral and dark dorsal feathers, but which are also expressed in other regions of the body, we also identified a suite of candidate genes that could be associated with fitness differences among the morphs. These include several immune-related genes, providing a plausible link between melanisation and parasite load. qPCR analysis of a subset of these genes revealed significant differences between ventral and dorsal feathers and an additional effect of morph.<br><br>CONCLUSION: This new resource provides preliminary insights into genes that could be involved in fitness differences between the buzzard colour morphs, and should facilitate future studies of raptors and their malaria-like parasites.}, }
@article {pmid26644569, year = {2015}, author = {Ibsen-Jensen, R and Chatterjee, K and Nowak, MA}, title = {Computational complexity of ecological and evolutionary spatial dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {51}, pages = {15636-15641}, pmid = {26644569}, issn = {1091-6490}, mesh = {Algorithms ; *Biological Evolution ; Computational Biology ; *Ecology ; Ecosystem ; Probability ; }, abstract = {There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).}, }
@article {pmid26643685, year = {2015}, author = {Power, DA and Watson, RA and Szathmáry, E and Mills, R and Powers, ST and Doncaster, CP and Czapp, B}, title = {What can ecosystems learn? Expanding evolutionary ecology with learning theory.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {69}, pmid = {26643685}, issn = {1745-6150}, mesh = {*Biological Evolution ; Ecology ; *Ecosystem ; *Models, Biological ; }, abstract = {BACKGROUND: The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole?<br><br>RESULTS: Here we answer this question by incorporating principles from connectionist learning, a previously unrelated discipline already using well-developed theories on how emergent behaviours arise in simple networks. Specifically, we show conditions where natural selection on ecological interactions is functionally equivalent to a simple type of connectionist learning, 'unsupervised learning', well-known in neural-network models of cognitive systems to produce many non-trivial collective behaviours. Accordingly, we find that a community can self-organise in a well-defined and non-trivial sense without selection at the community level; its organisation can be conditioned by past experience in the same sense as connectionist learning models habituate to stimuli. This conditioning drives the community to form a distributed ecological memory of multiple past states, causing the community to: a) converge to these states from any random initial composition; b) accurately restore historical compositions from small fragments; c) recover a state composition following disturbance; and d) to correctly classify ambiguous initial compositions according to their similarity to learned compositions. We examine how the formation of alternative stable states alters the community's response to changing environmental forcing, and we identify conditions under which the ecosystem exhibits hysteresis with potential for catastrophic regime shifts.<br><br>CONCLUSIONS: This work highlights the potential of connectionist theory to expand our understanding of evo-eco dynamics and collective ecological behaviours. Within this framework we find that, despite not being a Darwinian unit, ecological communities can behave like connectionist learning systems, creating internal conditions that habituate to past environmental conditions and actively recalling those conditions.}, }
@article {pmid26641818, year = {2015}, author = {Theobald, DM and Harrison-Atlas, D and Monahan, WB and Albano, CM}, title = {Ecologically-Relevant Maps of Landforms and Physiographic Diversity for Climate Adaptation Planning.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0143619}, pmid = {26641818}, issn = {1932-6203}, mesh = {Adaptation, Biological ; Animals ; *Biodiversity ; *Climate Change ; Ecology/methods ; Environment ; Environmental Monitoring/*methods ; Environmental Policy ; Geographic Information Systems ; Maps as Topic ; *Models, Theoretical ; }, abstract = {Key to understanding the implications of climate and land use change on biodiversity and natural resources is to incorporate the physiographic platform on which changes in ecological systems unfold. Here, we advance a detailed classification and high-resolution map of physiography, built by combining landforms and lithology (soil parent material) at multiple spatial scales. We used only relatively static abiotic variables (i.e., excluded climatic and biotic factors) to prevent confounding current ecological patterns and processes with enduring landscape features, and to make the physiographic classification more interpretable for climate adaptation planning. We generated novel spatial databases for 15 landform and 269 physiographic types across the conterminous United States of America. We examined their potential use by natural resource managers by placing them within a contemporary climate change adaptation framework, and found our physiographic databases could play key roles in four of seven general adaptation strategies. We also calculated correlations with common empirical measures of biodiversity to examine the degree to which the physiographic setting explains various aspects of current biodiversity patterns. Additionally, we evaluated the relationship between landform diversity and measures of climate change to explore how changes may unfold across a geophysical template. We found landform types are particularly sensitive to spatial scale, and so we recommend using high-resolution datasets when possible, as well as generating metrics using multiple neighborhood sizes to both minimize and characterize potential unknown biases. We illustrate how our work can inform current strategies for climate change adaptation. The analytical framework and classification of landforms and parent material are easily extendable to other geographies and may be used to promote climate change adaptation in other settings.}, }
@article {pmid26625892, year = {2016}, author = {Pelikan, C and Herbold, CW and Hausmann, B and Müller, AL and Pester, M and Loy, A}, title = {Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics.}, journal = {Environmental microbiology}, volume = {18}, number = {9}, pages = {2994-3009}, doi = {10.1111/1462-2920.13139}, pmid = {26625892}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; Computational Biology ; DNA Primers/*genetics ; DNA, Bacterial/genetics ; Hydrogensulfite Reductase/genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Sulfates/*metabolism ; Sulfites/*metabolism ; }, abstract = {Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB polymerase chain reaction (PCR) products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. Although tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.}, }
@article {pmid26611970, year = {2015}, author = {Kahime, K and Boussaa, S and El Mzabi, A and Boumezzough, A}, title = {Spatial relations among environmental factors and phlebotomine sand fly populations (Diptera: Psychodidae) in central and southern Morocco.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {40}, number = {2}, pages = {342-354}, doi = {10.1111/jvec.12173}, pmid = {26611970}, issn = {1948-7134}, mesh = {Altitude ; Animals ; Climate ; Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Insect Vectors ; Leishmaniasis, Cutaneous/transmission ; Leishmaniasis, Visceral/transmission ; Male ; Morocco ; Phlebotomus/physiology ; Principal Component Analysis ; Psychodidae/*physiology ; Soil ; }, abstract = {Phlebotomine sand flies (Diptera: Psychodidae, Phlebotominae) are of considerable public health importance because of their ability to transmit several human parasites, mainly as vectors of Leishmania spp. Over the past decade, the epidemiological situation of cutaneous leishmaniasis (CL) has significantly increased with its geographic expansion to previously free areas and the emergence of overlapping foci of cutaneous leishmaniasis and visceral leishmaniasis (VL) in several provinces of Morocco. A total of 15,313 specimens was collected during this entomological survey. The genera Phlebotomus (57.38%) and Sergentomyia (42.62%) were identified. Sergentomyia minuta (22.01%) was the most prevalent species, followed by S. fallax (18.21%), Phlebotomus perniciosus (14.35%), P. papatasi (14.06%), P. sergenti (12.85%), P. longicuspis (10.74%), P. ariasi (2.68%), S. dreyfussi (1.53%), P. alexandri (1.31%), P. bergeroti (1.14%), S. christophersi (0.62%), S. africana (0.25%), P. chabaudi (0.14%), P. chadlii (0.05%), and P. kazeruni (0.04%). We aimed to determine current distribution of leishmaniases vectors, their ecological characteristics, and the significance of the predominant species at any bioclimate stage, altitude range, and soil texture in terms of the risk of leishmaniasis transmission.}, }
@article {pmid26609082, year = {2015}, author = {Spiegel, O and Leu, ST and Sih, A and Godfrey, SS and Bull, CM}, title = {When the going gets tough: behavioural type-dependent space use in the sleepy lizard changes as the season dries.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1819}, pages = {}, pmid = {26609082}, issn = {1471-2954}, mesh = {Animals ; Bayes Theorem ; *Ecosystem ; Geographic Information Systems ; *Homing Behavior ; Lizards/*physiology ; Models, Biological ; *Seasons ; South Australia ; Spatial Analysis ; }, abstract = {Understanding space use remains a major challenge for animal ecology, with implications for species interactions, disease spread, and conservation. Behavioural type (BT) may shape the space use of individuals within animal populations. Bolder or more aggressive individuals tend to be more exploratory and disperse further. Yet, to date we have limited knowledge on how space use other than dispersal depends on BT. To address this question we studied BT-dependent space-use patterns of sleepy lizards (Tiliqua rugosa) in southern Australia. We combined high-resolution global positioning system (GPS) tracking of 72 free-ranging lizards with repeated behavioural assays, and with a survey of the spatial distributions of their food and refuge resources. Bayesian generalized linear mixed models (GLMM) showed that lizards responded to the spatial distribution of resources at the neighbourhood scale and to the intensity of space use by other conspecifics (showing apparent conspecific avoidance). BT (especially aggressiveness) affected space use by lizards and their response to ecological and social factors, in a seasonally dependent manner. Many of these effects and interactions were stronger later in the season when food became scarce and environmental conditions got tougher. For example, refuge and food availability became more important later in the season and unaggressive lizards were more responsive to these predictors. These findings highlight a commonly overlooked source of heterogeneity in animal space use and improve our mechanistic understanding of processes leading to behaviourally driven disease dynamics and social structure.}, }
@article {pmid26592351, year = {2016}, author = {Nawaz, S and Yuan, Y}, title = {Computational pathology: Exploring the spatial dimension of tumor ecology.}, journal = {Cancer letters}, volume = {380}, number = {1}, pages = {296-303}, doi = {10.1016/j.canlet.2015.11.018}, pmid = {26592351}, issn = {1872-7980}, support = {105104//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biopsy ; Breast Neoplasms/mortality/*pathology/therapy ; Female ; *High-Throughput Screening Assays/statistics &amp; numerical data ; Humans ; *Image Interpretation, Computer-Assisted ; Models, Statistical ; Pathology/*methods/statistics &amp; numerical data ; Pattern Recognition, Automated ; Phenotype ; Predictive Value of Tests ; Prognosis ; Time Factors ; *Tumor Microenvironment ; }, abstract = {Tumors are evolving ecosystems where cancer subclones and the microenvironment interact. This is analogous to interaction dynamics between species in their natural habitats, which is a prime area of study in ecology. Spatial statistics are frequently used in ecological studies to infer complex relations including predator-prey, resource dependency and co-evolution. Recently, the emerging field of computational pathology has enabled high-throughput spatial analysis by using image processing to identify different cell types and their locations within histological tumor samples. We discuss how these data may be analyzed with spatial statistics used in ecology to reveal patterns and advance our understanding of ecological interactions occurring among cancer cells and their microenvironment.}, }
@article {pmid26590126, year = {2016}, author = {Kim, J and Fabris, M and Baart, G and Kim, MK and Goossens, A and Vyverman, W and Falkowski, PG and Lun, DS}, title = {Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum.}, journal = {The Plant journal : for cell and molecular biology}, volume = {85}, number = {1}, pages = {161-176}, doi = {10.1111/tpj.13081}, pmid = {26590126}, issn = {1365-313X}, mesh = {Biofuels ; *Computational Biology ; Computer Simulation ; Databases, Factual ; Diatoms/growth &amp; development/*metabolism ; Genome/*genetics ; *Glycolysis ; *Metabolic Networks and Pathways ; Microalgae ; Mitochondria/metabolism ; *Models, Biological ; Photosynthesis ; Species Specificity ; }, abstract = {Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome-scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock-in transformants. Here we present a genome-scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms.}, }
@article {pmid26569270, year = {2015}, author = {Gong, J and Yang, J and Tang, W}, title = {Spatially Explicit Landscape-Level Ecological Risks Induced by Land Use and Land Cover Change in a National Ecologically Representative Region in China.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {11}, pages = {14192-14215}, pmid = {26569270}, issn = {1660-4601}, mesh = {Biodiversity ; China ; Cities ; Computer Simulation ; Conservation of Natural Resources ; Ecology/*methods ; Ecosystem ; *Environment ; Geographic Information Systems ; Humans ; *Models, Theoretical ; Risk ; Risk Assessment/methods ; }, abstract = {Land use and land cover change is driven by multiple influential factors from environmental and social dimensions in a land system. Land use practices of human decision-makers modify the landscape of the land system, possibly leading to landscape fragmentation, biodiversity loss, or environmental pollution-severe environmental or ecological impacts. While landscape-level ecological risk assessment supports the evaluation of these impacts, investigations on how these ecological risks induced by land use practices change over space and time in response to alternative policy intervention remain inadequate. In this article, we conducted spatially explicit landscape ecological risk analysis in Ezhou City, China. Our study area is a national ecologically representative region experiencing drastic land use and land cover change, and is regulated by multiple policies represented by farmland protection, ecological conservation, and urban development. We employed landscape metrics to consider the influence of potential landscape-level disturbance for the evaluation of landscape ecological risks. Using spatiotemporal simulation, we designed scenarios to examine spatiotemporal patterns in landscape ecological risks in response to policy intervention. Our study demonstrated that spatially explicit landscape ecological risk analysis combined with simulation-driven scenario analysis is of particular importance for guiding the sustainable development of ecologically vulnerable land systems.}, }
@article {pmid26556502, year = {2015}, author = {Roche, DG and Kruuk, LE and Lanfear, R and Binning, SA}, title = {Public Data Archiving in Ecology and Evolution: How Well Are We Doing?.}, journal = {PLoS biology}, volume = {13}, number = {11}, pages = {e1002295}, pmid = {26556502}, issn = {1545-7885}, mesh = {*Access to Information ; Animals ; *Biological Evolution ; Biology/*methods ; Data Accuracy ; Data Curation ; *Datasets as Topic/standards ; Ecology/*methods ; Guidelines as Topic ; Humans ; Internet ; *Periodicals as Topic ; Workforce ; }, abstract = {Policies that mandate public data archiving (PDA) successfully increase accessibility to data underlying scientific publications. However, is the data quality sufficient to allow reuse and reanalysis? We surveyed 100 datasets associated with nonmolecular studies in journals that commonly publish ecological and evolutionary research and have a strong PDA policy. Out of these datasets, 56% were incomplete, and 64% were archived in a way that partially or entirely prevented reuse. We suggest that cultural shifts facilitating clearer benefits to authors are necessary to achieve high-quality PDA and highlight key guidelines to help authors increase their data's reuse potential and compliance with journal data policies.}, }
@article {pmid26553774, year = {2016}, author = {Deshpande, V and Wang, Q and Greenfield, P and Charleston, M and Porras-Alfaro, A and Kuske, CR and Cole, JR and Midgley, DJ and Tran-Dinh, N}, title = {Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences.}, journal = {Mycologia}, volume = {108}, number = {1}, pages = {1-5}, doi = {10.3852/14-293}, pmid = {26553774}, issn = {0027-5514}, mesh = {Bayes Theorem ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Datasets as Topic ; Fungi/*classification/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Fungi are key organisms in many ecological processes and communities. Rapid and low cost surveys of the fungal members of a community can be undertaken by isolating and sequencing a taxonomically informative genomic region, such as the ITS (internal transcribed spacer), from DNA extracted from a metagenomic sample, and then classifying these sequences to determine which organisms are present. This paper announces the availability of the Warcup ITS training set and shows how it can be used with the Ribosomal Database Project (RDP) Bayesian Classifier to rapidly and accurately identify fungi using ITS sequences. The classifications can be down to species level and use conventional literature-based mycological nomenclature and taxonomic assignments.}, }
@article {pmid26544687, year = {2015}, author = {Abe, MS and Shimada, M}, title = {Lévy Walks Suboptimal under Predation Risk.}, journal = {PLoS computational biology}, volume = {11}, number = {11}, pages = {e1004601}, pmid = {26544687}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Computational Biology ; Computer Simulation ; *Models, Biological ; Movement ; Predatory Behavior/*physiology ; Risk ; }, abstract = {A key challenge in movement ecology is to understand how animals move in nature. Previous studies have predicted that animals should perform a special class of random walks, called Lévy walk, to obtain more targets. However, some empirical studies did not support this hypothesis, and the relationship between search strategy and ecological factors is still unclear. We focused on ecological factors, such as predation risk, and analyzed whether Lévy walk may not be favored. It was remarkable that the ecological factors often altered an optimal search strategy from Lévy walk to Brownian walk, depending on the speed of the predator's movement, density of predators, etc. This occurred because higher target encounter rates simultaneously led searchers to higher predation risks. Our findings indicate that animals may not perform Lévy walks often, and we suggest that it is crucial to consider the ecological context for evaluating the search strategy performed by animals in the field.}, }
@article {pmid26530215, year = {2016}, author = {Enrico, L and Díaz, S and Westoby, M and Rice, BL}, title = {Leaf mechanical resistance in plant trait databases: comparing the results of two common measurement methods.}, journal = {Annals of botany}, volume = {117}, number = {1}, pages = {209-214}, pmid = {26530215}, issn = {1095-8290}, mesh = {Biomechanical Phenomena ; *Databases as Topic ; Linear Models ; Plant Leaves/*physiology ; *Quantitative Trait, Heritable ; Statistics, Nonparametric ; }, abstract = {BACKGROUND AND AIMS: The influence of leaf mechanical properties on local ecosystem processes, such as trophic transfer, decomposition and nutrient cycling, has resulted in a growing interest in including leaf mechanical resistance in large-scale databases of plant functional traits. 'Specific work to shear' and 'force to tear' are two properties commonly used to describe mechanical resistance (toughness or strength) of leaves. Two methodologies have been widely used to measure them across large datasets. This study aimed to assess correlations and standardization between the two methods, as measured by two widely used apparatuses, in order to inter-convert existing data in those global datasets.<br><br>METHODS: Specific work to shear (W(SS)) and force to tear (FT) were measured in leaves of 72 species from south-eastern Australia. The measurements were made including and excluding midribs. Relationships between the variables were tested by Spearman correlations and ordinary least square regressions.<br><br>KEY RESULTS: A positive and significant correlation was found between the methods, but coefficients varied according to the inclusion or exclusion of the midrib in the measurements. Equations for prediction varied according to leaf venation pattern. A positive and significant (r = 0·90, P < 0·0001) correlation was also found between W(SS) values for fresh and rehydrated leaves, which is considered to be of practical relevance.<br><br>CONCLUSIONS: In the context of broad-scale ecological hypotheses and used within the constraints recommended here, leaf mechanical resistance data obtained with both methodologies could be pooled together into a single coarser variable, using the equations provided in this paper. However, more detailed datasets of FT cannot be safely filled in with estimations based on W(SS), or vice versa. In addition, W(SS) values of green leaves can be predicted with good accuracy from W(SS) of rehydrated leaves of the same species.}, }
@article {pmid26528407, year = {2015}, author = {Case, BS and Buckley, HL}, title = {Local-scale topoclimate effects on treeline elevations: a country-wide investigation of New Zealand's southern beech treelines.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1334}, pmid = {26528407}, issn = {2167-8359}, abstract = {Although treeline elevations are limited globally by growing season temperature, at regional scales treelines frequently deviate below their climatic limit. The cause of these deviations relate to a host of climatic, disturbance, and geomorphic factors that operate at multiple scales. The ability to disentangle the relative effects of these factors is currently hampered by the lack of reliable topoclimatic data, which describe how regional climatic characteristics are modified by topographic effects in mountain areas. In this study we present an analysis of the combined effects of local- and regional-scale factors on southern beech treeline elevation variability at 28 study areas across New Zealand. We apply a mesoscale atmospheric model to generate local-scale (200 m) meteorological data at these treelines and, from these data, we derive a set of topoclimatic indices that reflect possible detrimental and ameliorative influences on tree physiological functioning. Principal components analysis of meteorological data revealed geographic structure in how study areas were situated in multivariate space along gradients of topoclimate. Random forest and conditional inference tree modelling enabled us to tease apart the relative effects of 17 explanatory factors on local-scale treeline elevation variability. Overall, modelling explained about 50% of the variation in treeline elevation variability across the 28 study areas, with local landform and topoclimatic effects generally outweighing those from regional-scale factors across the 28 study areas. Further, the nature of the relationships between treeline elevation variability and the explanatory variables were complex, frequently non-linear, and consistent with the treeline literature. To our knowledge, this is the first study where model-generated meteorological data, and derived topoclimatic indices, have been developed and applied to explain treeline variation. Our results demonstrate the potential of such an approach for ecological research in mountainous environments.}, }
@article {pmid26519912, year = {2016}, author = {Santos, J and Al-Azzawi, M and Aronson, J and Flowers, TJ}, title = {eHALOPH a Database of Salt-Tolerant Plants: Helping put Halophytes to Work.}, journal = {Plant &amp; cell physiology}, volume = {57}, number = {1}, pages = {e10}, doi = {10.1093/pcp/pcv155}, pmid = {26519912}, issn = {1471-9053}, mesh = {Antioxidants/metabolism ; *Databases, Genetic ; Salinity ; Salt Tolerance ; Salt-Tolerant Plants/*genetics/physiology ; Sodium Chloride/metabolism ; }, abstract = {eHALOPH (http://www.sussex.ac.uk/affiliates/halophytes/) is a database of salt-tolerant plants-halophytes. Records of plant species tolerant of salt concentrations of around 80 mM sodium chloride or more have been collected, along with data on plant type, life form, ecotypes, maximum salinity tolerated, the presence or absence of salt glands, photosynthetic pathway, antioxidants, secondary metabolites, compatible solutes, habitat, economic use and whether there are publications on germination, microbial interactions and mycorrhizal status, bioremediation and of molecular data. The database eHALOPH can be used in the analysis of traits associated with tolerance and for informing choice of species that might be used for saline agriculture, bioremediation or ecological restoration and rehabilitation of degraded wetlands or other areas.}, }
@article {pmid26511852, year = {2015}, author = {Zhu, H and Ren, X and Jin, Y and Yang, K and Che, Y}, title = {Multilevel analysis of a riverscape under rapid urbanization in the Yangtze delta plain, China: 1965-2006.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {11}, pages = {711}, pmid = {26511852}, issn = {1573-2959}, mesh = {China ; Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; Models, Theoretical ; Multilevel Analysis ; Rivers/*chemistry ; *Urbanization ; }, abstract = {River networks are the typical hydrological characteristic of the Yangtze delta plain. They have important ecological service functions and a unique landscape, which has been significantly degraded during the past 50 years. Qingpu District in Shanghai has been used as study area to develop an integrated method for riverscape assessment in floodplain areas with a dense river network. This integrated method bridges geomorgraphy, landscape, and regional planning. Indicators of sinuosity, connectivity, and circuitry have been integrated into a three-level framework, including river, intersection, and river network level. Furthermore, this method was integrated by the geographic information system method and stepwise regression to identify the riverscape response to the changes in the use of the land. The spatial and temporal changes of the riverscape and land use were calculated for each grid (3000 m×3000 m) from 1965 to 2006. The results indicated that the riverscape had been significantly degraded during the study period in terms of sinuosity, connectivity, and circuitry reducing. The land use changed significantly with more building areas and less water regions and agricultural land. Additionally, the regression results indicated that several specific land use conversion types had had strong effects on the change in the riverscape structure. Finally, according to the assessing method, we have proposed specific planning and management recommendations based on the pressure-state-response model to protect the riverscape from the impact of rapid urbanization.}, }
@article {pmid26508349, year = {2015}, author = {Newey, S and Davidson, P and Nazir, S and Fairhurst, G and Verdicchio, F and Irvine, RJ and van der Wal, R}, title = {Limitations of recreational camera traps for wildlife management and conservation research: a practitioner's perspective.}, journal = {Ambio}, volume = {44 Suppl 4}, number = {}, pages = {624-635}, pmid = {26508349}, issn = {1654-7209}, mesh = {Animals ; *Animals, Wild ; Conservation of Natural Resources/*methods ; Data Collection/*methods ; Inventions ; Photography/*methods ; Recreation ; }, abstract = {The availability of affordable 'recreational' camera traps has dramatically increased over the last decade. We present survey results which show that many conservation practitioners use cheaper 'recreational' units for research rather than more expensive 'professional' equipment. We present our perspective of using two popular models of 'recreational' camera trap for ecological field-based studies. The models used (for >2 years) presented us with a range of practical problems at all stages of their use including deployment, operation, and data management, which collectively crippled data collection and limited opportunities for quantification of key issues arising. Our experiences demonstrate that prospective users need to have a sufficient understanding of the limitations camera trap technology poses, dimensions we communicate here. While the merits of different camera traps will be study specific, the performance of more expensive 'professional' models may prove more cost-effective in the long-term when using camera traps for research.}, }
@article {pmid26491393, year = {2015}, author = {de Jong, Y and Kouwenberg, J and Boumans, L and Hussey, C and Hyam, R and Nicolson, N and Kirk, P and Paton, A and Michel, E and Guiry, MD and Boegh, PS and Pedersen, HÆ and Enghoff, H and von Raab-Straube, E and Güntsch, A and Geoffroy, M and Müller, A and Kohlbecker, A and Berendsohn, W and Appeltans, W and Arvanitidis, C and Vanhoorne, B and Declerck, J and Vandepitte, L and Hernandez, F and Nash, R and Costello, MJ and Ouvrard, D and Bezard-Falgas, P and Bourgoin, T and Wetzel, FT and Glöckler, F and Korb, G and Ring, C and Hagedorn, G and Häuser, C and Aktaç, N and Asan, A and Ardelean, A and Borges, PA and Dhora, D and Khachatryan, H and Malicky, M and Ibrahimov, S and Tuzikov, A and De Wever, A and Moncheva, S and Spassov, N and Chobot, K and Popov, A and Boršić, I and Sfenthourakis, S and Kõljalg, U and Uotila, P and Olivier, G and Dauvin, JC and Tarkhnishvili, D and Chaladze, G and Tuerkay, M and Legakis, A and Peregovits, L and Gudmundsson, G and Ólafsson, E and Lysaght, L and Galil, BS and Raimondo, FM and Domina, G and Stoch, F and Minelli, A and Spungis, V and Budrys, E and Olenin, S and Turpel, A and Walisch, T and Krpach, V and Gambin, MT and Ungureanu, L and Karaman, G and Kleukers, RM and Stur, E and Aagaard, K and Valland, N and Moen, TL and Bogdanowicz, W and Tykarski, P and Węsławski, JM and Kędra, M and M de Frias Martins, A and Abreu, AD and Silva, R and Medvedev, S and Ryss, A and Šimić, S and Marhold, K and Stloukal, E and Tome, D and Ramos, MA and Valdés, B and Pina, F and Kullander, S and Telenius, A and Gonseth, Y and Tschudin, P and Sergeyeva, O and Vladymyrov, V and Rizun, VB and Raper, C and Lear, D and Stoev, P and Penev, L and Rubio, AC and Backeljau, T and Saarenmaa, H and Ulenberg, S}, title = {PESI - a taxonomic backbone for Europe.}, journal = {Biodiversity data journal}, volume = {}, number = {3}, pages = {e5848}, pmid = {26491393}, issn = {1314-2828}, abstract = {BACKGROUND: Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.<br><br>NEW INFORMATION: This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.}, }
@article {pmid26467174, year = {2016}, author = {Sabath, N and Goldberg, EE and Glick, L and Einhorn, M and Ashman, TL and Ming, R and Otto, SP and Vamosi, JC and Mayrose, I}, title = {Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms.}, journal = {The New phytologist}, volume = {209}, number = {3}, pages = {1290-1300}, doi = {10.1111/nph.13696}, pmid = {26467174}, issn = {1469-8137}, mesh = {*Biodiversity ; Computer Simulation ; Databases as Topic ; Magnoliopsida/*physiology ; *Phylogeny ; Probability ; Quantitative Trait, Heritable ; Reproduction ; }, abstract = {Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver.}, }
@article {pmid26458227, year = {2016}, author = {Jousselin, E and Clamens, AL and Galan, M and Bernard, M and Maman, S and Gschloessl, B and Duport, G and Meseguer, AS and Calevro, F and Coeur d'acier, A}, title = {Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {628-640}, doi = {10.1111/1755-0998.12478}, pmid = {26458227}, issn = {1755-0998}, mesh = {Animals ; Aphids/*microbiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; Symbiosis ; }, abstract = {The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiome studies. We aimed here to validate an Illumina 16S rRNA gene sequencing protocol and analytical pipeline for investigating endosymbiotic bacteria associated with aphids. Using replicate DNA samples from 12 species (Aphididae: Lachninae, Cinara) and several controls, we removed individual sequences not meeting a minimum threshold number of reads in each sample and carried out taxonomic assignment for the remaining sequences. With this approach, we show that (i) contaminants accounted for a negligible proportion of the bacteria identified in our samples; (ii) the taxonomic composition of our samples and the relative abundance of reads assigned to a taxon were very similar across PCR and DNA replicates for each aphid sample; in particular, bacterial DNA concentration had no impact on the results. Furthermore, by analysing the distribution of unique sequences across samples rather than aggregating them into operational taxonomic units (OTUs), we gained insight into the specificity of endosymbionts for their hosts. Our results confirm that Serratia symbiotica is often present in Cinara species, in addition to the primary symbiont, Buchnera aphidicola. Furthermore, our findings reveal new symbiotic associations with Erwinia- and Sodalis-related bacteria. We conclude with suggestions for generating and analysing 16S rRNA gene sequences for arthropod-endosymbiont studies.}, }
@article {pmid26415759, year = {2015}, author = {Accetto, T and Avguštin, G}, title = {Polysaccharide utilization locus and CAZYme genome repertoires reveal diverse ecological adaptation of Prevotella species.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {7}, pages = {453-461}, doi = {10.1016/j.syapm.2015.07.007}, pmid = {26415759}, issn = {1618-0984}, mesh = {*Computational Biology ; *Genetic Loci ; *Genetic Variation ; *Metabolic Networks and Pathways ; Polysaccharides/*metabolism ; Prevotella/*enzymology/*genetics/metabolism ; }, abstract = {The results of metagenomic studies have clearly established that bacteria of the genus Prevotella represent one of the important groups found in the oral cavity and large intestine of man, and they also dominate the rumen. They belong to the Bacteroidetes, a phylum well-known for its polysaccharide degrading potential that stems from the outer membrane-localized enzyme/binding protein complexes encoded in polysaccharide utilization loci (PULs). Dozens of Prevotella species have been described, primarily from the oral cavity, and many of them occur simultaneously at the same sites, but research on their ecological adaptation has been neglected. Therefore, in this study, the repertoires of PULs and carbohydrate acting enzymes (CAZYmes) found in Prevotella genomes were analyzed and it was concluded that the Prevotella species were widely heterogeneous in this respect and displayed several distinct adaptations with regard to the number, source and nature of the substrates apparently preferred for growth.}, }
@article {pmid26405731, year = {2015}, author = {Lajeunesse, MJ}, title = {Bias and correction for the log response ratio in ecological meta-analysis.}, journal = {Ecology}, volume = {96}, number = {8}, pages = {2056-2063}, pmid = {26405731}, issn = {0012-9658}, mesh = {Computer Simulation ; Data Interpretation, Statistical ; *Ecosystem ; Linear Models ; *Meta-Analysis as Topic ; *Models, Biological ; Monte Carlo Method ; Risk Assessment ; Sampling Studies ; }, abstract = {Ecologists widely use the log response ratio for summarizing the outcomes of studies for meta-analysis. However, little is known about the sampling distribution of this effect size estimator. Here I show with a Monte Carlo simulation that the log response ratio is biased when quantifying the outcome of studies with small sample sizes, and can yield erroneous variance estimates when the scale of study parameters are near zero. Given these challenges, I derive and compare two new estimators that help correct this small-sample bias, and update guidelines and diagnostics for assessing when the response ratio is appropriate for ecological meta-analysis. These new bias-corrected estimators retain much of the original utility of the response ratio and are aimed to improve the quality and reliability of inferences with effect sizes based on the log ratio of two means.}, }
@article {pmid26350795, year = {2015}, author = {Manaswini, G and Sudhakar Reddy, C}, title = {Geospatial monitoring and prioritization of forest fire incidences in Andhra Pradesh, India.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {10}, pages = {616}, pmid = {26350795}, issn = {1573-2959}, mesh = {Biodiversity ; Climate ; Conservation of Natural Resources/*methods ; Databases, Factual ; Ecology ; Environmental Monitoring/*methods ; *Fires/statistics &amp; numerical data ; *Forests ; Incidence ; India ; Spatio-Temporal Analysis ; Trees ; }, abstract = {Forest fire has been identified as one of the key environmental issue for long-term conservation of biodiversity and has impact on global climate. Spatially multiple observations are necessary for monitoring of forest fires in tropics for understanding conservation efficacy and sustaining biodiversity in protected areas. The present work was carried out to estimate the spatial extent of forest burnt areas and fire frequency using Resourcesat Advanced Wide Field Sensor (AWiFS) data (2009, 2010, 2012, 2013 and 2014) in Andhra Pradesh, India. The spatio-temporal analysis shows that an area of 7514.10 km(2) (29.22% of total forest cover) has been affected by forest fires. Six major forest types are distributed in Andhra Pradesh, i.e. semi-evergreen, moist deciduous, dry deciduous, dry evergreen, thorn and mangroves. Of the total forest burnt area, dry deciduous forests account for >75%. District-wise analysis shows that Kurnool, Prakasam and Cuddapah have shown >100 km(2) of burnt area every year. The total forest burnt area estimate covering protected areas ranges between 6.9 and 22.3% during the study period. Spatial burnt area analysis for protected areas in 2014 indicates 37.2% of fire incidences in the Nagarjunasagar Srisailam Tiger Reserve followed by 20.2 % in the Sri Lankamalleswara Wildlife Sanctuary, 20.1% in the Sri Venkateswara Wildlife Sanctuary and 17.4% in the Gundla Brahmeswaram Wildlife Sanctuary. The analysis of cumulative fire occurrences from 2009 to 2014 has helped in delineation of conservation priority hotspots using a spatial grid cell approach. Conservation priority hotspots I and II are distributed in major parts of study area including protected areas of the Nagarjunasagar Srisailam Tiger Reserve and Gundla Brahmeswaram Wildlife Sanctuary. The spatial database generated will be useful in studies related to influence of fires on species adaptability, ecological damage assessment and conservation planning.}, }
@article {pmid26348291, year = {2015}, author = {Meyer, C and Kreft, H and Guralnick, R and Jetz, W}, title = {Global priorities for an effective information basis of biodiversity distributions.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8221}, pmid = {26348291}, issn = {2041-1723}, mesh = {*Animal Distribution ; Animals ; *Biodiversity ; Conservation of Natural Resources/*methods ; Databases, Factual ; *Internationality ; Vertebrates/*classification/*physiology ; }, abstract = {Gaps in digital accessible information (DAI) on species distributions hamper prospects of safeguarding biodiversity and ecosystem services, and addressing central ecological and evolutionary questions. Achieving international targets on biodiversity knowledge requires that information gaps be identified and actions prioritized. Integrating 157 million point records and distribution maps for 21,170 terrestrial vertebrate species, we find that outside a few well-sampled regions, DAI on point occurrences provides very limited and spatially biased inventories of species. Surprisingly, many large, emerging economies are even more under-represented in global DAI than species-rich, developing countries in the tropics. Multi-model inference reveals that completeness is mainly limited by distance to researchers, locally available research funding and participation in data-sharing networks, rather than transportation infrastructure, or size and funding of Western data contributors as often assumed. Our results highlight the urgent need for integrating non-Western data sources and intensifying cooperation to more effectively address societal biodiversity information needs.}, }
@article {pmid26340990, year = {2015}, author = {Li, K and Hong, W and Jiao, H and Wang, GD and Rodriguez, KA and Buffenstein, R and Zhao, Y and Nevo, E and Zhao, H}, title = {Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {38}, pages = {11905-11910}, pmid = {26340990}, issn = {1091-6490}, support = {K99 AG049940/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Gene Ontology ; *Genetic Speciation ; *Genetic Variation ; *Genome ; Linkage Disequilibrium/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Population Dynamics ; Proteolysis ; Receptors, Odorant/genetics ; Sequence Analysis, DNA ; Spalax/*genetics ; Sympatry/*genetics ; }, abstract = {Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an important mode of speciation as first envisaged by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection].}, }
@article {pmid26339034, year = {2015}, author = {Hatton, IA and McCann, KS and Fryxell, JM and Davies, TJ and Smerlak, M and Sinclair, AR and Loreau, M}, title = {The predator-prey power law: Biomass scaling across terrestrial and aquatic biomes.}, journal = {Science (New York, N.Y.)}, volume = {349}, number = {6252}, pages = {aac6284}, doi = {10.1126/science.aac6284}, pmid = {26339034}, issn = {1095-9203}, mesh = {Animals ; *Biomass ; *Databases, Factual ; *Food Chain ; Invertebrates ; Mammals ; Plankton ; }, abstract = {Ecosystems exhibit surprising regularities in structure and function across terrestrial and aquatic biomes worldwide. We assembled a global data set for 2260 communities of large mammals, invertebrates, plants, and plankton. We find that predator and prey biomass follow a general scaling law with exponents consistently near ¾. This pervasive pattern implies that the structure of the biomass pyramid becomes increasingly bottom-heavy at higher biomass. Similar exponents are obtained for community production-biomass relations, suggesting conserved links between ecosystem structure and function. These exponents are similar to many body mass allometries, and yet ecosystem scaling emerges independently from individual-level scaling, which is not fully understood. These patterns suggest a greater degree of ecosystem-level organization than previously recognized and a more predictive approach to ecological theory.}, }
@article {pmid26338071, year = {2015}, author = {Guo, S and Qiang, M and Luan, X and Xu, P and He, G and Yin, X and Xi, L and Jin, X and Shao, J and Chen, X and Fang, D and Li, B}, title = {The application of the Internet of Things to animal ecology.}, journal = {Integrative zoology}, volume = {10}, number = {6}, pages = {572-578}, doi = {10.1111/1749-4877.12162}, pmid = {26338071}, issn = {1749-4877}, mesh = {*Animal Distribution ; Animals ; Ecology/instrumentation/*methods ; Geographic Information Systems ; *Internet ; Radio Frequency Identification Device ; Remote Sensing Technology ; }, abstract = {For ecologists, understanding the reaction of animals to environmental changes is critical. Using networked sensor technology to measure wildlife and environmental parameters can provide accurate, real-time and comprehensive data for monitoring, research and conservation of wildlife. This paper reviews: (i) conventional detection technology; (ii) concepts and applications of the Internet of Things (IoT) in animal ecology; and (iii) the advantages and disadvantages of IoT. The current theoretical limits of IoT in animal ecology are also discussed. Although IoT offers a new direction in animal ecological research, it still needs to be further explored and developed as a theoretical system and applied to the appropriate scientific frameworks for understanding animal ecology.}, }
@article {pmid26313959, year = {2015}, author = {Li, HF and Lan, YC and Fujisaki, I and Kanzaki, N and Lee, HJ and Su, NY}, title = {Termite Assemblage Pattern and Niche Partitioning in a Tropical Forest Ecosystem.}, journal = {Environmental entomology}, volume = {44}, number = {3}, pages = {546-556}, doi = {10.1093/ee/nvv038}, pmid = {26313959}, issn = {1938-2936}, mesh = {Animals ; *Ecosystem ; Forests ; Geographic Information Systems ; Isoptera/*physiology ; Taiwan ; *Tropical Climate ; }, abstract = {Termites are major plant decomposers in tropical forest ecosystems, but their cryptic nature poses an obstacle for studying their ecological roles in depth. In the current study, we quantified climatic and geographic information of 137 termite collection sites in the Kenting National Park, Taiwan, and described the ecological niches and assemblage patterns of 13 termite species of three families. Three major assemblage patterns are reported. First, the three termite families were found in most landcovering types with similar number of species, which indicated that each family played a unique role in the ecosystem. Second, average numbers of termite species were not different among collection sites, but the total number of termite species found in each landcovering type was different, which indicated that termite niche capacity in each small area was the same but some landcovering types were composed of diverse microhabitats to host more termite species. Third, termite species of every family showed distinct moisture preferences in their habitat choices. In addition to the three assemblage patterns, we found that niche size of the advanced termite family, Termitidae, was larger than that of the primitive termite families, Rhinotermitidae or Kalotermitidae. The broader choices of cellulosic materials as food sources may allow Termitidae to adapt to more diverse environments than exclusive wood feeders. Termite niche quantification could further be used to study termite pest adaption in urban areas, interspecific competition between native and invasive species, and plant decomposition processes.}, }
@article {pmid26311086, year = {2015}, author = {Steenberg, JW and Millward, AA and Duinker, PN and Nowak, DJ and Robinson, PJ}, title = {Neighbourhood-scale urban forest ecosystem classification.}, journal = {Journal of environmental management}, volume = {163}, number = {}, pages = {134-145}, doi = {10.1016/j.jenvman.2015.08.008}, pmid = {26311086}, issn = {1095-8630}, mesh = {Canada ; *Cities ; Cluster Analysis ; Decision Support Techniques ; Ecology/classification/*methods ; *Ecosystem ; *Forests ; Humans ; Population Density ; Residence Characteristics ; Trees ; }, abstract = {Urban forests are now recognized as essential components of sustainable cities, but there remains uncertainty concerning how to stratify and classify urban landscapes into units of ecological significance at spatial scales appropriate for management. Ecosystem classification is an approach that entails quantifying the social and ecological processes that shape ecosystem conditions into logical and relatively homogeneous management units, making the potential for ecosystem-based decision support available to urban planners. The purpose of this study is to develop and propose a framework for urban forest ecosystem classification (UFEC). The multifactor framework integrates 12 ecosystem components that characterize the biophysical landscape, built environment, and human population. This framework is then applied at the neighbourhood scale in Toronto, Canada, using hierarchical cluster analysis. The analysis used 27 spatially-explicit variables to quantify the ecosystem components in Toronto. Twelve ecosystem classes were identified in this UFEC application. Across the ecosystem classes, tree canopy cover was positively related to economic wealth, especially income. However, education levels and homeownership were occasionally inconsistent with the expected positive relationship with canopy cover. Open green space and stocking had variable relationships with economic wealth and were more closely related to population density, building intensity, and land use. The UFEC can provide ecosystem-based information for greening initiatives, tree planting, and the maintenance of the existing canopy. Moreover, its use has the potential to inform the prioritization of limited municipal resources according to ecological conditions and to concerns of social equity in the access to nature and distribution of ecosystem service supply.}, }
@article {pmid26308326, year = {2015}, author = {McAvoy, A and Hauert, C}, title = {Asymmetric Evolutionary Games.}, journal = {PLoS computational biology}, volume = {11}, number = {8}, pages = {e1004349}, pmid = {26308326}, issn = {1553-7358}, mesh = {Animals ; Biological Evolution ; Computational Biology/*methods ; Cultural Evolution ; Ecology ; *Game Theory ; Genotype ; Humans ; *Models, Theoretical ; }, abstract = {Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.}, }
@article {pmid26298253, year = {2015}, author = {Isigonis, P and Ciffroy, P and Zabeo, A and Semenzin, E and Critto, A and Giove, S and Marcomini, A}, title = {A Multi-Criteria Decision Analysis based methodology for quantitatively scoring the reliability and relevance of ecotoxicological data.}, journal = {The Science of the total environment}, volume = {538}, number = {}, pages = {102-116}, doi = {10.1016/j.scitotenv.2015.06.016}, pmid = {26298253}, issn = {1879-1026}, mesh = {*Decision Support Techniques ; Ecotoxicology ; Environmental Monitoring/*methods ; Fuzzy Logic ; Risk Assessment ; Water Pollutants, Chemical/*analysis ; }, abstract = {Ecotoxicological data are highly important for risk assessment processes and are used for deriving environmental quality criteria, which are enacted for assuring the good quality of waters, soils or sediments and achieving desirable environmental quality objectives. Therefore, it is of significant importance the evaluation of the reliability of available data for analysing their possible use in the aforementioned processes. The thorough analysis of currently available frameworks for the assessment of ecotoxicological data has led to the identification of significant flaws but at the same time various opportunities for improvement. In this context, a new methodology, based on Multi-Criteria Decision Analysis (MCDA) techniques, has been developed with the aim of analysing the reliability and relevance of ecotoxicological data (which are produced through laboratory biotests for individual effects), in a transparent quantitative way, through the use of expert knowledge, multiple criteria and fuzzy logic. The proposed methodology can be used for the production of weighted Species Sensitivity Weighted Distributions (SSWD), as a component of the ecological risk assessment of chemicals in aquatic systems. The MCDA aggregation methodology is described in detail and demonstrated through examples in the article and the hierarchically structured framework that is used for the evaluation and classification of ecotoxicological data is shortly discussed. The methodology is demonstrated for the aquatic compartment but it can be easily tailored to other environmental compartments (soil, air, sediments).}, }
@article {pmid26287466, year = {2015}, author = {van Kleunen, M and Dawson, W and Essl, F and Pergl, J and Winter, M and Weber, E and Kreft, H and Weigelt, P and Kartesz, J and Nishino, M and Antonova, LA and Barcelona, JF and Cabezas, FJ and Cárdenas, D and Cárdenas-Toro, J and Castaño, N and Chacón, E and Chatelain, C and Ebel, AL and Figueiredo, E and Fuentes, N and Groom, QJ and Henderson, L and Inderjit,  and Kupriyanov, A and Masciadri, S and Meerman, J and Morozova, O and Moser, D and Nickrent, DL and Patzelt, A and Pelser, PB and Baptiste, MP and Poopath, M and Schulze, M and Seebens, H and Shu, WS and Thomas, J and Velayos, M and Wieringa, JJ and Pyšek, P}, title = {Global exchange and accumulation of non-native plants.}, journal = {Nature}, volume = {525}, number = {7567}, pages = {100-103}, pmid = {26287466}, issn = {1476-4687}, mesh = {*Biodiversity ; Databases, Factual ; *Geographic Mapping ; Introduced Species/*statistics &amp; numerical data ; North America ; Pacific Islands ; Phylogeography ; *Plants ; }, abstract = {All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage. So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.}, }
@article {pmid26261300, year = {2015}, author = {Bibi, F and Kiessling, W}, title = {Continuous evolutionary change in Plio-Pleistocene mammals of eastern Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {34}, pages = {10623-10628}, pmid = {26261300}, issn = {1091-6490}, mesh = {Adaptation, Physiological ; Africa, Eastern ; Animals ; Antelopes/physiology ; *Biological Evolution ; Body Weight ; *Climate Change/history ; Databases, Factual ; Ecology ; Extinction, Biological ; Fossils ; Genetic Speciation ; History, Ancient ; Humidity ; Mammals/*physiology ; Temperature ; }, abstract = {Much debate has revolved around the question of whether the mode of evolutionary and ecological turnover in the fossil record of African mammals was continuous or pulsed, and the degree to which faunal turnover tracked changes in global climate. Here, we assembled and analyzed large specimen databases of the fossil record of eastern African Bovidae (antelopes) and Turkana Basin large mammals. Our results indicate that speciation and extinction proceeded continuously throughout the Pliocene and Pleistocene, as did increases in the relative abundance of arid-adapted bovids, and in bovid body mass. Species durations were similar among clades with different ecological attributes. Occupancy patterns were unimodal, with long and nearly symmetrical origination and extinction phases. A single origination pulse may be present at 2.0-1.75 Ma, but besides this, there is no evidence that evolutionary or ecological changes in the eastern African record tracked rapid, 100,000-y-scale changes in global climate. Rather, eastern African large mammal evolution tracked global or regional climatic trends at long (million year) time scales, while local, basin-scale changes (e.g., tectonic or hydrographic) and biotic interactions ruled at shorter timescales.}, }
@article {pmid26260166, year = {2015}, author = {Steyaert, SM and Zedrosser, A and Rosell, F}, title = {Socio-ecological features other than sex affect habitat selection in the socially obligate monogamous Eurasian beaver.}, journal = {Oecologia}, volume = {179}, number = {4}, pages = {1023-1032}, pmid = {26260166}, issn = {1432-1939}, mesh = {Animals ; Avoidance Learning/*physiology ; *Ecosystem ; Female ; Geographic Information Systems ; Humans ; Male ; Pair Bond ; Rodentia/*growth &amp; development/physiology ; Sex Characteristics ; Sexual Behavior, Animal/*physiology ; *Social Behavior ; Territoriality ; }, abstract = {Habitat selection is a context-dependent mechanism, in which both the internal state as well as external factors affect the behavior and decisions of an individual. This is well known for polygamous mammals, which are typically sexually dimorphic, and often express great variability in behavior and habitat selection between individuals as well between the sexes. Among monogamous mammals, however, variability in habitat selection should be explained by group characteristics and the presence of offspring rather than by sex. We evaluated this hypothesis in a socially monogamous rodent, the Eurasian beaver (Castor fiber), in a saturated Norwegian population. For the first time in this species we applied GPS tracking devices (N = 22 adult beavers, in 15 territories, 2009-2013), and used resource selection functions (i) to document population-wide habitat selection and the importance of 'territory' therein, and (ii) to evaluate which socio-ecological factors explained potential individual differences in habitat selection. We found that variation in habitat selection was stronger between territories than between years or individuals nested by territory. We identified that family size and the presence of kits, but not sex, explained individual variation in habitat selection. Adults with kits and/or larger families tended to exhibit low risk-taking behavior (avoiding human-related variables such as roads, buildings, and agricultural land), and stayed close to their main lodge (parental care). Our results show that habitat selection is a context-dependent mechanism even in a species which expresses very little behavioral and morphological dimorphism.}, }
@article {pmid26236474, year = {2015}, author = {Tedersoo, L and Ramirez, KS and Nilsson, RH and Kaljuvee, A and Kõljalg, U and Abarenkov, K}, title = {Standardizing metadata and taxonomic identification in metabarcoding studies.}, journal = {GigaScience}, volume = {4}, number = {}, pages = {34}, pmid = {26236474}, issn = {2047-217X}, mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; Sequence Alignment ; }, abstract = {High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.}, }
@article {pmid26233048, year = {2015}, author = {Matias, L and Harris, D}, title = {A single-station method for the detection, classification and location of fin whale calls using ocean-bottom seismic stations.}, journal = {The Journal of the Acoustical Society of America}, volume = {138}, number = {1}, pages = {504-520}, doi = {10.1121/1.4922706}, pmid = {26233048}, issn = {1520-8524}, mesh = {Acoustics/*instrumentation ; Animals ; Balaenoptera/*physiology ; Datasets as Topic ; Equipment Design ; Fin Whale/*physiology ; Homing Behavior ; Marine Biology/*instrumentation ; Oceans and Seas ; Sound Localization ; *Vocalization, Animal ; }, abstract = {Passive seismic monitoring in the oceans uses long-term deployments of Ocean Bottom Seismometers (OBSs). An OBS usually records the three components of ground motion and pressure, typically at 100 Hz. This makes the OBS an ideal tool to investigate fin and blue whales that vocalize at frequencies below 45 Hz. Previous applications of OBS data to locate whale calls have relied on single channel analyses that disregard the information that is conveyed by the horizontal seismic channels. Recently, Harris, Matias, Thomas, Harwood, and Geissler [J. Acoust. Soc. Am. 134, 3522-3535 (2013)] presented a method that used all four channels recorded by one OBS to derive the range and azimuth of fin whale calls. In this work, the detection, classification, and ranging of calls using this four-channel method were further investigated, focusing on methods to increase the accuracy of range estimates to direct path arrivals. Corrections to account for the influences of the sound speed in the water layer and the velocity structure in the top strata of the seabed were considered. The single station method discussed here is best implemented when OBSs have been deployed in deep water on top of seabed strata with low P-wave velocity. These conditions maximize the ability to detect and estimate ranges to fin whale calls.}, }
@article {pmid26227803, year = {2015}, author = {Byers, JE and Smith, RS and Pringle, JM and Clark, GF and Gribben, PE and Hewitt, CL and Inglis, GJ and Johnston, EL and Ruiz, GM and Stachowicz, JJ and Bishop, MJ}, title = {Invasion Expansion: Time since introduction best predicts global ranges of marine invaders.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12436}, pmid = {26227803}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms ; Australia ; Databases, Factual ; Ecosystem ; Environment ; *Introduced Species ; *Invertebrates/physiology ; Marine Biology ; New Zealand ; Ships ; Time Factors ; United States ; }, abstract = {Strategies for managing biological invasions are often based on the premise that characteristics of invading species and the invaded environment are key predictors of the invader's distribution. Yet, for either biological traits or environmental characteristics to explain distribution, adequate time must have elapsed for species to spread to all potential habitats. We compiled and analyzed a database of natural history and ecological traits of 138 coastal marine invertebrate species, the environmental conditions at sites to which they have been introduced, and their date of first introduction. We found that time since introduction explained the largest fraction (20%) of the variability in non-native range size, while traits of the species and environmental variables had significant, but minimal, influence on non-native range size. The positive relationship between time since introduction and range size indicates that non-native marine invertebrate species are not at equilibrium and are still spreading, posing a major challenge for management of coastal ecosystems.}, }
@article {pmid26225933, year = {2015}, author = {Kidd, AM and Monz, C and D'Antonio, A and Manning, RE and Reigner, N and Goonan, KA and Jacobi, C}, title = {The effect of minimum impact education on visitor spatial behavior in parks and protected areas: An experimental investigation using GPS-based tracking.}, journal = {Journal of environmental management}, volume = {162}, number = {}, pages = {53-62}, doi = {10.1016/j.jenvman.2015.07.007}, pmid = {26225933}, issn = {1095-8630}, mesh = {Conservation of Natural Resources/*methods ; Ecology/*education ; Education, Nonprofessional/*methods ; Geographic Information Systems ; Humans ; Knowledge ; Maine ; Recreation/*psychology ; Spatial Analysis ; Spatial Behavior ; Travel ; }, abstract = {The unmanaged impacts of recreation and tourism can often result in unacceptable changes in resource conditions and quality of the visitor experience. Minimum impact visitor education programs aim to reduce the impacts of recreation by altering visitor behaviors. Specifically, education seeks to reduce impacts resulting from lack of knowledge both about the consequences of one's actions and impact-minimizing best practices. In this study, three different on-site minimum impact education strategies (&quot;treatments&quot;) and a control condition were applied on the trails and summit area of Sargent Mountain in Acadia National Park, Maine. Treatment conditions were designed to encourage visitors to stay on marked trails and minimize off-trail travel. Treatments included a message delivered via personal contact, and both an ecological-based message and an amenity-based message posted on signs located alongside the trail. A control condition of current trail markings and directional signs was also assessed. The efficacy of the messaging was evaluated through the use of Global Positioning System (GPS) tracking of visitor spatial behavior on/off trails. Spatial analysis of GPS tracks revealed statistically significant differences among treatments, with the personal contact treatment yielding significantly less dispersion of visitors on the mountain summit. Results also indicate that the signs deployed in the study were ineffective at limiting off-trail use beyond what can be accomplished with trail markers and directional signs. These findings suggest that personal contact by a uniformed ranger or volunteer may be the most effective means of message delivery for on-site minimum impact education.}, }
@article {pmid26220359, year = {2016}, author = {Mueller, JC and Kuhl, H and Timmermann, B and Kempenaers, B}, title = {Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {549-561}, doi = {10.1111/1755-0998.12450}, pmid = {26220359}, issn = {1755-0998}, mesh = {Animals ; Databases, Genetic ; Databases, Nucleic Acid ; Female ; *Gene Expression Profiling ; *Genetic Variation ; *Genome ; Internet ; Male ; Passeriformes/*genetics ; Polymorphism, Single Nucleotide ; RNA, Messenger/analysis ; Sequence Analysis, DNA ; Sex Factors ; }, abstract = {Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus--a long-time ecological model species--has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500,000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de.}, }
@article {pmid26157601, year = {2015}, author = {Coutinho, FH and Meirelles, PM and Moreira, AP and Paranhos, RP and Dutilh, BE and Thompson, FL}, title = {Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1008}, pmid = {26157601}, issn = {2167-8359}, abstract = {Associations between microorganisms occur extensively throughout Earth's oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. A total of 1,906 correlations amongst 297 organisms were detected, segregating them into 11 major groups that occupy distinct ecological niches. Additionally, by analyzing the oceanographic parameters measured for a selected number of sampling sites, we characterized the influence of environmental variables over each of these 11 groups. Clustering organisms into groups of taxa that have similar ecology, allowed the detection of several significant correlations that could not be observed for the taxa individually.}, }
@article {pmid26142451, year = {2015}, author = {Messina, JP and Pigott, DM and Golding, N and Duda, KA and Brownstein, JS and Weiss, DJ and Gibson, H and Robinson, TP and Gilbert, M and William Wint, GR and Nuttall, PA and Gething, PW and Myers, MF and George, DB and Hay, SI}, title = {The global distribution of Crimean-Congo hemorrhagic fever.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {109}, number = {8}, pages = {503-513}, pmid = {26142451}, issn = {1878-3503}, support = {095066//Wellcome Trust/United Kingdom ; R01 LM010812/LM/NLM NIH HHS/United States ; }, mesh = {Abattoirs ; Animal Husbandry ; Animals ; Arachnid Vectors/*virology ; Disease Outbreaks/*prevention &amp; control ; Farmers ; Geography ; *Global Health ; Hemorrhagic Fever Virus, Crimean-Congo/*pathogenicity ; Hemorrhagic Fever, Crimean/blood/prevention &amp; control/*transmission ; Humans ; Occupational Diseases/*prevention &amp; control/virology ; Occupational Exposure/*prevention &amp; control ; Phylogeny ; Ticks/virology ; }, abstract = {BACKGROUND: Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne infection caused by a virus (CCHFV) from the Bunyaviridae family. Domestic and wild vertebrates are asymptomatic reservoirs for the virus, putting animal handlers, slaughter-house workers and agricultural labourers at highest risk in endemic areas, with secondary transmission possible through contact with infected blood and other bodily fluids. Human infection is characterized by severe symptoms that often result in death. While it is known that CCHFV transmission is limited to Africa, Asia and Europe, definitive global extents and risk patterns within these limits have not been well described.<br><br>METHODS: We used an exhaustive database of human CCHF occurrence records and a niche modeling framework to map the global distribution of risk for human CCHF occurrence.<br><br>RESULTS: A greater proportion of shrub or grass land cover was the most important contributor to our model, which predicts highest levels of risk around the Black Sea, Turkey, and some parts of central Asia. Sub-Saharan Africa shows more focalized areas of risk throughout the Sahel and the Cape region.<br><br>CONCLUSIONS: These new risk maps provide a valuable starting point for understanding the zoonotic niche of CCHF, its extent and the risk it poses to humans.}, }
@article {pmid26123545, year = {2015}, author = {Rosser, N and Kozak, KM and Phillimore, AB and Mallet, J}, title = {Extensive range overlap between heliconiine sister species: evidence for sympatric speciation in butterflies?.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {125}, pmid = {26123545}, issn = {1471-2148}, support = {BB/G006903/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; Butterflies/anatomy &amp; histology/*classification/*genetics ; Climate ; Computer Simulation ; Databases, Factual ; Ecology ; Genetic Speciation ; Phylogeny ; Sympatry ; Wings, Animal/anatomy &amp; histology ; }, abstract = {BACKGROUND: Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry.<br><br>RESULTS: Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32%-95% of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved.<br><br>CONCLUSIONS: Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on &quot;strict and &quot; &quot;relaxed&quot; biological species concepts (BSC), as well as on a surrogate for the widely-used &quot;diagnostic&quot; version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two groups. To establish whether heliconiines are exceptional will require biogeographic comparative studies for a wider range of animal taxa including many more invertebrates.}, }
@article {pmid26107170, year = {2015}, author = {Wang, Z and Zhou, J and Loaiciga, H and Guo, H and Hong, S}, title = {A DPSIR model for ecological security assessment through indicator screening: a case study at Dianchi Lake in China.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0131732}, pmid = {26107170}, issn = {1932-6203}, mesh = {Algorithms ; China ; Conservation of Natural Resources/*methods ; Cyanobacteria ; Databases, Factual ; Ecology/*methods ; Ecosystem ; Environmental Monitoring/*methods ; Eutrophication ; Human Activities ; Lakes ; Models, Theoretical ; Principal Component Analysis ; Risk ; Risk Assessment ; }, abstract = {Given the important role of lake ecosystems in social and economic development, and the current severe environmental degradation in China, a systematic diagnosis of the ecological security of lakes is essential for sustainable development. A Driving-force, Pressure, Status, Impact, and Risk (DPSIR) model, combined with data screening for lake ecological security assessment was developed to overcome the disadvantages of data selection in existing assessment methods. Correlation and principal component analysis were used to select independent and representative data. The DPSIR model was then applied to evaluate the ecological security of Dianchi Lake in China during 1988-2007 using an ecological security index. The results revealed a V-shaped trend. The application of the DPSIR model with data screening provided useful information regarding the status of the lake's ecosystem, while ensuring information efficiency and eliminating multicollinearity. The modeling approach described here is practical and operationally efficient, and provides an attractive alternative approach to assess the ecological security of lakes.}, }
@article {pmid26099482, year = {2015}, author = {Bayliss, HR and Beyer, FR}, title = {Information retrieval for ecological syntheses.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {136-148}, doi = {10.1002/jrsm.1120}, pmid = {26099482}, issn = {1759-2887}, mesh = {Data Accuracy ; *Data Interpretation, Statistical ; Data Mining/*methods ; Ecology/*methods ; Evidence-Based Medicine/methods ; *Meta-Analysis as Topic ; *Research Design ; *Review Literature as Topic ; }, abstract = {Research syntheses are increasingly being conducted within the fields of ecology and environmental management. Information retrieval is crucial in any synthesis in identifying data for inclusion whilst potentially reducing biases in the dataset gathered, yet the nature of ecological information provides several challenges when compared with medicine that should be considered when planning and undertaking searches. We present ten recommendations for anyone considering undertaking information retrieval for ecological research syntheses that highlight the main differences with medicine and, if adopted, may help reduce biases in the dataset retrieved, increase search efficiency and improve reporting standards. They are as follows: (1) plan for information retrieval at an early stage, (2) identify and use sources of help, (3) clearly define the question to be addressed, (4) ensure that provisions for managing, recording and reporting the search are in place, (5) select an appropriate search type, (6) identify sources to be used, (7) identify limitations of the sources, (8) ensure that the search vocabulary is appropriate, (9) identify limits and filters that can help direct the search, and (10) test the strategy to ensure that it is realistic and manageable. These recommendations may be of value for other disciplines where search infrastructures are not yet sufficiently well developed.}, }
@article {pmid26099481, year = {2015}, author = {Shrier, I}, title = {How to critically read ecological meta-analyses.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {134-135}, doi = {10.1002/jrsm.1150}, pmid = {26099481}, issn = {1759-2887}, mesh = {*Data Accuracy ; *Data Interpretation, Statistical ; Data Mining/*methods ; Ecology/*methods ; *Meta-Analysis as Topic ; *Research Design ; }, }
@article {pmid26099480, year = {2015}, author = {Lortie, CJ and Stewart, G and Rothstein, H and Lau, J}, title = {How to critically read ecological meta-analyses.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {124-133}, doi = {10.1002/jrsm.1109}, pmid = {26099480}, issn = {1759-2887}, mesh = {*Data Accuracy ; *Data Interpretation, Statistical ; Data Mining/*methods ; Ecology/*methods ; *Meta-Analysis as Topic ; Reading ; *Research Design ; }, abstract = {Meta-analysis offers ecologists a powerful tool for knowledge synthesis. Albeit a form of review, it also shares many similarities with primary empirical research. Consequently, critical reading of meta-analyses incorporates criteria from both sets of approaches particularly because ecology is a discipline that embraces heterogeneity and broad methodologies. The most important issues in critically assessing a meta-analysis initially include transparency, replicability, and clear statement of purpose by the authors. Specific to ecology, more so than other disciplines, tests of the same hypothesis are generally conducted at different study sites, have variable ecological contexts (i.e., seasonality), and use very different methods. Clear reporting and careful examination of heterogeneity in ecological meta-analyses is thus crucial. Ecologists often also test similar hypotheses with different species, and in these meta-analyses, the reader should expect exploration of phylogenetic dependencies. Finally, observational studies not only provide the substrate for potential current manipulative experiments in this discipline but also form an important body of literature historically for synthesis. Sensitivity analyses of observational versus manipulative experiments when aggregated in the same ecological meta-analysis are also frequent and appropriate. This brief conceptual review is not intended as an instrument to rate meta-analyses for ecologists but does provide the appropriate framing for those purposes and directs the reader to ongoing developments in this direction in other disciplines.}, }
@article {pmid26099478, year = {2015}, author = {Mengersen, K and MacNeil, MA and Caley, MJ}, title = {The potential for meta-analysis to support decision analysis in ecology.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {111-121}, doi = {10.1002/jrsm.1105}, pmid = {26099478}, issn = {1759-2887}, mesh = {*Data Interpretation, Statistical ; *Decision Support Techniques ; Ecology/*methods ; Feasibility Studies ; *Meta-Analysis as Topic ; *Research Design ; }, abstract = {Meta-analysis and decision analysis are underpinned by well-developed methods that are commonly applied to a variety of problems and disciplines. While these two fields have been closely linked in some disciplines such as medicine, comparatively little attention has been paid to the potential benefits of linking them in ecology, despite reasonable expectations that benefits would be derived from doing so. Meta-analysis combines information from multiple studies to provide more accurate parameter estimates and to reduce the uncertainty surrounding them. Decision analysis involves selecting among alternative choices using statistical information that helps to shed light on the uncertainties involved. By linking meta-analysis to decision analysis, improved decisions can be made, with quantification of the costs and benefits of alternate decisions supported by a greater density of information. Here, we briefly review concepts of both meta-analysis and decision analysis, illustrating the natural linkage between them and the benefits from explicitly linking one to the other. We discuss some examples in which this linkage has been exploited in the medical arena and how improvements in precision and reduction of structural uncertainty inherent in a meta-analysis can provide substantive improvements to decision analysis outcomes by reducing uncertainty in expected loss and maximising information from across studies. We then argue that these significant benefits could be translated to ecology, in particular to the problem of making optimal ecological decisions in the face of uncertainty.}, }
@article {pmid26098107, year = {2015}, author = {Ayanu, Y and Conrad, C and Jentsch, A and Koellner, T}, title = {Unveiling Undercover Cropland Inside Forests Using Landscape Variables: A Supplement to Remote Sensing Image Classification.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0130079}, pmid = {26098107}, issn = {1932-6203}, mesh = {Agriculture ; Conservation of Natural Resources/methods ; Crops, Agricultural/*growth &amp; development ; Ecosystem ; Environmental Monitoring/*methods ; Ethiopia ; Food ; Food Supply ; Forests ; *Geographic Information Systems ; Remote Sensing Technology/*methods ; Satellite Imagery/*methods ; }, abstract = {The worldwide demand for food has been increasing due to the rapidly growing global population, and agricultural lands have increased in extent to produce more food crops. The pattern of cropland varies among different regions depending on the traditional knowledge of farmers and availability of uncultivated land. Satellite images can be used to map cropland in open areas but have limitations for detecting undergrowth inside forests. Classification results are often biased and need to be supplemented with field observations. Undercover cropland inside forests in the Bale Mountains of Ethiopia was assessed using field observed percentage cover of land use/land cover classes, and topographic and location parameters. The most influential factors were identified using Boosted Regression Trees and used to map undercover cropland area. Elevation, slope, easterly aspect, distance to settlements, and distance to national park were found to be the most influential factors determining undercover cropland area. When there is very high demand for growing food crops, constrained under restricted rights for clearing forest, cultivation could take place within forests as an undercover. Further research on the impact of undercover cropland on ecosystem services and challenges in sustainable management is thus essential.}, }
@article {pmid26093894, year = {2015}, author = {Sudhakar Reddy, C and Vazeed Pasha, S and Jha, CS and Dadhwal, VK}, title = {Geospatial characterization of deforestation, fragmentation and forest fires in Telangana state, India: conservation perspective.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {7}, pages = {455}, pmid = {26093894}, issn = {1573-2959}, mesh = {Biodiversity ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/*methods ; *Fires ; Forests ; Geographic Information Systems ; Geography ; India ; *Trees ; }, abstract = {Conservation of biodiversity has been put to the highest priority throughout the world. The process of identifying threatened ecosystems will search for different drivers related to biodiversity loss. The present study aimed to generate spatial information on deforestation and ecological degradation indicators of fragmentation and forest fires using systematic conceptual approach in Telangana state, India. Identification of ecosystems facing increasing vulnerability can help to safeguard the extinctions of species and useful for conservation planning. The technological advancement of satellite remote sensing and Geographical Information System has increased greatly in assessment and monitoring of ecosystem-level changes. The areas of threat were identified by creating grid cells (5 × 5 km) in Geographical Information System (GIS). Deforestation was assessed using multi-source data of 1930, 1960, 1975, 1985, 1995, 2005 and 2013. The forest cover of 40,746 km(2), 29,299 km(2), 18,652 km(2), 18,368 km(2), 18,006 km(2), 17,556 km(2) and 17,520 km(2) was estimated during 1930, 1960, 1975, 1985, 1995, 2005 and 2013, respectively. Historical evaluation of deforestation revealed that major changes had occurred in forests of Telangana and identified 1095 extinct, 397 critically endangered, 523 endangered and 311 vulnerable ecosystem grid cells. The fragmentation analysis has identified 307 ecosystem grid cells under critically endangered status. Forest burnt area information was extracted using AWiFS data of 2005 to 2014. Spatial analysis indicates total fire-affected forest in Telangana as 58.9% in a decadal period. Conservation status has been recorded depending upon values of threat for each grid, which forms the basis for conservation priority hotspots. Of existing forest, 2.1% grids had severe ecosystem collapse and had been included under the category of conservation priority hotspot-I, followed by 27.2% in conservation priority hotspot-II and 51.5% in conservation priority hotspot-III. This analysis complements assessment of ecosystems undergoing multiple threats. An integrated approach involving the deforestation and degradation indicators is useful in formulating the strategies to take appropriate conservation measures.}, }
@article {pmid26082541, year = {2015}, author = {Reyers, B and Nel, JL and O'Farrell, PJ and Sitas, N and Nel, DC}, title = {Navigating complexity through knowledge coproduction: Mainstreaming ecosystem services into disaster risk reduction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {24}, pages = {7362-7368}, pmid = {26082541}, issn = {1091-6490}, mesh = {Conservation of Natural Resources/*methods ; Decision Making ; *Disasters ; Droughts ; *Ecosystem ; Fires ; Floods ; Knowledge Bases ; Risk Reduction Behavior ; South Africa ; Tidal Waves ; }, abstract = {Achieving the policy and practice shifts needed to secure ecosystem services is hampered by the inherent complexities of ecosystem services and their management. Methods for the participatory production and exchange of knowledge offer an avenue to navigate this complexity together with the beneficiaries and managers of ecosystem services. We develop and apply a knowledge coproduction approach based on social-ecological systems research and assess its utility in generating shared knowledge and action for ecosystem services. The approach was piloted in South Africa across four case studies aimed at reducing the risk of disasters associated with floods, wildfires, storm waves, and droughts. Different configurations of stakeholders (knowledge brokers, assessment teams, implementers, and bridging agents) were involved in collaboratively designing each study, generating and exchanging knowledge, and planning for implementation. The approach proved useful in the development of shared knowledge on the sizable contribution of ecosystem services to disaster risk reduction. This knowledge was used by stakeholders to design and implement several actions to enhance ecosystem services, including new investments in ecosystem restoration, institutional changes in the private and public sector, and innovative partnerships of science, practice, and policy. By bringing together multiple disciplines, sectors, and stakeholders to jointly produce the knowledge needed to understand and manage a complex system, knowledge coproduction approaches offer an effective avenue for the improved integration of ecosystem services into decision making.}, }
@article {pmid26058704, year = {2015}, author = {Semenzin, E and Lanzellotto, E and Hristozov, D and Critto, A and Zabeo, A and Giubilato, E and Marcomini, A}, title = {Species sensitivity weighted distribution for ecological risk assessment of engineered nanomaterials: the n-TiO2 case study.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {11}, pages = {2644-2659}, doi = {10.1002/etc.3103}, pmid = {26058704}, issn = {1552-8618}, mesh = {Animals ; Bacteria/drug effects ; Ecology ; Fresh Water ; Invertebrates/drug effects/physiology ; Metal Nanoparticles/*chemistry/toxicity ; Risk Assessment ; Species Specificity ; Titanium/*chemistry ; Vertebrates/physiology ; }, abstract = {Societal concerns about the environmental risks of engineered nanomaterials (ENMs) have recently increased, but nano-ecological risk assessments are constrained by significant gaps in basic information on long-term effects and exposures, for example. An approach to the ecological risk assessment of ENMs is proposed that can operate in the context of high uncertainty. This approach further develops species sensitivity weighted distribution (SSWD) by including 3 weighting criteria (species relevance, trophic level abundance, and nanotoxicity data quality) to address nano-specific needs (n-SSWD). The application of n-SSWD is illustrated for nanoscale titanium dioxide (n-TiO2), which is available in different crystal forms; it was selected because of its widespread use in consumer products (e.g., cosmetics) and the ample availability of data from ecotoxicological studies in the literature (including endpoints for algae, invertebrates, bacteria, and vertebrates in freshwater, saltwater, and terrestrial compartments). The n-SSWD application resulted in estimation of environmental quality criteria (hazard concentration affecting 5% and 50% of the species) and ecological risk (potentially affected fraction of species), which were then compared with similar results obtained by applying the traditional species sensitivity distribution (SSD) approach to the same dataset. The n-SSWDs were also built for specific trophic levels (e.g., primary producers) and taxonomic groups (e.g., algae), which helped to identify the most sensitive organisms. These results showd that n-SSWD is a valuable risk tool, although further testing is suggested.}, }
@article {pmid26058066, year = {2015}, author = {Forcino, FL and Leighton, LR and Twerdy, P and Cahill, JF}, title = {Reexamining Sample Size Requirements for Multivariate, Abundance-Based Community Research: When Resources are Limited, the Research Does Not Have to Be.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128379}, pmid = {26058066}, issn = {1932-6203}, mesh = {*Community-Based Participatory Research ; Databases as Topic ; *Health Resources ; Multivariate Analysis ; *Research Design ; Sample Size ; }, abstract = {Community ecologists commonly perform multivariate techniques (e.g., ordination, cluster analysis) to assess patterns and gradients of taxonomic variation. A critical requirement for a meaningful statistical analysis is accurate information on the taxa found within an ecological sample. However, oversampling (too many individuals counted per sample) also comes at a cost, particularly for ecological systems in which identification and quantification is substantially more resource consuming than the field expedition itself. In such systems, an increasingly larger sample size will eventually result in diminishing returns in improving any pattern or gradient revealed by the data, but will also lead to continually increasing costs. Here, we examine 396 datasets: 44 previously published and 352 created datasets. Using meta-analytic and simulation-based approaches, the research within the present paper seeks (1) to determine minimal sample sizes required to produce robust multivariate statistical results when conducting abundance-based, community ecology research. Furthermore, we seek (2) to determine the dataset parameters (i.e., evenness, number of taxa, number of samples) that require larger sample sizes, regardless of resource availability. We found that in the 44 previously published and the 220 created datasets with randomly chosen abundances, a conservative estimate of a sample size of 58 produced the same multivariate results as all larger sample sizes. However, this minimal number varies as a function of evenness, where increased evenness resulted in increased minimal sample sizes. Sample sizes as small as 58 individuals are sufficient for a broad range of multivariate abundance-based research. In cases when resource availability is the limiting factor for conducting a project (e.g., small university, time to conduct the research project), statistically viable results can still be obtained with less of an investment.}, }
@article {pmid26047160, year = {2015}, author = {Gao, P and Niu, X and Wang, B and Zheng, Y}, title = {Land use changes and its driving forces in hilly ecological restoration area based on gis and RS of northern China.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11038}, pmid = {26047160}, issn = {2045-2322}, mesh = {Agriculture ; China ; *Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; Forests ; Geographic Information Systems ; Remote Sensing Technology ; }, abstract = {Land use change is one of the important aspects of the regional ecological restoration research. With remote sensing (RS) image in 2003, 2007 and 2012, using geographic information system (GIS) technologies, the land use pattern changes in Yimeng Mountain ecological restoration area in China and its driving force factors were studied. Results showed that: (1) Cultivated land constituted the largest area during 10 years, and followed by forest land and grass land; cultivated land and unused land were reduced by 28.43% and 44.32%, whereas forest land, water area and land for water facilities and others were increased. (2) During 2003-2007, forest land change showed the largest, followed by unused land and grass land; however, during 2008-2012, water area and land for water facilities change showed the largest, followed by grass land and unused land. (3) Land use degree was above the average level, it was in the developing period during 2003-2007 and in the degenerating period during 2008-2012. (4) Ecological Restoration Projects can greatly change the micro topography, increase vegetation coverage, and then induce significant changes in the land use distribution, which were the main driving force factors of the land use pattern change in the ecological restoration area.}, }
@article {pmid26047146, year = {2015}, author = {Singh, KS and Thual, D and Spurio, R and Cannata, N}, title = {SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {6}, pages = {6352-6366}, pmid = {26047146}, issn = {1660-4601}, mesh = {Ecology/methods ; *Environmental Microbiology ; Environmental Monitoring/methods ; Information Management/*methods ; *Microarray Analysis ; *Software ; }, abstract = {One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies.}, }
@article {pmid26042592, year = {2015}, author = {Alexander, KA and Sanderson, CE and Marathe, M and Lewis, BL and Rivers, CM and Shaman, J and Drake, JM and Lofgren, E and Dato, VM and Eisenberg, MC and Eubank, S}, title = {What factors might have led to the emergence of Ebola in West Africa?.}, journal = {PLoS neglected tropical diseases}, volume = {9}, number = {6}, pages = {e0003652}, pmid = {26042592}, issn = {1935-2735}, support = {R01 GM109718/GM/NIGMS NIH HHS/United States ; U01 GM110744/GM/NIGMS NIH HHS/United States ; U01 GM110748/GM/NIGMS NIH HHS/United States ; T15 LM007059/LM/NLM NIH HHS/United States ; R01 GM100467/GM/NIGMS NIH HHS/United States ; 5U01GM070694-11/GM/NIGMS NIH HHS/United States ; 5T15 LM007059-28/LM/NLM NIH HHS/United States ; U01 GM070694/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa, Western/epidemiology ; Communicable Diseases, Emerging/*epidemiology ; Disease Outbreaks/*prevention &amp; control ; Ebolavirus/*physiology ; Hemorrhagic Fever, Ebola/*epidemiology ; Humans ; Risk Factors ; }, abstract = {An Ebola outbreak of unprecedented scope emerged in West Africa in December 2013 and presently continues unabated in the countries of Guinea, Sierra Leone, and Liberia. Ebola is not new to Africa, and outbreaks have been confirmed as far back as 1976. The current West African Ebola outbreak is the largest ever recorded and differs dramatically from prior outbreaks in its duration, number of people affected, and geographic extent. The emergence of this deadly disease in West Africa invites many questions, foremost among these: why now, and why in West Africa? Here, we review the sociological, ecological, and environmental drivers that might have influenced the emergence of Ebola in this region of Africa and its spread throughout the region. Containment of the West African Ebola outbreak is the most pressing, immediate need. A comprehensive assessment of the drivers of Ebola emergence and sustained human-to-human transmission is also needed in order to prepare other countries for importation or emergence of this disease. Such assessment includes identification of country-level protocols and interagency policies for outbreak detection and rapid response, increased understanding of cultural and traditional risk factors within and between nations, delivery of culturally embedded public health education, and regional coordination and collaboration, particularly with governments and health ministries throughout Africa. Public health education is also urgently needed in countries outside of Africa in order to ensure that risk is properly understood and public concerns do not escalate unnecessarily. To prevent future outbreaks, coordinated, multiscale, early warning systems should be developed that make full use of these integrated assessments, partner with local communities in high-risk areas, and provide clearly defined response recommendations specific to the needs of each community.}, }
@article {pmid26039741, year = {2015}, author = {North, AC and Hodgson, DJ and Price, SJ and Griffiths, AG}, title = {Anthropogenic and ecological drivers of amphibian disease (ranavirosis).}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0127037}, pmid = {26039741}, issn = {1932-6203}, mesh = {Animals ; *DNA Virus Infections/epidemiology/veterinary ; *Databases, Factual ; *Extinction, Biological ; Rana temporaria/*virology ; *Ranavirus ; United Kingdom/epidemiology ; }, abstract = {Ranaviruses are causing mass amphibian die-offs in North America, Europe and Asia, and have been implicated in the decline of common frog (Rana temporaria) populations in the UK. Despite this, we have very little understanding of the environmental drivers of disease occurrence and prevalence. Using a long term (1992-2000) dataset of public reports of amphibian mortalities, we assess a set of potential predictors of the occurrence and prevalence of Ranavirus-consistent common frog mortality events in Britain. We reveal the influence of biotic and abiotic drivers of this disease, with many of these abiotic characteristics being anthropogenic. Whilst controlling for the geographic distribution of mortality events, disease prevalence increases with increasing frog population density, presence of fish and wild newts, increasing pond depth and the use of garden chemicals. The presence of an alternative host reduces prevalence, potentially indicating a dilution effect. Ranavirosis occurrence is associated with the presence of toads, an urban setting and the use of fish care products, providing insight into the causes of emergence of disease. Links between occurrence, prevalence, pond characteristics and garden management practices provides useful management implications for reducing the impacts of Ranavirus in the wild.}, }
@article {pmid26035530, year = {2015}, author = {Rodríguez, A and Rodríguez, B and Negro, JJ}, title = {GPS tracking for mapping seabird mortality induced by light pollution.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10670}, pmid = {26035530}, issn = {2045-2322}, mesh = {Animals ; *Birds ; *Environmental Pollution ; *Geographic Information Systems ; Geography ; *Light ; Spain ; *Spatial Analysis ; }, abstract = {Light pollution and its consequences on ecosystems are increasing worldwide. Knowledge on the threshold levels of light pollution at which significant ecological impacts emerge and the size of dark refuges to maintain natural nocturnal processes is crucial to mitigate its negative consequences. Seabird fledglings are attracted by artificial lights when they leave their nest at night, causing high mortality. We used GPS data-loggers to track the flights of Cory's shearwater Calonectris diomedea fledglings from nest-burrows to ground, and to evaluate the light pollution levels of overflown areas on Tenerife, Canary Islands, using nocturnal, high-resolution satellite imagery. Birds were grounded at locations closer than 16 km from colonies in their maiden flights, and 50% were rescued within a 3 km radius from the nest-site. Most birds left the nests in the first three hours after sunset. Rescue locations showed radiance values greater than colonies, and flight distance was positively related to light pollution levels. Breeding habitat alteration by light pollution was more severe for inland colonies. We provide scientific-based information to manage dark refuges facilitating that fledglings from inland colonies reach the sea successfully. We also offer methodological approaches useful for other critically threatened petrel species grounded by light pollution.}, }
@article {pmid26034279, year = {2015}, author = {Slik, JW and Arroyo-Rodríguez, V and Aiba, S and Alvarez-Loayza, P and Alves, LF and Ashton, P and Balvanera, P and Bastian, ML and Bellingham, PJ and van den Berg, E and Bernacci, L and da Conceição Bispo, P and Blanc, L and Böhning-Gaese, K and Boeckx, P and Bongers, F and Boyle, B and Bradford, M and Brearley, FQ and Breuer-Ndoundou Hockemba, M and Bunyavejchewin, S and Calderado Leal Matos, D and Castillo-Santiago, M and Catharino, EL and Chai, SL and Chen, Y and Colwell, RK and Chazdon, RL and Clark, C and Clark, DB and Clark, DA and Culmsee, H and Damas, K and Dattaraja, HS and Dauby, G and Davidar, P and DeWalt, SJ and Doucet, JL and Duque, A and Durigan, G and Eichhorn, KA and Eisenlohr, PV and Eler, E and Ewango, C and Farwig, N and Feeley, KJ and Ferreira, L and Field, R and de Oliveira Filho, AT and Fletcher, C and Forshed, O and Franco, G and Fredriksson, G and Gillespie, T and Gillet, JF and Amarnath, G and Griffith, DM and Grogan, J and Gunatilleke, N and Harris, D and Harrison, R and Hector, A and Homeier, J and Imai, N and Itoh, A and Jansen, PA and Joly, CA and de Jong, BH and Kartawinata, K and Kearsley, E and Kelly, DL and Kenfack, D and Kessler, M and Kitayama, K and Kooyman, R and Larney, E and Laumonier, Y and Laurance, S and Laurance, WF and Lawes, MJ and Amaral, IL and Letcher, SG and Lindsell, J and Lu, X and Mansor, A and Marjokorpi, A and Martin, EH and Meilby, H and Melo, FP and Metcalfe, DJ and Medjibe, VP and Metzger, JP and Millet, J and Mohandass, D and Montero, JC and de Morisson Valeriano, M and Mugerwa, B and Nagamasu, H and Nilus, R and Ochoa-Gaona, S and Onrizal,  and Page, N and Parolin, P and Parren, M and Parthasarathy, N and Paudel, E and Permana, A and Piedade, MT and Pitman, NC and Poorter, L and Poulsen, AD and Poulsen, J and Powers, J and Prasad, RC and Puyravaud, JP and Razafimahaimodison, JC and Reitsma, J and Dos Santos, JR and Roberto Spironello, W and Romero-Saltos, H and Rovero, F and Rozak, AH and Ruokolainen, K and Rutishauser, E and Saiter, F and Saner, P and Santos, BA and Santos, F and Sarker, SK and Satdichanh, M and Schmitt, CB and Schöngart, J and Schulze, M and Suganuma, MS and Sheil, D and da Silva Pinheiro, E and Sist, P and Stevart, T and Sukumar, R and Sun, IF and Sunderland, T and Suresh, HS and Suzuki, E and Tabarelli, M and Tang, J and Targhetta, N and Theilade, I and Thomas, DW and Tchouto, P and Hurtado, J and Valencia, R and van Valkenburg, JL and Van Do, T and Vasquez, R and Verbeeck, H and Adekunle, V and Vieira, SA and Webb, CO and Whitfeld, T and Wich, SA and Williams, J and Wittmann, F and Wöll, H and Yang, X and Adou Yao, CY and Yap, SL and Yoneda, T and Zahawi, RA and Zakaria, R and Zang, R and de Assis, RL and Garcia Luize, B and Venticinque, EM}, title = {An estimate of the number of tropical tree species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {24}, pages = {7472-7477}, pmid = {26034279}, issn = {1091-6490}, mesh = {*Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; *Forests ; Phylogeography ; Rainforest ; Species Specificity ; Statistics, Nonparametric ; *Trees/classification ; *Tropical Climate ; }, abstract = {The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.}, }
@article {pmid25999513, year = {2015}, author = {Sunagawa, S and Coelho, LP and Chaffron, S and Kultima, JR and Labadie, K and Salazar, G and Djahanschiri, B and Zeller, G and Mende, DR and Alberti, A and Cornejo-Castillo, FM and Costea, PI and Cruaud, C and d'Ovidio, F and Engelen, S and Ferrera, I and Gasol, JM and Guidi, L and Hildebrand, F and Kokoszka, F and Lepoivre, C and Lima-Mendez, G and Poulain, J and Poulos, BT and Royo-Llonch, M and Sarmento, H and Vieira-Silva, S and Dimier, C and Picheral, M and Searson, S and Kandels-Lewis, S and ,  and Bowler, C and de Vargas, C and Gorsky, G and Grimsley, N and Hingamp, P and Iudicone, D and Jaillon, O and Not, F and Ogata, H and Pesant, S and Speich, S and Stemmann, L and Sullivan, MB and Weissenbach, J and Wincker, P and Karsenti, E and Raes, J and Acinas, SG and Bork, P}, title = {Ocean plankton. Structure and function of the global ocean microbiome.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6237}, pages = {1261359}, doi = {10.1126/science.1261359}, pmid = {25999513}, issn = {1095-9203}, mesh = {Databases, Genetic ; Ecosystem ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Humans ; Metagenome ; Microbiota/*genetics ; Oceans and Seas ; Plankton/*classification/genetics/isolation &amp; purification ; Seawater/*microbiology ; }, abstract = {Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.}, }
@article {pmid25980726, year = {2015}, author = {Xiao, Y and Xiao, Q and Ouyang, Z and Maomao, Q}, title = {Assessing changes in water flow regulation in Chongqing region, China.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {6}, pages = {362}, pmid = {25980726}, issn = {1573-2959}, mesh = {Altitude ; China ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Models, Theoretical ; Rivers/*chemistry ; *Water Movements ; }, abstract = {Water flow regulation is an important ecosystem service that significantly impacts on ecological quality and social benefits. With the aim of improving our understanding of ecosystems and proposing strategies for optimizing ecosystem services, a geographic information system (GIS)-based approach was designed to estimate and map regulated water flow in the Chongqing region of China. In this study, we applied the integrated valuation of environmental services and tradeoffs (InVEST) model and mathematical simulations to estimate the provision of the regulated water flow across space and time in 2000, 2005, and 2010. The results indicated that this ecosystem service had improved by 2.07 % from 2000 to 2010 as a result of human activities (such as vegetation restoration) and climatic interaction. Places with positive changes mainly occurred in high mountain areas, whereas places with negative changes were mainly distributed in resettlement areas along the Yangtze River. The type of ecosystem in areas with high mountains and steep slopes was a relatively minor contributor to the total service, but this ecosystem had the higher water flow regulation capacity. Moreover, with the increase in altitude and slope, the percentage contribution of forest increased significantly from 2000 to 2010; by contrast, the percentage contribution of cropland decreased rapidly. As for the impacts, the spatial variation of water flow regulation in the Chongqing region had a significant relation with climate and human activities at the regional scale. These results provided specific information that could be used to strengthen necessary public awareness about the protection and restoration of ecosystems.}, }
@article {pmid25980407, year = {2015}, author = {Levy, R and Carr, R and Kreimer, A and Freilich, S and Borenstein, E}, title = {NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {164}, pmid = {25980407}, issn = {1471-2105}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*metabolism ; Computational Biology/*methods ; *Host-Parasite Interactions ; Humans ; Internet ; *Metabolic Networks and Pathways ; *Microbial Interactions ; Models, Biological ; *Software ; }, abstract = {BACKGROUND: Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm.<br><br>RESULTS: NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds.<br><br>CONCLUSIONS: The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.}, }
@article {pmid25971519, year = {2015}, author = {Zhu, J and Zhou, Y and Wang, S and Wang, L and Wang, F and Liu, W and Guo, B}, title = {Multicriteria decision analysis for monitoring ecosystem service function of the Three-River Headwaters region of the Qinghai-Tibet Plateau, China.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {6}, pages = {355}, pmid = {25971519}, issn = {1573-2959}, mesh = {China ; Climate ; Conservation of Natural Resources/methods ; *Decision Support Techniques ; Ecology ; *Ecosystem ; Environment ; Environmental Monitoring/*methods ; Rivers ; Tibet ; }, abstract = {The Three-River Headwaters (TRH) region in the Qinghai-Tibet Plateau, China, is of key importance to the ecological security of China and Southeast Asia and contains some of the most sensitive and fragile ecosystems. Monitoring and evaluating the ecosystem service function and its changes in the TRH region could support decision-making for regional ecological protection and restoration programs. Referencing the concept of ecosystem service and the Millennium Ecosystem Assessment (MA) framework, this study built a system of indicators for monitoring and evaluating the ecosystem service function. Thus, combining a multicriteria decision analysis (MCDA) and weighted linear combination (WLC) with analytic hierarchy process (AHP), we applied the ecosystem service function index (ESFI) based on remote sensing data at 1-km spatial resolution to spatiotemporally monitor the changes during the period 2005-2010. The study results indicated that ESFI had a good performance for monitoring the ecosystem service function and showed an improving trend in the TRH region over the past 5 years. Ecosystem environment recovery not only reflected the changing trend of warm and wet climate but was also a response of the ecological protection project of the Key Ecological Function Zone in the TRH region.}, }
@article {pmid25965051, year = {2015}, author = {Dafforn, KA and Mayer-Pinto, M and Morris, RL and Waltham, NJ}, title = {Application of management tools to integrate ecological principles with the design of marine infrastructure.}, journal = {Journal of environmental management}, volume = {158}, number = {}, pages = {61-73}, doi = {10.1016/j.jenvman.2015.05.001}, pmid = {25965051}, issn = {1095-8630}, mesh = {*Conservation of Natural Resources ; *Decision Support Techniques ; Ecology ; *Ecosystem ; Environment Design ; Humans ; *Oceans and Seas ; }, abstract = {Globally the coastal zone is suffering the collateral damage from continuing urban development and construction, expanding resource sectors, increasing population, regulation to river flow, and on-going land change and degradation. While protection of natural coastal habitat is recommended, balancing conservation with human services is now the challenge for managers. Marine infrastructure such as seawalls, marinas and offshore platforms is increasingly used to support and provide services, but has primarily been designed for engineering purposes without consideration of the ecological consequences. Increasingly developments are seeking alternatives to hard engineering and a range of ecological solutions has begun to replace or be incorporated into marine and coastal infrastructure. But too often, hard engineering remains the primary strategy because the tools for managers to implement ecological solutions are either lacking or not supported by policy and stakeholders. Here we outline critical research needs for marine urban development and emerging strategies that seek to mitigate the impacts of marine infrastructure. We present case studies to highlight the strategic direction necessary to support management decisions internationally.}, }
@article {pmid25948716, year = {2015}, author = {Pearse, WD and Cadotte, MW and Cavender-Bares, J and Ives, AR and Tucker, CM and Walker, SC and Helmus, MR}, title = {pez: phylogenetics for the environmental sciences.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {17}, pages = {2888-2890}, doi = {10.1093/bioinformatics/btv277}, pmid = {25948716}, issn = {1367-4811}, mesh = {*Biodiversity ; *Databases, Genetic ; *Ecology ; Phenotype ; *Phylogeny ; *Software ; }, abstract = {UNLABELLED: pez is an R package that permits measurement, modelling and simulation of phylogenetic structure in ecological data. pez contains the first implementation of many methods in R, and aggregates existing data structures and methods into a single, coherent package.<br><br>pez is released under the GPL v3 open-source license, available on the Internet from CRAN (http://cran.r-project.org). The package is under active development, and the authors welcome contributions (see http://github.com/willpearse/pez).<br><br>CONTACT: will.pearse@gmail.com.}, }
@article {pmid25914427, year = {2014}, author = {Ulrich, W and Soliveres, S and Kryszewski, W and Maestre, FT and Gotelli, NJ}, title = {Matrix models for quantifying competitive intransitivity.}, journal = {Oikos (Copenhagen, Denmark)}, volume = {123}, number = {9}, pages = {1057-1070}, pmid = {25914427}, issn = {0030-1299}, support = {242658//European Research Council/International ; }, abstract = {Assessing the relative importance of intransitive competition networks in nature has been difficult because it requires a large number of pairwise competition experiments linked to observed field abundances of interacting species. Here we introduce metrics and statistical tests for evaluating the contribution of intransitivity to community structure using two kinds of data: competition matrices derived from the outcomes of pairwise experimental studies (C matrices) and species abundance matrices. We use C matrices to develop patch transition matrices (P) that predict community structure in a simple Markov chain model. We propose a randomization test to evaluate the degree of intransitivity from these P matrices in combination with empirical or simulated C matrices. Benchmark tests revealed that the methods could correctly detect intransitive competition networks, even in the absence of direct measures of pairwise competitive strength. These tests represent the first tools for estimating the degree of intransitivity in competitive networks from observational datasets. They can be applied to both spatio-temporal data sampled in homogeneous environments or across environmental gradients, and to experimental measures of pairwise interactions. To illustrate the methods, we analyzed empirical data matrices on the colonization of slug carrion by necrophagous flies and their parasitoids.}, }
@article {pmid25913208, year = {2015}, author = {Charlop-Powers, Z and Brady, SF}, title = {phylogeo: an R package for geographic analysis and visualization of microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {17}, pages = {2909-2911}, pmid = {25913208}, issn = {1367-4811}, support = {F32 AI110029/AI/NIAID NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; AI110029/AI/NIAID NIH HHS/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {*Computer Graphics ; Data Interpretation, Statistical ; Humans ; *Metagenome ; Microbiota/*genetics ; *Phylogeny ; *Programming Languages ; Sequence Analysis, DNA/*methods ; *Software ; Web Browser ; }, abstract = {MOTIVATION: We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language.<br><br>phylogeo is documented and freely available http://zachcp.github.io/phylogeo<br><br>CONTACT: : zcharlop@rockefeller.edu.}, }
@article {pmid25903634, year = {2015}, author = {Parker, IM and Saunders, M and Bontrager, M and Weitz, AP and Hendricks, R and Magarey, R and Suiter, K and Gilbert, GS}, title = {Phylogenetic structure and host abundance drive disease pressure in communities.}, journal = {Nature}, volume = {520}, number = {7548}, pages = {542-544}, pmid = {25903634}, issn = {1476-4687}, mesh = {*Biodiversity ; California ; Databases, Factual ; *Grassland ; Introduced Species/trends ; *Phylogeny ; Plant Diseases/*statistics &amp; numerical data ; Plants/*classification ; Population Density ; }, abstract = {Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a 'rare-species advantage'. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species. Here we show that the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure. We found that the amount of tissue lost to disease increased with the relative abundance of a species across a grassland plant community, and that this rare-species advantage had an additional phylogenetic component: disease pressure was stronger on species with many close relatives. We used a global model of pathogen sharing as a function of relatedness between hosts, which provided a robust predictor of relative disease pressure at the local scale. In our grassland, the total amount of disease was most accurately explained not by the abundance of the focal host alone, but by the abundance of all species in the community weighted by their phylogenetic distance to the host. Furthermore, the model strongly predicted observed disease pressure for 44 novel host species we introduced experimentally to our study site, providing evidence for a mechanism to explain why phylogenetically rare species are more likely to become invasive when introduced. Our results demonstrate how the phylogenetic and ecological structure of communities can have a key role in disease dynamics, with implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry.}, }
@article {pmid25898571, year = {2014}, author = {Liu, X and Huang, H and Yang, YF and Wu, HZ}, title = {[Analysis of effect of topographical conditions on content of total alkaloid in Coptidis Rhizoma in Chongqin, China].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {39}, number = {24}, pages = {4748-4753}, pmid = {25898571}, issn = {1001-5302}, mesh = {Alkaloids/*analysis/metabolism ; China ; Coptis/*chemistry ; Ecology ; Environment ; Geographic Information Systems ; Geography ; Plants, Medicinal ; Rhizome/*chemistry ; }, abstract = {To study ecology suitability rank dividing of the total alkaloid content of Coptis Rhizoma for selecting artificial planting base and high-quality industrial raw material in Chongqing province. Based on the investigation of PCB and DEM data of Chongqing province, the relationship between the total alkaloid content in Coptis Rhizoma and topographical conditions was analyzed by statistical analysis. The geographic information systems (GIS)-based assessment and landscape ecological principles were applied to assess eco logy suitability areas of Coptis Rhizoma in Chongqing. slope, aspect and altitude are main topographical factors that affect the content of the total alkaloid content in Coptis Rhizoma The total alkaloid content in Coptis Rhizoma is higher in the lower altitude, shady slope and bigger slope areas. The total alkaloid content is higher in the south areas of Chongqing province and lower in the northeast. Terrain conditions of the southern region of Chongqing are most suitable for The accumulated of total alkaloid Coptis Rhizoma content.}, }
@article {pmid25891686, year = {2015}, author = {Specht, A and Guru, S and Houghton, L and Keniger, L and Driver, P and Ritchie, EG and Lai, K and Treloar, A}, title = {Data management challenges in analysis and synthesis in the ecosystem sciences.}, journal = {The Science of the total environment}, volume = {534}, number = {}, pages = {144-158}, doi = {10.1016/j.scitotenv.2015.03.092}, pmid = {25891686}, issn = {1879-1026}, mesh = {Australia ; Conservation of Natural Resources/*methods ; Database Management Systems ; *Ecology ; Ecosystem ; }, abstract = {Open-data has created an unprecedented opportunity with new challenges for ecosystem scientists. Skills in data management are essential to acquire, manage, publish, access and re-use data. These skills span many disciplines and require trans-disciplinary collaboration. Science synthesis centres support analysis and synthesis through collaborative 'Working Groups' where domain specialists work together to synthesise existing information to provide insight into critical problems. The Australian Centre for Ecological Analysis and Synthesis (ACEAS) served a wide range of stakeholders, from scientists to policy-makers to managers. This paper investigates the level of sophistication in data management in the ecosystem science community through the lens of the ACEAS experience, and identifies the important factors required to enable us to benefit from this new data-world and produce innovative science. ACEAS promoted the analysis and synthesis of data to solve transdisciplinary questions, and promoted the publication of the synthesised data. To do so, it provided support in many of the key skillsets required. Analysis and synthesis in multi-disciplinary and multi-organisational teams, and publishing data were new for most. Data were difficult to discover and access, and to make ready for analysis, largely due to lack of metadata. Data use and publication were hampered by concerns about data ownership and a desire for data citation. A web portal was created to visualise geospatial datasets to maximise data interpretation. By the end of the experience there was a significant increase in appreciation of the importance of a Data Management Plan. It is extremely doubtful that the work would have occurred or data delivered without the support of the Synthesis centre, as few of the participants had the necessary networks or skills. It is argued that participation in the Centre provided an important learning opportunity, and has resulted in improved knowledge and understanding of good data management practices.}, }
@article {pmid25882668, year = {2015}, author = {Rodrigues, L and Calheiros, M and Pereira, C}, title = {The decision of out-of-home placement in residential care after parental neglect: Empirically testing a psychosocial model.}, journal = {Child abuse &amp; neglect}, volume = {49}, number = {}, pages = {35-49}, doi = {10.1016/j.chiabu.2015.03.014}, pmid = {25882668}, issn = {1873-7757}, mesh = {Adult ; Child ; Child Abuse/*prevention &amp; control ; Child Protective Services/*methods ; *Child Welfare ; *Decision Making ; *Decision Support Techniques ; Empirical Research ; Female ; Foster Home Care ; Humans ; Infant ; Male ; Middle Aged ; *Models, Psychological ; Portugal ; Reproducibility of Results ; Social Workers ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Out-of-home placement decisions in residential care are complex, ambiguous and full of uncertainty, especially in cases of parental neglect. Literature on this topic is so far unable to understand and demonstrate the source of errors involved in those decisions and still fails to focus on professional's decision making process. Therefore, this work intends to test a socio-psychological model of decision-making that is a more integrated, dualistic and ecological version of the Theory of Planned Behavior's model. It describes the process through which the decision maker takes into account personal, contextual and social factors of the Decision-Making Ecology in the definition of his/her decision threshold. One hundred and ninety-five professionals from different Children and Youth Protection Units, throughout the Portuguese territory, participated in this online study. After reading a vignette of a (psychological and physical) neglect case toward a one-year-old child, participants were presented with a group of questions that measured worker's assessment of risk, intention, attitude, subjective norm, behavior control and beliefs toward residential care placement decision, as well as worker's behavior experience, emotions and family/child-related-values involved in that decision. A set of structural equation modeling analyses have proven the good fit of the proposed model. The intention to propose a residential care placement decision was determined by cognitive, social, affective, value-laden and experience variables and the perceived risk. Altogether our model explained 61% of professional's decision toward a parental neglect case. The theoretical and practical implications of these results are discussed, namely the importance of raising awareness about the existence of these biased psychosocial determinants.}, }
@article {pmid25880302, year = {2015}, author = {Kushwaha, SK and Manoharan, L and Meerupati, T and Hedlund, K and Ahrén, D}, title = {MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {65}, pmid = {25880302}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; DNA Primers/genetics ; Ecology ; Environment ; *Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; *Software ; Soil/*chemistry ; }, abstract = {BACKGROUND: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families.<br><br>RESULTS: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 400,000 probes that match more than 300,000 [corrected] publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/ .<br><br>CONCLUSION: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.}, }
@article {pmid25864941, year = {2015}, author = {Mahboubi, P and Parkes, M and Stephen, C and Chan, HM}, title = {Using expert informed GIS to locate important marine social-ecological hotspots.}, journal = {Journal of environmental management}, volume = {160}, number = {}, pages = {342-352}, doi = {10.1016/j.jenvman.2015.03.055}, pmid = {25864941}, issn = {1095-8630}, mesh = {*Biodiversity ; British Columbia ; Ecology ; *Geographic Information Systems ; Humans ; *Marine Biology ; }, abstract = {The marine environment provides significant benefits to many local communities. Pressure to develop coastal waterways worldwide creates an urgent need for tools to locate marine spaces that have important social or ecological values, and to quantify their relative importance. The primary objective of this study was to develop, apply and critically assess a tool to identify important social-ecological hotspots in the marine environment. The study was conducted in a typical coastal community in northern British Columbia, Canada. This expert-informed GIS, or xGIS, tool used a survey instrument to draw on the knowledge of local experts from a range of backgrounds with respect to a series of 12 social-ecological value attributes, such as biodiversity, cultural and economic values. We identified approximately 1500 polygons on marine maps and assigned relative values to them using a token distribution exercise. A series of spatial statistical analyses were performed to locate and quantify the relative social-ecological importance of marine spaces and the results were ultimately summarized in a single hotspot map of the entire study area. This study demonstrates the utility of xGIS as a useful tool for stakeholders and environmental managers engaged in the planning and management of marine resources at the local and regional levels.}, }
@article {pmid25863290, year = {2015}, author = {Ramos, AA and Weydmann, A and Cox, CJ and Canário, AV and Serrão, EA and Pearson, GA}, title = {A transcriptome resource for the copepod Calanus glacialis across a range of culture temperatures.}, journal = {Marine genomics}, volume = {23}, number = {}, pages = {27-29}, doi = {10.1016/j.margen.2015.03.014}, pmid = {25863290}, issn = {1876-7478}, mesh = {Animals ; Computational Biology ; Copepoda/*genetics ; Gene Expression Regulation/*physiology ; *Temperature ; *Transcriptome ; }, abstract = {The copepod Calanus glacialis plays a key role in the Arctic pelagic ecosystem. Despite its ecological importance and ongoing climate changes, limited knowledge at the genomic level has hindered the understanding of the molecular processes underlying environmental stress responses and ecological adaptation. Transcriptome data was generated from an experiment with C. glacialis copepodite (CV) subjected to five different temperatures. We obtained a total of 512,352 high-quality 454 pyrosequencing reads, which were assembled into 55,562 contigs distributed in 128 KEGG pathways. Functional analysis revealed numerous genes related to diverse biological functions and processes, including members of all major conserved signaling pathways. Comparative analysis of acclimated individuals to experimental temperatures has provided information about gene variations observed in several pathways (e.g. genes involved in energy, lipid and amino acid metabolism were shown to be down-regulated with increasing temperatures). These mRNA sequence resources will facilitate further studies on genomics and physiology-driven molecular processes in C. glacialis and related species.}, }
@article {pmid25854193, year = {2015}, author = {Rico, A and Van den Brink, PJ}, title = {Evaluating aquatic invertebrate vulnerability to insecticides based on intrinsic sensitivity, biological traits, and toxic mode of action.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {8}, pages = {1907-1917}, doi = {10.1002/etc.3008}, pmid = {25854193}, issn = {1552-8618}, mesh = {Animals ; Arthropods/drug effects/physiology ; Chloride Channels/antagonists &amp; inhibitors/metabolism ; Cholinesterases/chemistry/metabolism ; Databases, Factual ; Ecosystem ; Insecticides/*toxicity ; Invertebrates/*drug effects/physiology ; Linear Models ; Motor Activity/drug effects ; Risk Assessment ; Sodium Channels/chemistry/metabolism ; }, abstract = {In the present study, the authors evaluated the vulnerability of aquatic invertebrates to insecticides based on their intrinsic sensitivity and their population-level recovery potential. The relative sensitivity of invertebrates to 5 different classes of insecticides was calculated at the genus, family, and order levels using the acute toxicity data available in the US Environmental Protection Agency ECOTOX database. Biological trait information was linked to the calculated relative sensitivity to evaluate correlations between traits and sensitivity and to calculate a vulnerability index, which combines intrinsic sensitivity and traits describing the recovery potential of populations partially exposed to insecticides (e.g., voltinism, flying strength, occurrence in drift). The analysis shows that the relative sensitivity of arthropods depends on the insecticide mode of action. Traits such as degree of sclerotization, size, and respiration type showed good correlation to sensitivity and can be used to make predictions for invertebrate taxa without a priori sensitivity knowledge. The vulnerability analysis revealed that some of the Ephemeroptera, Plecoptera, and Trichoptera taxa were vulnerable to all insecticide classes and indicated that particular gastropod and bivalve species were potentially vulnerable. Microcrustaceans (e.g., daphnids, copepods) showed low potential vulnerability, particularly in lentic ecosystems. The methods described in the present study can be used for the selection of focal species to be included as part of ecological scenarios and higher tier risk assessments.}, }
@article {pmid25840699, year = {2015}, author = {Kozak, JP and Bennett, MG and Hayden-Lesmeister, A and Fritz, KA and Nickolotsky, A}, title = {Using Flow-Ecology Relationships to Evaluate Ecosystem Service Trade-Offs and Complementarities in the Nation's Largest River Swamp.}, journal = {Environmental management}, volume = {55}, number = {6}, pages = {1327-1342}, pmid = {25840699}, issn = {1432-1009}, mesh = {Animals ; Brachyura/growth &amp; development ; Decision Support Techniques ; Ecology/*methods ; *Ecosystem ; Fisheries ; Hydrology ; Ictaluridae/growth &amp; development ; Louisiana ; Models, Theoretical ; Principal Component Analysis ; Rivers/*chemistry ; *Water Movements ; *Wetlands ; }, abstract = {Large river systems are inextricably linked with social systems; consequently, management decisions must be made within a given ecological, social, and political framework that often defies objective, technical resolution. Understanding flow-ecology relationships in rivers is necessary to assess potential impacts of management decisions, but translating complex flow-ecology relationships into stakeholder-relevant information remains a struggle. The concept of ecosystem services provides a bridge between flow-ecology relationships and stakeholder-relevant data. Flow-ecology relationships were used to explore complementary and trade-off relationships among 12 ecosystem services and related variables in the Atchafalaya River Basin, Louisiana. Results from Indicators of Hydrologic Alteration were reduced to four management-relevant hydrologic variables using principal components analysis. Multiple regression was used to determine flow-ecology relationships and Pearson correlation coefficients, along with regression results, were used to determine complementary and trade-off relationships among ecosystem services and related variables that were induced by flow. Seven ecosystem service variables had significant flow-ecology relationships for at least one hydrologic variable (R (2) = 0.19-0.64). River transportation and blue crab (Callinectes sapidus) landings exhibited a complementary relationship mediated by flow; whereas transportation and crawfish landings, crawfish landings and crappie (Pomoxis spp.) abundance, and blue crab landings and blue catfish (Ictalurus furcatus) abundance exhibited trade-off relationships. Other trade-off and complementary relationships among ecosystem services and related variables, however, were not related to flow. These results give insight into potential conflicts among stakeholders, can reduce the dimensions of management decisions, and provide initial hypotheses for experimental flow modifications.}, }
@article {pmid25824671, year = {2015}, author = {Belcaid, M and Toonen, RJ}, title = {Demystifying computer science for molecular ecologists.}, journal = {Molecular ecology}, volume = {24}, number = {11}, pages = {2619-2640}, doi = {10.1111/mec.13175}, pmid = {25824671}, issn = {1365-294X}, support = {G12MD00760/MD/NIMHD NIH HHS/United States ; P20GM103516/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Artificial Intelligence ; *Computational Biology ; Computer Literacy ; Ecology/*education ; Programming Languages ; }, abstract = {In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle &amp; Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373-389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated.}, }
@article {pmid25811842, year = {2015}, author = {Visser, MD and McMahon, SM and Merow, C and Dixon, PM and Record, S and Jongejans, E}, title = {Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists.}, journal = {PLoS computational biology}, volume = {11}, number = {3}, pages = {e1004140}, pmid = {25811842}, issn = {1553-7358}, mesh = {Cluster Analysis ; Computational Biology/*methods ; *Computing Methodologies ; Ecology/*methods ; Genetics, Population/*methods ; Humans ; }, abstract = {Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1-S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research.}, }
@article {pmid25810242, year = {2015}, author = {Pollet, TV and Stulp, G and Henzi, SP and Barrett, L}, title = {Taking the aggravation out of data aggregation: A conceptual guide to dealing with statistical issues related to the pooling of individual-level observational data.}, journal = {American journal of primatology}, volume = {77}, number = {7}, pages = {727-740}, doi = {10.1002/ajp.22405}, pmid = {25810242}, issn = {1098-2345}, mesh = {Animals ; Behavior, Animal ; *Bias ; Data Collection/*methods ; *Data Interpretation, Statistical ; Meta-Analysis as Topic ; Models, Statistical ; Papio ; }, abstract = {Field data often include multiple observations taken from the same individual. In order to avoid pseudoreplication, it is commonplace to aggregate data, generating a mean score per individual, and then using these aggregated data in subsequent analyses. Aggregation, however, can generate problems of its own. Not only does it lead to a loss of information, it can also leave analyses vulnerable to the &quot;ecological fallacy&quot;: the drawing of false inferences about individual behavior on the basis of population level (&quot;ecological&quot;) data. It can also result in Simpson's paradox, where relationships seen at the individual level can be completely reversed when analyzed at the aggregate level. These phenomena have been documented widely in the medical and social sciences but tend to go unremarked in primatological studies that rely on observational data from the field. Here, we provide a conceptual guide that explains how and why aggregate data are vulnerable to the ecological fallacy and Simpson's paradox, illustrating these points using data on baboons. We then discuss one particular analytical approach, namely multi-level modeling, that can potentially eliminate these problems. By highlighting the issue of the ecological fallacy, and increasing awareness of how datasets are often organized into a number of different levels, we also highlight the manner in which researchers can more positively exploit the structure of their datasets, without any information loss. These analytical approaches may thus provide greater insight into behavior by permitting more thorough investigation of interactions and cross-level effects.}, }
@article {pmid25808888, year = {2015}, author = {Polansky, L and Kilian, W and Wittemyer, G}, title = {Elucidating the significance of spatial memory on movement decisions by African savannah elephants using state-space models.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1805}, pages = {}, pmid = {25808888}, issn = {1471-2954}, mesh = {Animals ; Decision Making ; Elephants/*physiology ; Female ; Geographic Information Systems ; Hippocampus/physiology ; Male ; Markov Chains ; *Models, Biological ; *Movement ; Namibia ; Seasons ; *Spatial Memory ; }, abstract = {Spatial memory facilitates resource acquisition where resources are patchy, but how it influences movement behaviour of wide-ranging species remains to be resolved. We examined African elephant spatial memory reflected in movement decisions regarding access to perennial waterholes. State-space models of movement data revealed a rapid, highly directional movement behaviour almost exclusively associated with visiting perennial water. Behavioural change point (BCP) analyses demonstrated that these goal-oriented movements were initiated on average 4.59 km, and up to 49.97 km, from the visited waterhole, with the closest waterhole accessed 90% of the time. Distances of decision points increased when switching to different waterholes, during the dry season, or for female groups relative to males, while selection of the closest waterhole decreased when switching. Overall, our analyses indicated detailed spatial knowledge over large scales, enabling elephants to minimize travel distance through highly directional movement when accessing water. We discuss the likely cognitive and socioecological mechanisms driving these spatially precise movements that are most consistent with our findings. By applying modern analytic techniques to high-resolution movement data, this study illustrates emerging approaches for studying how cognition structures animal movement behaviour in different ecological and social contexts.}, }
@article {pmid25803280, year = {2015}, author = {Reeder, TW and Townsend, TM and Mulcahy, DG and Noonan, BP and Wood, PL and Sites, JW and Wiens, JJ}, title = {Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0118199}, pmid = {25803280}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Databases, Factual ; Databases, Genetic ; *Fossils ; Lizards/*classification/genetics ; Phylogeny ; Snakes/*classification/genetics ; }, abstract = {Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.}, }
@article {pmid25796906, year = {2014}, author = {Li, XF and Liu, LM and Qi, X and Zhang, JX and Zhao, TB and Wang, Y and Liu, XF and Zhou, YB}, title = {[Land use change dynamics and driving forces of the vulnerable ecological region in northwestern Shanxi Province, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {25}, number = {10}, pages = {2959-2967}, pmid = {25796906}, issn = {1001-9332}, mesh = {Agriculture ; China ; *Conservation of Natural Resources ; Ecology ; *Ecosystem ; Environmental Restoration and Remediation ; Forests ; Geographic Information Systems ; Grassland ; Industry ; Remote Sensing Technology ; }, abstract = {By using remote sensing and GIS technology, this paper collected land use information of 1980, 1990, 2000 and 2010 and the relevant statistical data, and analyzed the characteristics of land use change and its driving forces in northwestern Shanxi Province, the typical ecological fragile area. The results showed that there were significant changes in land use patterns in the past 30 years. During 1980-1990, 1990-2000 and 2000-2010 periods, the area of farmland decreased continuously, while the areas of grassland and woodland experienced increase-decrease-increase and decrease-increase-decrease patterns of change, respectively. The areas of industrial and resident lands increased continuously, but the water body and unused land decreased. The farmland was mainly transformed to grassland and woodland, and the areas of industrial and resident lands increased from the farmland. The lost area of water body was transformed to grassland and farmland. The decrease of unused land was due to the implementation of ecological engineering and urban ex-panding. In general, the changes of land use types were significantly higher before 2000 than after 2000. The industrial and resident lands, unused land and grassland changed drastically. The relationships between land use types and driving forces indicated that population pressure and economic development led to the changes of industrial land and farmland; policy of forestry ecological engi- neering drove the changes of woodland and grassland; the drought-characterized climate was the major cause inducing the decrease of water area and hindering the restoration of forest.}, }
@article {pmid25774033, year = {2015}, author = {Camacho, A and Trefaut Rodrigues, M and Navas, C}, title = {Extreme operative temperatures are better descriptors of the thermal environment than mean temperatures.}, journal = {Journal of thermal biology}, volume = {49-50}, number = {}, pages = {106-111}, doi = {10.1016/j.jtherbio.2015.02.007}, pmid = {25774033}, issn = {0306-4565}, mesh = {Brazil ; Data Interpretation, Statistical ; *Environment ; *Temperature ; }, abstract = {In ecological studies of thermal biology the thermal environment is most frequently described using the mean or other measures of central tendency in environmental temperatures. However, this procedure may hide biologically relevant thermal variation for ectotherms, potentially misleading interpretations. Extremes of operative temperatures (EOT) can help with this problem by bracketing the thermal environment of focal animals. Within this paper, we quantify how mean operative temperatures relate to the range of simultaneously available operative temperatures (a measure of error). We also show how EOT: 1) detect more thermal differences among microsites than measures of central tendency, like the mean OT, 2) allow inferring on microsite use by ectothermic animals, and 3) clarify the relationships between field operative temperatures and temperatures measured at weather stations (WS). To do that, we explored operative temperatures measured at four sites of the Brazilian Caatingas and their correspondent nearest weather stations. We found that the daily mean OT can hide temperature ranges of 41 °C simultaneously available at our study sites. In addition, EOT detected more thermal differences among microsites than central quantiles. We also show how EOT allow inferring about microsite use of ectothermic animals in a given site. Finally, the daily maximum temperature and the daily temperature range measured at WSs predicted well the minimum available field OT at localities many kilometers away. Based on our results, we recommend the use of EOT, instead of mean OT, in thermal ecology studies.}, }
@article {pmid25772004, year = {2016}, author = {Berninger, JP and LaLone, CA and Villeneuve, DL and Ankley, GT}, title = {Prioritization of pharmaceuticals for potential environmental hazard through leveraging a large-scale mammalian pharmacological dataset.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {4}, pages = {1007-1020}, doi = {10.1002/etc.2965}, pmid = {25772004}, issn = {1552-8618}, mesh = {Animals ; Aquatic Organisms ; *Databases, Factual ; *Drug-Related Side Effects and Adverse Reactions ; Fishes ; Half-Life ; Hazardous Substances/pharmacokinetics/*toxicity ; Humans ; Mammals ; Pharmaceutical Preparations/*metabolism ; Probability ; Risk Assessment ; Species Specificity ; United States ; Water Pollutants, Chemical/pharmacokinetics/*toxicity ; }, abstract = {The potential for pharmaceuticals in the environment to cause adverse ecological effects is of increasing concern. Given the thousands of active pharmaceutical ingredients (APIs) that can enter the aquatic environment through human and/or animal (e.g., livestock) waste, a current challenge in aquatic toxicology is identifying those that pose the greatest risk. Because empirical toxicity information for aquatic species is generally lacking for pharmaceuticals, an important data source for prioritization is that generated during the mammalian drug development process. Applying concepts of species read-across, mammalian pharmacokinetic data were used to systematically prioritize APIs by estimating their potential to cause adverse biological consequences to aquatic organisms, using fish as an example. Mammalian absorption, distribution, metabolism, and excretion (ADME) data (e.g., peak plasma concentration, apparent volume of distribution, clearance rate, and half-life) were collected and curated, creating the Mammalian Pharmacokinetic Prioritization For Aquatic Species Targeting (MaPPFAST) database representing 1070 APIs. From these data, a probabilistic model and scoring system were developed and evaluated. Individual APIs and therapeutic classes were ranked based on clearly defined read-across assumptions for translating mammalian-derived ADME parameters to estimate potential hazard in fish (i.e., greatest predicted hazard associated with lowest mammalian peak plasma concentrations, total clearance and highest volume of distribution, half-life). It is anticipated that the MaPPFAST database and the associated API prioritization approach will help guide research and/or inform ecological risk assessment.}, }
@article {pmid25762112, year = {2015}, author = {Forster, D and Bittner, L and Karkar, S and Dunthorn, M and Romac, S and Audic, S and Lopez, P and Stoeck, T and Bapteste, E}, title = {Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms.}, journal = {BMC biology}, volume = {13}, number = {}, pages = {16}, pmid = {25762112}, issn = {1741-7007}, mesh = {Animal Migration/*physiology ; Animals ; Base Sequence ; Ciliophora/*genetics/physiology ; DNA, Complementary/genetics ; Databases, Genetic ; *Ecosystem ; *Gene Regulatory Networks ; Genetic Variation ; *Geography ; *Models, Biological ; *Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br><br>RESULTS: Our broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals.<br><br>CONCLUSIONS: Currently available 'universal' primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity.}, }
@article {pmid25728598, year = {2015}, author = {Choi, YJ and Beakes, G and Glockling, S and Kruse, J and Nam, B and Nigrelli, L and Ploch, S and Shin, HD and Shivas, RG and Telle, S and Voglmayr, H and Thines, M}, title = {Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci.}, journal = {Molecular ecology resources}, volume = {15}, number = {6}, pages = {1275-1288}, pmid = {25728598}, issn = {1755-0998}, support = {P 22739//Austrian Science Fund FWF/Austria ; }, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Oomycetes/*classification/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.}, }
@article {pmid25682266, year = {2015}, author = {Pert, PL and Ens, EJ and Locke, J and Clarke, PA and Packer, JM and Turpin, G}, title = {An online spatial database of Australian Indigenous Biocultural Knowledge for contemporary natural and cultural resource management.}, journal = {The Science of the total environment}, volume = {534}, number = {}, pages = {110-121}, doi = {10.1016/j.scitotenv.2015.01.073}, pmid = {25682266}, issn = {1879-1026}, mesh = {Australia ; Conservation of Natural Resources/*methods ; *Databases, Factual ; Humans ; *Oceanic Ancestry Group ; }, abstract = {With growing international calls for the enhanced involvement of Indigenous peoples and their biocultural knowledge in managing conservation and the sustainable use of physical environment, it is timely to review the available literature and develop cross-cultural approaches to the management of biocultural resources. Online spatial databases are becoming common tools for educating land managers about Indigenous Biocultural Knowledge (IBK), specifically to raise a broad awareness of issues, identify knowledge gaps and opportunities, and to promote collaboration. Here we describe a novel approach to the application of internet and spatial analysis tools that provide an overview of publically available documented Australian IBK (AIBK) and outline the processes used to develop the online resource. By funding an AIBK working group, the Australian Centre for Ecological Analysis and Synthesis (ACEAS) provided a unique opportunity to bring together cross-cultural, cross-disciplinary and trans-organizational contributors who developed these resources. Without such an intentionally collaborative process, this unique tool would not have been developed. The tool developed through this process is derived from a spatial and temporal literature review, case studies and a compilation of methods, as well as other relevant AIBK papers. The online resource illustrates the depth and breadth of documented IBK and identifies opportunities for further work, partnerships and investment for the benefit of not only Indigenous Australians, but all Australians. The database currently includes links to over 1500 publically available IBK documents, of which 568 are geo-referenced and were mapped. It is anticipated that as awareness of the online resource grows, more documents will be provided through the website to build the database. It is envisaged that this will become a well-used tool, integral to future natural and cultural resource management and maintenance.}, }
@article {pmid25681255, year = {2015}, author = {Konstantinidis, KT and Rosselló-Móra, R}, title = {Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {4}, pages = {223-230}, doi = {10.1016/j.syapm.2015.01.001}, pmid = {25681255}, issn = {1618-0984}, mesh = {*Bacteria/classification/genetics ; *Bacteriological Techniques ; *Computational Biology ; *Metagenomics ; *Single-Cell Analysis ; }, abstract = {Microbial taxonomists have generally been reluctant to accept the valid publication of names of uncultured taxa given that only pure cultures allow for a thorough description of the genealogy, genetics and phenotype of the putative taxa to be classified. The classification of conspicuous uncultured organisms has been considered into the Candidatus provisional status, but this is only possible with organisms for which it is possible to retrieve basic data on phylogeny, morphology, ecology and some metabolic traits that unequivocally identify them. The current developments on modern sequencing techniques, and especially metagenomics, allow the recognition of discrete populations of DNA sequences in environmental samples, which can be considered to belong to individual closely related populations that may be identified as members of yet-to-be described species. The recognition of such populations of (meta)genomes allow the retrieval of valuable taxonomic information, i.e. genealogy, genome, phenotypic coherence with other populations, and ecological relevant traits. Such traits may be included in the Candidatus proposals of environmentally occurring, yet uncultured species not exhibiting exceptional morphologies, phenotypes or ecological relevancies.}, }
@article {pmid25669144, year = {2015}, author = {Campbell, HA and Beyer, HL and Dennis, TE and Dwyer, RG and Forester, JD and Fukuda, Y and Lynch, C and Hindell, MA and Menke, N and Morales, JM and Richardson, C and Rodgers, E and Taylor, G and Watts, ME and Westcott, DA}, title = {Finding our way: On the sharing and reuse of animal telemetry data in Australasia.}, journal = {The Science of the total environment}, volume = {534}, number = {}, pages = {79-84}, doi = {10.1016/j.scitotenv.2015.01.089}, pmid = {25669144}, issn = {1879-1026}, mesh = {Animals ; Australasia ; *Biodiversity ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Telemetry ; }, abstract = {The presence and movements of organisms both reflect and influence the distribution of ecological resources in space and time. The monitoring of animal movement by telemetry devices is being increasingly used to inform management of marine, freshwater and terrestrial ecosystems. Here, we brought together academics, and environmental managers to determine the extent of animal movement research in the Australasian region, and assess the opportunities and challenges in the sharing and reuse of these data. This working group was formed under the Australian Centre for Ecological Analysis and Synthesis (ACEAS), whose overall aim was to facilitate trans-organisational and transdisciplinary synthesis. We discovered that between 2000 and 2012 at least 501 peer-reviewed scientific papers were published that report animal location data collected by telemetry devices from within the Australasian region. Collectively, this involved the capture and electronic tagging of 12 656 animals. The majority of studies were undertaken to address specific management questions; rarely were these data used beyond their original intent. We estimate that approximately half (~500) of all animal telemetry projects undertaken remained unpublished, a similar proportion were not discoverable via online resources, and less than 8.8% of all animals tagged and tracked had their data stored in a discoverable and accessible manner. Animal telemetry data contain a wealth of information about how animals and species interact with each other and the landscapes they inhabit. These data are expensive and difficult to collect and can reduce survivorship of the tagged individuals, which implies an ethical obligation to make the data available to the scientific community. This is the first study to quantify the gap between telemetry devices placed on animals and findings/data published, and presents methods for improvement. Instigation of these strategies will enhance the cost-effectiveness of the research and maximise its impact on the management of natural resources.}, }
@article {pmid25653834, year = {2014}, author = {Strasser, C and Kunze, J and Abrams, S and Cruse, P}, title = {DataUp: A tool to help researchers describe and share tabular data.}, journal = {F1000Research}, volume = {3}, number = {}, pages = {6}, pmid = {25653834}, issn = {2046-1402}, abstract = {Scientific datasets have immeasurable value, but they lose their value over time without proper documentation, long-term storage, and easy discovery and access. Across disciplines as diverse as astronomy, demography, archeology, and ecology, large numbers of small heterogeneous datasets (i.e., the long tail of data) are especially at risk unless they are properly documented, saved, and shared. One unifying factor for many of these at-risk datasets is that they reside in spreadsheets. In response to this need, the California Digital Library (CDL) partnered with Microsoft Research Connections and the Gordon and Betty Moore Foundation to create the DataUp data management tool for Microsoft Excel. Many researchers creating these small, heterogeneous datasets use Excel at some point in their data collection and analysis workflow, so we were interested in developing a data management tool that fits easily into those work flows and minimizes the learning curve for researchers. The DataUp project began in August 2011. We first formally assessed the needs of researchers by conducting surveys and interviews of our target research groups: earth, environmental, and ecological scientists. We found that, on average, researchers had very poor data management practices, were not aware of data centers or metadata standards, and did not understand the benefits of data management or sharing. Based on our survey results, we composed a list of desirable components and requirements and solicited feedback from the community to prioritize potential features of the DataUp tool. These requirements were then relayed to the software developers, and DataUp was successfully launched in October 2012.}, }
@article {pmid25625634, year = {2015}, author = {Hu, X and Hong, W and Qiu, R and Hong, T and Chen, C and Wu, C}, title = {Geographic variations of ecosystem service intensity in Fuzhou City, China.}, journal = {The Science of the total environment}, volume = {512-513}, number = {}, pages = {215-226}, doi = {10.1016/j.scitotenv.2015.01.035}, pmid = {25625634}, issn = {1879-1026}, mesh = {China ; Cities ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; }, abstract = {Ecosystem services are strongly influenced by the landscape configuration of natural and human systems. So they are heterogeneous across landscapes. However lack of the knowledge of spatial variations of ecosystem services constrains the effective management and conservation of ecosystems. We presented a spatially explicit and quantitative assessment of the geographic variations in ecosystem services for the Fuzhou City in 2009 using exploratory spatial data analysis (ESDA) and semivariance analysis. Results confirmed a significant and positive spatial autocorrelation, and revealed several hot-spots and cold-spots for the spatial distribution of ecosystem service intensity (ESI) in the study area. Also the trend surface analysis indicated that the level of ESI tended to be reduced gradually from north to south and from west to east, with a trough in the urban central area, which was quite in accordance with land-use structure. A more precise cluster map was then developed using the range of lag distance, deriving from semivariance analysis, as neighborhood size instead of default value in the software of ESRI ArcGIS 10.0, and geographical clusters where population growth and land-use pressure varied significantly and positively with ESI across the city were also created by geographically weighted regression (GWR). This study has good policy implications applicable to prioritize areas for conservation or construction, and design ecological corridor to improve ecosystem service delivery to benefiting areas.}, }
@article {pmid25591712, year = {2014}, author = {Winder, IC}, title = {The biogeography of the Papio baboons: a GIS-based analysis of range characteristics and variability.}, journal = {Folia primatologica; international journal of primatology}, volume = {85}, number = {5}, pages = {292-318}, doi = {10.1159/000362545}, pmid = {25591712}, issn = {1421-9980}, mesh = {Africa ; *Animal Distribution ; Animals ; *Ecosystem ; Geographic Information Systems ; Papio/*physiology ; }, abstract = {The Papio baboons are known for their ecological flexibility and wide geographic ranges, as well as their uncertain taxonomy. There have, however, been few systematic comparisons of the environments occupied by the 6 major Papio species, and how differences in range conditions and variability might affect their evolutionary ecology remains unknown. This paper uses geographical information system techniques to explore the environmental associations of all 6 major species. It argues that despite some small differences in the average conditions encountered by each, it is in fact variation within individual ranges that is most apparent. In fact, the differences between the environments occupied by adjacent troops in well-known national parks may be as large or larger than the average differences in the ranges of different species, and this may have important implications for baboon biogeography.}, }
@article {pmid25567233, year = {2015}, author = {Molnár, Z and Gellény, K and Margóczi, K and Biró, M}, title = {Landscape ethnoecological knowledge base and management of ecosystem services in a Székely-Hungarian pre-capitalistic village system (Transylvania, Romania).}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {11}, number = {}, pages = {3}, pmid = {25567233}, issn = {1746-4269}, mesh = {Agriculture/*organization &amp; administration ; *Conservation of Natural Resources ; Crops, Agricultural ; *Ecosystem ; Female ; Forests ; Humans ; Hungary ; *Knowledge Bases ; Male ; Romania/ethnology ; Rural Population ; }, abstract = {BACKGROUND: Previous studies showed an in-depth ecological understanding by traditional people of managing natural resources. We studied the landscape ethnoecological knowledge (LEEK) of Székelys on the basis of 16-19(th) century village laws. We analyzed the habitat types, ecosystem services and sustainable management types on which village laws had focused.<br><br>METHODS: Székelys had self-governed communities formed mostly of &quot;noble peasants&quot;. Land-use was dominated by commons and regulated by village laws framed by the whole community. Seventy-two archival laws from 52 villages, resulting in 898 regulations, were analyzed using the DPSIR framework. Explicit and implicit information about the contemporary ecological knowledge of Székelys was extracted. We distinguished between responses that limited use and supported regeneration and those that protected produced/available ecosystem services and ensured their fair distribution.<br><br>RESULTS: Most regulations referred to forests (674), arable lands (562), meadows (448) and pastures (134). Székelys regulated the proportion of arable land, pasture and forest areas consciously in order to maximize long-term exploitation of ecosystem services. The inner territory was protected against overuse by relocating certain uses to the outer territory. Competition for ecosystem services was demonstrated by conflicts of pressure-related (mostly personal) and response-related (mostly communal) driving forces. Felling of trees (oaks), grazing of forests, meadows and fallows, masting, use of wild apple/pear trees and fishing were strictly regulated. Cutting of leaf-fodder, grazing of green crops, burning of forest litter and the polluting of streams were prohibited. Marketing by villagers and inviting outsiders to use the ecosystem services were strictly regulated, and mostly prohibited. Székelys recognized at least 71 folk habitat types, understood ecological regeneration and degradation processes, the history of their landscape and the management possibilities of ecosystem services. Some aspects of LEEK were so well known within Székely communities that they were not made explicit in village laws, others remained implicit because they were not related to regulations.<br><br>CONCLUSIONS: Based on explicit and implicit information, we argue that Székelys possessed detailed knowledge of the local ecological system. Moreover the world's first known explicit mention of ecosystem services (&quot;Benefits that are provided by Nature for free&quot;) originated from this region from 1786.}, }
@article {pmid25559385, year = {2015}, author = {Gryseels, S and Rieger, T and Oestereich, L and Cuypers, B and Borremans, B and Makundi, R and Leirs, H and Günther, S and Goüy de Bellocq, J}, title = {Gairo virus, a novel arenavirus of the widespread Mastomys natalensis: Genetically divergent, but ecologically similar to Lassa and Morogoro viruses.}, journal = {Virology}, volume = {476}, number = {}, pages = {249-256}, doi = {10.1016/j.virol.2014.12.011}, pmid = {25559385}, issn = {1096-0341}, mesh = {Animals ; Antibodies, Viral/immunology ; Arenaviridae Infections/immunology/*veterinary/virology ; Arenavirus/classification/genetics/*isolation &amp; purification ; Disease Reservoirs/virology ; Female ; *Genetic Variation ; Lassa virus/classification/genetics/isolation &amp; purification ; Male ; Molecular Sequence Data ; Murinae/immunology/*virology ; Phylogeny ; Rodent Diseases/immunology/*virology ; Tanzania ; }, abstract = {Despite its near pan-African range, the Natal multimammate mouse, Mastomys natalensis, carries the human pathogen Lassa virus only in West Africa, while the seemingly non-pathogenic arenaviruses Mopeia, Morogoro, and Luna have been detected in this semi-commensal rodent in Mozambique/Zimbabwe, Tanzania and Zambia, respectively. Here, we describe a novel arenavirus in M. natalensis from Gairo district of central Tanzania, for which we propose the name &quot;Gairo virus&quot;. Surprisingly, the virus is not closely related with Morogoro virus that infects M. natalensis only 90km south of Gairo, but clusters phylogenetically with Mobala-like viruses that infect non-M. natalensis host species in Central African Republic and Ethiopia. Despite the evolutionary distance, Gairo virus shares basic ecological features with the other M. natalensis-borne viruses Lassa and Morogoro. Our data show that M. natalensis, carrying distantly related viruses even in the same geographical area, is a potent reservoir host for a variety of arenaviruses.}, }
@article {pmid25551223, year = {2014}, author = {Eriksen, RL and Hierro, JL and Eren, Ö and Andonian, K and Török, K and Becerra, PI and Montesinos, D and Khetsuriani, L and Diaconu, A and Kesseli, R}, title = {Dispersal pathways and genetic differentiation among worldwide populations of the invasive weed Centaurea solstitialis L. (Asteraceae).}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114786}, pmid = {25551223}, issn = {1932-6203}, mesh = {Centaurea/*genetics/*physiology ; Databases, Genetic ; Expressed Sequence Tags/metabolism ; Gene Frequency ; Genetic Loci/genetics ; *Genetic Variation ; *Introduced Species ; Microsatellite Repeats/genetics ; *Plant Dispersal ; Plant Weeds/*genetics/*physiology ; }, abstract = {The natural history of introduced species is often unclear due to a lack of historical records. Even when historical information is readily available, important factors of the invasions such as genetic bottlenecks, hybridization, historical relationships among populations and adaptive changes are left unknown. In this study, we developed a set of nuclear, simple sequence repeat markers and used these to characterize the genetic diversity and population structure among native (Eurasian) and non-native (North and South American) populations of Centaurea solstitialis L., (yellow starthistle). We used these data to test hypotheses about the invasion pathways of the species that were based on historical and geographical records, and we make inferences about historical relationships among populations and demographic processes following invasion. We confirm that the center of diversity and the native range of the species is likely the eastern Mediterranean region in the vicinity of Turkey. From this region, the species likely proceeded to colonize other parts of Europe and Asia via a slow, stepwise range expansion. Spanish populations were the primary source of seed to invade South America via human-mediated events, as was evident from historical records, but populations from the eastern Mediterranean region were also important. North American populations were largely derived from South America, but had secondary contributors. We suggest that the introduction history of non-native populations from disparate parts of the native range have allowed not just one, but multiple opportunities first in South America then again in North America for the creation of novel genotypes via intraspecific hybridization. We propose that multiple intraspecific hybridization events may have created especially potent conditions for the selection of a noxious invader, and may explain differences in genetic patterns among North and South America populations, inferred differences in demographic processes, as well as morphological differences previously reported from common garden experiments.}, }
@article {pmid25500135, year = {2015}, author = {Barros, A and Pickering, C and Gudes, O}, title = {Desktop analysis of potential impacts of visitor use: a case study for the highest park in the Southern Hemisphere.}, journal = {Journal of environmental management}, volume = {150}, number = {}, pages = {179-195}, doi = {10.1016/j.jenvman.2014.11.004}, pmid = {25500135}, issn = {1095-8630}, mesh = {Argentina ; *Biodiversity ; Conservation of Natural Resources ; *Environment ; Geographic Information Systems ; Humans ; Ice Cover ; *Mountaineering ; *Recreation ; }, abstract = {Nature-based tourism and recreation activities have a range of environmental impacts, but most protected area agencies have limited capacity to assess them. To prioritise where and what impacts to monitor and manage, we conducted a desktop assessment using Geographical Information Systems (GIS) by combining recreation ecology research with data on visitor usage and key environmental features for a popular protected area used for mountaineering and trekking, Aconcagua Provincial Park (2400-6962 m a.s.l.) in the Andes of Argentina. First, we integrated visitor data from permits with environmental data using GIS. We then identified key impact indicators for different activities based on the recreation ecology literature. Finally, we integrated this data to identify likely ecological impacts based on the types of activities, amount of use and altitudinal zones. Visitors only used 2% of the Park, but use was concentrated in areas of high conservation value including in alpine meadows and glacier lakes. Impacts on water resources were likely to be concentrated in campsites from the intermediate to the nival/glacial zones of the Park while impacts on terrestrial biodiversity were likely to be more severe in the low and intermediate alpine zones (2400-3800 m a.s.l.). These results highlight how visitor data can be used to identify priority areas for on-ground assessment of impacts in key locations. Improvements to the management of visitors in this Park involves more effective ways of dealing with water extraction and human waste in high altitude campsites and the impacts of hikers and pack animals in the low and intermediate alpine zones.}, }
@article {pmid25470737, year = {2015}, author = {Austin, T and Denoyelle, M and Chaudry, A and Stradling, S and Eadsforth, C}, title = {European Chemicals Agency dossier submissions as an experimental data source: refinement of a fish toxicity model for predicting acute LC50 values.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {2}, pages = {369-378}, doi = {10.1002/etc.2817}, pmid = {25470737}, issn = {1552-8618}, mesh = {Animals ; Cyprinidae/*physiology ; *Databases as Topic ; Ecotoxicology ; Europe ; Inhibitory Concentration 50 ; *Models, Biological ; Oncorhynchus mykiss/*physiology ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; *Toxicity Tests, Acute ; }, abstract = {As a result of the stringent data requirements of the Registration, Evaluation, Authorisation, and Restriction of Chemicals (REACH) regulation, a vast amount of ecotoxicological data has become available through the dissemination portal of the European Chemicals Agency (ECHA). As of April 2014, the database contained 12,439 unique substances from 47,909 dossiers. This vast database could be used to refine existing, or to create new, non-testing methods, such as quantitative structure-activity relationships (QSARs). Acute fish toxicity data were mined from the ECHA database using the eChemPortal; after filtering for single organic substances, 1159 experimental data points remained, representing 564 compounds. To evaluate the quality and accessibility of this data, the authors used the data to refine and improve an existing QSAR. The reliability of the data submitted to the ECHA database, as well as the effectiveness of the Klimisch scoring system, were assessed by comparing the refined QSAR with established QSAR benchmarks. The model developed meets all Organisation for Economic Co-operation and Development principles, has strong internal (leave-one-out internally cross-validated correlation coefficient [Q(2)(LOO)] = 0.91) and external (external coefficient of determination (predicted vs experimental [test set])) validation statistics, and can provide reliable fish median lethal concentration (LC50) predictions for non-polar narcotics. Although some issues with dossier misinformation were discovered, it was found that the ECHA dissemination portal is a valuable and reliable data source. When queried using the eChemPortal, chemical dossiers containing reliable data could be found quickly. The ECHA dissemination portal holds great potential for future QSAR development and improvement, such as updating QSARs within the Ecological Structure-Activity Relationships (ECOSAR) program.}, }
@article {pmid25466378, year = {2014}, author = {Villeneuve, DL and Crump, D and Garcia-Reyero, N and Hecker, M and Hutchinson, TH and LaLone, CA and Landesmann, B and Lettieri, T and Munn, S and Nepelska, M and Ottinger, MA and Vergauwen, L and Whelan, M}, title = {Adverse outcome pathway (AOP) development I: strategies and principles.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {142}, number = {2}, pages = {312-320}, pmid = {25466378}, issn = {1096-0929}, mesh = {Animals ; Biomedical Research/*methods ; *Databases, Factual ; Humans ; *Models, Biological ; Toxicology/*methods ; }, abstract = {An adverse outcome pathway (AOP) is a conceptual framework that organizes existing knowledge concerning biologically plausible, and empirically supported, links between molecular-level perturbation of a biological system and an adverse outcome at a level of biological organization of regulatory relevance. Systematic organization of information into AOP frameworks has potential to improve regulatory decision-making through greater integration and more meaningful use of mechanistic data. However, for the scientific community to collectively develop a useful AOP knowledgebase that encompasses toxicological contexts of concern to human health and ecological risk assessment, it is critical that AOPs be developed in accordance with a consistent set of core principles. Based on the experiences and scientific discourse among a group of AOP practitioners, we propose a set of five fundamental principles that guide AOP development: (1) AOPs are not chemical specific; (2) AOPs are modular and composed of reusable components-notably key events (KEs) and key event relationships (KERs); (3) an individual AOP, composed of a single sequence of KEs and KERs, is a pragmatic unit of AOP development and evaluation; (4) networks composed of multiple AOPs that share common KEs and KERs are likely to be the functional unit of prediction for most real-world scenarios; and (5) AOPs are living documents that will evolve over time as new knowledge is generated. The goal of the present article was to introduce some strategies for AOP development and detail the rationale behind these 5 key principles. Consideration of these principles addresses many of the current uncertainties regarding the AOP framework and its application and is intended to foster greater consistency in AOP development.}, }
@article {pmid25461969, year = {2015}, author = {von Dassow, P and John, U and Ogata, H and Probert, I and Bendif, el M and Kegel, JU and Audic, S and Wincker, P and Da Silva, C and Claverie, JM and Doney, S and Glover, DM and Flores, DM and Herrera, Y and Lescot, M and Garet-Delmas, MJ and de Vargas, C}, title = {Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.}, journal = {The ISME journal}, volume = {9}, number = {6}, pages = {1365-1377}, pmid = {25461969}, issn = {1751-7370}, mesh = {Animals ; Biomass ; Chlorophyll/chemistry ; Computational Biology ; Diploidy ; Ecology ; Flagella/metabolism ; Gene Expression Profiling ; Genetic Markers/genetics ; Genome ; Genomics ; Genotype ; Haptophyta/*genetics ; Life Cycle Stages ; *Oceans and Seas ; Phytoplankton/*genetics ; }, abstract = {Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.}, }
@article {pmid25423027, year = {2015}, author = {Lallias, D and Hiddink, JG and Fonseca, VG and Gaspar, JM and Sung, W and Neill, SP and Barnes, N and Ferrero, T and Hall, N and Lambshead, PJ and Packer, M and Thomas, WK and Creer, S}, title = {Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems.}, journal = {The ISME journal}, volume = {9}, number = {5}, pages = {1208-1221}, pmid = {25423027}, issn = {1751-7370}, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA Barcoding, Taxonomic ; *Ecosystem ; Environmental Monitoring ; *Estuaries ; *Eukaryota ; Geography ; Phenotype ; RNA, Ribosomal, 18S/genetics ; Salinity ; United Kingdom ; Water Microbiology ; }, abstract = {Assessing how natural environmental drivers affect biodiversity underpins our understanding of the relationships between complex biotic and ecological factors in natural ecosystems. Of all ecosystems, anthropogenically important estuaries represent a 'melting pot' of environmental stressors, typified by extreme salinity variations and associated biological complexity. Although existing models attempt to predict macroorganismal diversity over estuarine salinity gradients, attempts to model microbial biodiversity are limited for eukaryotes. Although diatoms commonly feature as bioindicator species, additional microbial eukaryotes represent a huge resource for assessing ecosystem health. Of these, meiofaunal communities may represent the optimal compromise between functional diversity that can be assessed using morphology and phenotype-environment interactions as compared with smaller life fractions. Here, using 454 Roche sequencing of the 18S nSSU barcode we investigate which of the local natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of the estuarine ecosystem. In order to investigate potential variation at the ecosystem scale, we compare two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress. The data show that although community turnover is likely to be predictable, taxa are likely to respond to different environmental drivers and, in particular, hydrodynamics, salinity range and granulometry, according to varied life-history characteristics. At the ecosystem level, communities exhibited patterns of estuary-specific similarity within different salinity range habitats, highlighting the environmental sequencing biomonitoring potential of meiofauna, dispersal effects or both.}, }
@article {pmid25398865, year = {2015}, author = {Gibbons, SM and Schwartz, T and Fouquier, J and Mitchell, M and Sangwan, N and Gilbert, JA and Kelley, ST}, title = {Ecological succession and viability of human-associated microbiota on restroom surfaces.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {2}, pages = {765-773}, pmid = {25398865}, issn = {1098-5336}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; 5T-32EB-009412/EB/NIBIB NIH HHS/United States ; }, mesh = {Bacteria/*classification/*isolation &amp; purification ; *Biota ; *Environmental Microbiology ; Humans ; Microbial Viability ; Viruses/*classification/*isolation &amp; purification ; }, abstract = {Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in four public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late-successional community developed within 5 to 8 h on restroom floors and showed remarkable stability over weeks to months. Despite late-successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivable community, even after several hours of human exclusion. Methicillin-resistant Staphylococcus aureus (MRSA)-associated virulence genes were found on floors but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophages, human papilloma virus, and herpesviruses, were significantly correlated with bacterial abundances and showed an unexpectedly low virus-to-bacterium ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces.}, }
@article {pmid25386926, year = {2014}, author = {Brotons, L}, title = {Species distribution models and impact factor growth in environmental journals: methodological fashion or the attraction of global change science.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e111996}, pmid = {25386926}, issn = {1932-6203}, mesh = {Bibliometrics ; *Climate Change ; Databases, Bibliographic ; *Ecology ; *Environment ; Journal Impact Factor ; *Periodicals as Topic ; *Research ; }, abstract = {In this work, I evaluate the impact of species distribution models (SDMs) on the current status of environmental and ecological journals by asking the question to which degree development of SDMs in the literature is related to recent changes in the impact factors of ecological journals. The hypothesis evaluated states that research fronts are likely to attract research attention and potentially drive citation patterns, with journals concentrating papers related to the research front receiving more attention and benefiting from faster increases in their impact on the ecological literature. My results indicate a positive relationship between the number of SDM related articles published in a journal and its impact factor (IF) growth during the period 2000-09. However, the percentage of SDM related papers in a journal was strongly and positively associated with the percentage of papers on climate change and statistical issues. The results support the hypothesis that global change science has been critical in the development of SDMs and that interest in climate change research in particular, rather than the usage of SDM per se, appears as an important factor behind journal IF increases in ecology and environmental sciences. Finally, our results on SDM application in global change science support the view that scientific interest rather than methodological fashion appears to be the major driver of research attraction in the scientific literature.}, }
@article {pmid25383874, year = {2014}, author = {Blonder, B and Sloat, L and Enquist, BJ and McGill, B}, title = {Separating macroecological pattern and process: comparing ecological, economic, and geological systems.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e112850}, pmid = {25383874}, issn = {1932-6203}, mesh = {*Biodiversity ; Databases, Factual ; Economics ; Ecosystem ; Geology ; Population Dynamics ; }, abstract = {Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions for these patterns despite disparate assumptions. A troubling implication is that these patterns may not reflect anything unique about organizational principles of biology or the functioning of ecological systems. To test this, we analyze five datasets from ecological, economic, and geological systems that describe the distribution of objects across categories in the United States. At the level of functional form ('first-order effects'), these patterns are not unique to ecological systems, indicating they may reveal little about biological process. However, we show that mechanism can be better revealed in the scale-dependency of first-order patterns ('second-order effects'). These results provide a roadmap for biodiversity theory to move beyond traditional patterns, and also suggest ways in which macroecological theory can constrain the dynamics of economic systems.}, }
@article {pmid25375134, year = {2014}, author = {Simental-Rodríguez, SL and Quiñones-Pérez, CZ and Moya, D and Hernández-Tecles, E and López-Sánchez, CA and Wehenkel, C}, title = {The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e111623}, pmid = {25375134}, issn = {1932-6203}, mesh = {Amplified Fragment Length Polymorphism Analysis ; *Biodiversity ; Databases, Genetic ; Evolution, Molecular ; Genetic Drift ; Genetic Variation ; Genome, Plant ; Mexico ; Phylogeny ; Phylogeography ; Picea/*classification/*genetics ; }, abstract = {Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as &quot;Endangered&quot; on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between genetic variants and species diversity may be crucial in shaping tree communities.}, }
@article {pmid25343723, year = {2014}, author = {Beas-Luna, R and Novak, M and Carr, MH and Tinker, MT and Black, A and Caselle, JE and Hoban, M and Malone, D and Iles, A}, title = {An online database for informing ecological network models: http://kelpforest.ucsc.edu.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109356}, pmid = {25343723}, issn = {1932-6203}, mesh = {Databases, Factual ; *Ecosystem ; Humans ; *Internet ; North America ; *Software ; User-Computer Interface ; }, abstract = {Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can provide the life history, demographic and species interaction information necessary to parameterize ecological network models. Faced with the difficulty of synthesizing the information required to construct models for kelp forest ecosystems along the West Coast of North America, we developed an online database (http://kelpforest.ucsc.edu/) to facilitate the collation and dissemination of such information. Many of the database's attributes are novel yet the structure is applicable and adaptable to other ecosystem modeling efforts. Information for each taxonomic unit includes stage-specific life history, demography, and body-size allometries. Species interactions include trophic, competitive, facilitative, and parasitic forms. Each data entry is temporally and spatially explicit. The online data entry interface allows researchers anywhere to contribute and access information. Quality control is facilitated by attributing each entry to unique contributor identities and source citations. The database has proven useful as an archive of species and ecosystem-specific information in the development of several ecological network models, for informing management actions, and for education purposes (e.g., undergraduate and graduate training). To facilitate adaptation of the database by other researches for other ecosystems, the code and technical details on how to customize this database and apply it to other ecosystems are freely available and located at the following link (https://github.com/kelpforest-cameo/databaseui).}, }
@article {pmid25335280, year = {2014}, author = {Kang, CZ and Wang, QQ and Zhou, T and Jiang, WK and Xiao, CH and Xie, Y}, title = {[Study on ecological suitability regionalization of Eucommia ulmoides in Guizhou].}, journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials}, volume = {37}, number = {5}, pages = {760-766}, pmid = {25335280}, issn = {1001-4454}, mesh = {Adaptation, Biological ; China ; Climate ; *Ecology ; Eucommiaceae/chemistry/*growth &amp; development/physiology ; Geographic Information Systems ; *Geography, Medical ; Lignans/analysis ; Models, Theoretical ; Plant Bark/chemistry/growth &amp; development ; Plants, Medicinal/chemistry/*growth &amp; development/physiology ; Soil ; }, abstract = {OBJECTIVE: To study the ecological suitability regionalization of Eucommia ulmoides, for selecting artificial planting base and high-quality industrial raw material purchase area of the herb in Guizhou.<br><br>METHODS: Based on the investigation of 14 Eucommia ulmoides producing areas, pinoresinol diglucoside content and ecological factors were obtained. Using spatial analysis method to carry on ecological suitability regionalization. Meanwhile, combining pinoresinol diglucoside content, the correlation of major active components and environmental factors were analyzed by statistical analysis.<br><br>RESULTS: The most suitability planting area of Eucommia ulmoides was the northwest of Guizhou. The distribution of Eucommia ulmoides was mainly affected by the type and pH value of soil, and monthly precipitation. The spatial structure of major active components in Eucommia ulmoides were randomly distributed in global space, but had only one aggregation point which had a high positive correlation in local space. The major active components of Eucommia ulmoides had no correlation with altitude, longitude or latitude.<br><br>CONCLUSION: Using the spatial analysis method and statistical analysis method, based on environmental factor and pinoresinol diglucoside content, the ecological suitability regionalization of Eucommia ulmoides can provide reference for the selection of suitable planting area, artificial planting base and directing production layout.}, }
@article {pmid25332377, year = {2015}, author = {Beck, D and Dennis, C and Foster, JA}, title = {Seed: a user-friendly tool for exploring and visualizing microbial community data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {4}, pages = {602-603}, pmid = {25332377}, issn = {1367-4811}, support = {F31 GM016448/GM/NIGMS NIH HHS/United States ; P20 GM103408/GM/NIGMS NIH HHS/United States ; P20GM016454/GM/NIGMS NIH HHS/United States ; P20GM16448/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; Computational Biology/*methods ; *Computer Graphics ; *Ecology ; *Software ; }, abstract = {SUMMARY: In this article we present Simple Exploration of Ecological Data (Seed), a data exploration tool for microbial communities. Seed is written in R using the Shiny library. This provides access to powerful R-based functions and libraries through a simple user interface. Seed allows users to explore ecological datasets using principal coordinate analyses, scatter plots, bar plots, hierarchal clustering and heatmaps.<br><br>Seed is open source and available at https://github.com/danlbek/Seed.<br><br>CONTACT: danlbek@gmail.com<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid25299459, year = {2014}, author = {Nzeyimana, I and Hartemink, AE and Geissen, V}, title = {GIS-based multi-criteria analysis for Arabica coffee expansion in Rwanda.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e107449}, doi = {10.1371/journal.pone.0107449}, pmid = {25299459}, issn = {1932-6203}, mesh = {Coffea/*growth &amp; development ; Coffee ; Congo ; Ecology ; Geographic Information Systems ; Rwanda ; Soil ; }, abstract = {The Government of Rwanda is implementing policies to increase the area of Arabica coffee production. Information on the suitable areas for sustainably growing Arabica coffee is still scarce. This study aimed to analyze suitable areas for Arabica coffee production. We analyzed the spatial distribution of actual and potential production zones for Arabica coffee, their productivity levels and predicted potential yields. We used a geographic information system (GIS) for a weighted overlay analysis to assess the major production zones of Arabica coffee and their qualitative productivity indices. Actual coffee yields were measured in the field and were used to assess potential productivity zones and yields using ordinary kriging with ArcGIS software. The production of coffee covers about 32 000 ha, or 2.3% of all cultivated land in the country. The major zones of production are the Kivu Lake Borders, Central Plateau, Eastern Plateau, and Mayaga agro-ecological zones, where coffee is mainly cultivated on moderate slopes. In the highlands, coffee is grown on steep slopes that can exceed 55%. About 21% percent of the country has a moderate yield potential, ranging between 1.0 and 1.6 t coffee ha-1, and 70% has a low yield potential (<1.0 t coffee ha-1). Only 9% of the country has a high yield potential of 1.6-2.4 t coffee ha-1. Those areas are found near Lake Kivu where the dominant soil Orders are Inceptisols and Ultisols. Moderate yield potential is found in the Birunga (volcano), Congo-Nile watershed Divide, Impala and Imbo zones. Low-yield regions (<1 t ha-1) occur in the eastern semi-dry lowlands, Central Plateau, Eastern Plateau, Buberuka Highlands, and Mayaga zones. The weighted overlay analysis and ordinary kriging indicated a large spatial variability of potential productivity indices. Increasing the area and productivity of coffee in Rwanda thus has considerable potential.}, }
@article {pmid25277059, year = {2014}, author = {Stewart, MJ and Favrel, P and Rotgans, BA and Wang, T and Zhao, M and Sohail, M and O'Connor, WA and Elizur, A and Henry, J and Cummins, SF}, title = {Neuropeptides encoded by the genomes of the Akoya pearl oyster Pinctata fucata and Pacific oyster Crassostrea gigas: a bioinformatic and peptidomic survey.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {840}, pmid = {25277059}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Animals ; Crassostrea/*genetics ; Data Mining ; Genome/genetics ; Molecular Sequence Data ; Neuropeptides/chemistry/*genetics ; Pinctada/*genetics/metabolism ; *Proteomics ; }, abstract = {BACKGROUND: Oysters impart significant socio-ecological benefits from primary production of food supply, to estuarine ecosystems via reduction of water column nutrients, plankton and seston biomass. Little though is known at the molecular level of what genes are responsible for how oysters reproduce, filter nutrients, survive stressful physiological events and form reef communities. Neuropeptides represent a diverse class of chemical messengers, instrumental in orchestrating these complex physiological events in other species.<br><br>RESULTS: By a combination of in silico data mining and peptide analysis of ganglia, 74 putative neuropeptide genes were identified from genome and transcriptome databases of the Akoya pearl oyster, Pinctata fucata and the Pacific oyster, Crassostrea gigas, encoding precursors for over 300 predicted bioactive peptide products, including three newly identified neuropeptide precursors PFGx8amide, RxIamide and Wx3Yamide. Our findings also include a gene for the gonadotropin-releasing hormone (GnRH) and two egg-laying hormones (ELH) which were identified from both oysters. Multiple sequence alignments and phylogenetic analysis supports similar global organization of these mature peptides. Computer-based peptide modeling of the molecular tertiary structures of ELH highlights the structural homologies within ELH family, which may facilitate ELH activity leading to the release of gametes.<br><br>CONCLUSION: Our analysis demonstrates that oysters possess conserved molluscan neuropeptide domains and overall precursor organization whilst highlighting many previously unrecognized bivalve idiosyncrasies. This genomic analysis provides a solid foundation from which further studies aimed at the functional characterization of these molluscan neuropeptides can be conducted to further stimulate advances in understanding the ecology and cultivation of oysters.}, }
@article {pmid25262405, year = {2014}, author = {Kiedrzyńska, E and Jóźwik, A and Kiedrzyński, M and Zalewski, M}, title = {Hierarchy of factors exerting an impact on nutrient load of the Baltic Sea and sustainable management of its drainage basin.}, journal = {Marine pollution bulletin}, volume = {88}, number = {1-2}, pages = {162-173}, doi = {10.1016/j.marpolbul.2014.09.010}, pmid = {25262405}, issn = {1879-3363}, mesh = {*Agriculture ; Animals ; Baltic States ; Cattle ; Cluster Analysis ; Conservation of Natural Resources ; *Environment ; Eutrophication ; *Forests ; Humans ; Nitrogen/*analysis ; Oceans and Seas ; Phosphorus/*analysis ; Rivers ; Swine ; Waste Disposal, Fluid ; }, abstract = {The aim of the paper was to evaluate 23 catchment factors that determine total phosphorus and total nitrogen load to the Baltic Sea. Standard correlation analysis and clustering were used. Both phosphorus and nitrogen loads were found to be positively related to the number of pigs and the human population associated with wastewater treatment plants (WWTPs) per km(2), while the number of cattle and agricultural area were found to influence nitrogen rather than phosphorus load, and the area of forests is negatively related to loads of both nutrients. Clustering indicates an overall north-south pattern in the spatial co-occurrence of socio-ecological factors, with some exceptions discussed in the paper. Positive steps in the Baltic Sea region have already been taken, but much remains to be done. The development of coherent response policies to reduce eutrophication in the Baltic Sea should be based on a comprehensive knowledge base, an appropriate information strategy and learning alliance platform in each drainage river catchments.}, }
@article {pmid25258734, year = {2014}, author = {Wang, Y and Li, X and Li, J}, title = {Study on the response of ecological capacity to land-use/cover change in Wuhan city: a remote sensing and GIS based approach.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {794323}, pmid = {25258734}, issn = {1537-744X}, mesh = {Agriculture/trends ; *Algorithms ; China ; Conservation of Natural Resources/*methods/trends ; Ecology/methods/trends ; Ecosystem ; *Geographic Information Systems ; Geography ; Remote Sensing Technology/*methods ; Time Factors ; Urbanization/trends ; }, abstract = {This research examined the spatiotemporal patterns of land-use/cover and the dynamics of ecological capacity in response to land-use/cover change in Wuhan city, central China. The data were derived from five years' remote-sensed images, that is, 1990, 1995, 2000, 2005, and 2010. This paper used an integrated approach of remote sensing and GIS techniques, ecological capacity and the bilateral dynamic degree models. The results are as follows. (1) From 1990 to 2010, remarkable changes in land-use/cover have occurred within the studied area, and the most prominent characteristics of the changes were continuous decline of arable land and rapid increase of built-up land. (2) The total ecological capacity dropped from 450.55 × 10(4) ghm(2) in 1990 to 447.35 × 10(4) ghm(2) in 2010. The eastern, western, and southern parts had higher ecological capacity whereas the northwestern hilly areas and the central district had lower ecological capacity. (3) Due to the conversion from arable land to built-up land, the ecological capacity losses during 1990-1995, 1995-2000, 2000-2005, and 2005-2010 were 155.52 × 10(2) ghm(2), 114.12 × 10(2) ghm(2), 455.48 × 10(2) ghm(2), and 325.26 × 10(2) ghm(2), respectively. The study would contribute to better understanding of the effects of land-use dynamics and the evolution of ecological capacity, which can provide scientific basis for land management and environment protection.}, }
@article {pmid25211603, year = {2014}, author = {Vincenzi, S and Mangel, M and Crivelli, AJ and Munch, S and Skaug, HJ}, title = {Determining individual variation in growth and its implication for life-history and population processes using the empirical Bayes method.}, journal = {PLoS computational biology}, volume = {10}, number = {9}, pages = {e1003828}, pmid = {25211603}, issn = {1553-7358}, mesh = {Animals ; *Bayes Theorem ; Body Size ; Computational Biology/*methods ; *Growth and Development ; *Models, Biological ; Models, Statistical ; Trout/growth &amp; development ; }, abstract = {The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics. Modern statistical and computational methods allow the investigation of individual and shared (among homogeneous groups) determinants of the observed variation in growth. We use an Empirical Bayes approach to estimate individual and shared variation in somatic growth using a von Bertalanffy growth model with random effects. To illustrate the power and generality of the method, we consider two populations of marble trout Salmo marmoratus living in Slovenian streams, where individually tagged fish have been sampled for more than 15 years. We use year-of-birth cohort, population density during the first year of life, and individual random effects as potential predictors of the von Bertalanffy growth function's parameters k (rate of growth) and L∞ (asymptotic size). Our results showed that size ranks were largely maintained throughout marble trout lifetime in both populations. According to the Akaike Information Criterion (AIC), the best models showed different growth patterns for year-of-birth cohorts as well as the existence of substantial individual variation in growth trajectories after accounting for the cohort effect. For both populations, models including density during the first year of life showed that growth tended to decrease with increasing population density early in life. Model validation showed that predictions of individual growth trajectories using the random-effects model were more accurate than predictions based on mean size-at-age of fish.}, }
@article {pmid25209572, year = {2015}, author = {Schmitt, CA and Di Fiore, A}, title = {Predation risk sensitivity and the spatial organization of primate groups: a case study using GIS in lowland Woolly Monkeys (Lagothrix lagotricha poeppigii).}, journal = {American journal of physical anthropology}, volume = {156}, number = {1}, pages = {158-165}, doi = {10.1002/ajpa.22612}, pmid = {25209572}, issn = {1096-8644}, mesh = {Animals ; Atelinae/*physiology ; Female ; Geographic Information Systems ; Male ; Risk ; *Social Behavior ; Spatial Behavior/*physiology ; }, abstract = {Predation risk is thought to be a potent force influencing intragroup cohesion, and the level of risk experienced by an individual is expected to vary with both group size and spatial position within a group. Smaller-bodied and less-experienced individuals are presumed to be more vulnerable to predators, suggesting that within-group spatial organization should show size- and age-dependent patterns in predator sensitive positioning. However, such effects have been difficult to evaluate for arboreal primates living in large groups. We conducted a preliminary study using a novel, spatially explicit method of assessing group spatial organization using GIS data in two groups of wild lowland Woolly monkeys, in which one group had a membership roughly twice as large as the second. In the larger group, group spread was more diffuse and large adult males were more frequently on the outskirts of the group than other age/sex classes, while immatures and females with dependents were more often in the center. Leaf cover around an individual-presumed to index an animal's perception of risk-increased significantly with distance from the group center for all immatures, although they were typically under lower leaf cover than adults; the number of groupmates in proximity also had an effect, but nearest neighbor distance did not. These differences were not detectable in the smaller group. This preliminary study suggests that thorough studies of spatial organization and predation risk sensitivity in arboreal primates are possible and could yield valuable information on how gregarious individuals offset ecological risks through social spacing.}, }
@article {pmid25126580, year = {2014}, author = {Marszalek, J and Morgulec-Adamowicz, N and Rutkowska, I and Kosmol, A}, title = {Using ecological momentary assessment to evaluate current physical activity.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {915172}, pmid = {25126580}, issn = {2314-6141}, mesh = {Adolescent ; Adult ; Child ; *Ecology ; Humans ; MEDLINE ; *Motor Activity ; PubMed ; }, abstract = {OBJECTIVE: The purpose of this study was to assess the value of ecological momentary assessment in evaluating physical activity among children, adolescents, and adults. It also determines whether ecological momentary assessment fulfills the criteria of validity, reliability, objectivity, norms, and standardization applied to the tools used for the evaluation of physical activity.<br><br>METHODS: The EBSCO-CINHAL, Medline, PsycINFO, PubMed, and SPORTDiscuss databases were reviewed in December 2012 for articles associated with EMA.<br><br>RESULTS: Of the 20 articles examined, half (10) used electronic methods for data collection, although various methods were used, ranging from pen and paper to smartphone applications. Ten studies used objective monitoring equipment. Nineteen studies were performed over 4 days. While the validity of the EMA method was discussed in 18 studies, only four found it to be objective. In all cases, the EMA procedures were precisely documented and confirmed to be feasible.<br><br>CONCLUSIONS: Ecological momentary assessment is a valid, reliable, and feasible approach to evaluate activity and sedentary behavior. Researchers should be aware that while ecological momentary assessment offers many benefits, it simultaneously imposes many limitations which should be considered when studying physical activity.}, }
@article {pmid25117551, year = {2014}, author = {Yan, X and Dong, X and Zhang, W and Yin, H and Xiao, H and Chen, P and Ma, XF}, title = {Reference gene selection for quantitative real-time PCR normalization in Reaumuria soongorica.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104124}, pmid = {25117551}, issn = {1932-6203}, mesh = {Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genes, Plant ; RNA Stability ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; Seeds/genetics ; Tamaricaceae/*genetics ; }, abstract = {Despite its superiority for evaluating gene expression, real-time quantitative polymerase chain reaction (qPCR) results can be significantly biased by the use of inappropriate reference genes under different experimental conditions. Reaumuria soongorica is a dominant species of desert ecosystems in arid central Asia. Given the increasing interest in ecological engineering and potential genetic resources for arid agronomy, it is important to analyze gene function. However, systematic evaluation of stable reference genes should be performed prior to such analyses. In this study, the stabilities of 10 candidate reference genes were analyzed under 4 kinds of abiotic stresses (drought, salt, dark, and heat) within 4 accessions (HG010, HG020, XGG030, and XGG040) from 2 different habitats using 3 algorithms (geNorm, NormFinder, and BestKeeper). After validation of the ribulose-1,5-bisphosphate carboxylase/oxygenase large unite (rbcL) expression pattern, our data suggested that histone H2A (H2A) and eukaryotic initiation factor 4A-2 (EIF4A2) were the most stable reference genes, cyclophilin (CYCL) was moderate, and elongation factor 1α (EF1α) was the worst choice. This first systematic analysis for stably expressed genes will facilitate future functional analyses and deep mining of genetic resources in R. soongorica and other species of the Reaumuria genus.}, }
@article {pmid25063050, year = {2015}, author = {Wohlfahrt, G and Tasser, E}, title = {A mobile system for quantifying the spatial variability of the surface energy balance: design and application.}, journal = {International journal of biometeorology}, volume = {59}, number = {5}, pages = {617-627}, pmid = {25063050}, issn = {1432-1254}, mesh = {*Energy Transfer ; Environmental Monitoring/*instrumentation ; Equipment Design ; Equipment Failure Analysis ; Humidity ; Information Storage and Retrieval/methods ; Meteorology/*instrumentation ; Miniaturization ; Radiometry/instrumentation ; Reproducibility of Results ; Sensitivity and Specificity ; Soil/*chemistry ; Surface Properties ; Systems Integration ; Thermography/*instrumentation ; Water/analysis ; *Wind ; }, abstract = {We present a mobile device for the quantification of the small-scale (a few square meters) spatial variability in the surface energy balance components and several auxiliary variables of short-statured (<1 m) canopies. The key element of the mobile device is a handheld four-component net radiometer for the quantification of net radiation, albedo and infrared surface temperature, which is complemented with measurements of air temperature, wind speed, soil temperature and soil water content. Data are acquired by a battery-powered data logger, which is mounted on a backpack together with the auxiliary sensors. The proposed device was developed to bridge between the spatial scales of satellite/airborne remote sensing and fixed, stationary tower-based measurements with an emphasis on micrometeorological, catchment hydrological and landscape-ecological research questions. The potential of the new device is demonstrated through four selected case studies, which cover the issues of net radiation heterogeneity within the footprint of eddy covariance flux measurements due to (1) land use and (2) slope and aspect of the underlying surface, (3) controls on landscape-scale variability in soil temperature and albedo and (4) the estimation of evapotranspiration based exclusively on measurements with the mobile device.}, }
@article {pmid25055119, year = {2014}, author = {Jobstvogt, N and Townsend, M and Witte, U and Hanley, N}, title = {How can we identify and communicate the ecological value of deep-sea ecosystem services?.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e100646}, pmid = {25055119}, issn = {1932-6203}, mesh = {Conservation of Natural Resources/*methods ; Ecology/*methods ; *Ecosystem ; Geographic Information Systems ; Geography ; Humans ; *Oceans and Seas ; Portugal ; Seawater/chemistry ; Water Movements ; }, abstract = {Submarine canyons are considered biodiversity hotspots which have been identified for their important roles in connecting the deep sea with shallower waters. To date, a huge gap exists between the high importance that scientists associate with deep-sea ecosystem services and the communication of this knowledge to decision makers and to the wider public, who remain largely ignorant of the importance of these services. The connectivity and complexity of marine ecosystems makes knowledge transfer very challenging, and new communication tools are necessary to increase understanding of ecological values beyond the science community. We show how the Ecosystem Principles Approach, a method that explains the importance of ocean processes via easily understandable ecological principles, might overcome this challenge for deep-sea ecosystem services. Scientists were asked to help develop a list of clear and concise ecosystem principles for the functioning of submarine canyons through a Delphi process to facilitate future transfers of ecological knowledge. These ecosystem principles describe ecosystem processes, link such processes to ecosystem services, and provide spatial and temporal information on the connectivity between deep and shallow waters. They also elucidate unique characteristics of submarine canyons. Our Ecosystem Principles Approach was successful in integrating ecological information into the ecosystem services assessment process. It therefore has a high potential to be the next step towards a wider implementation of ecological values in marine planning. We believe that successful communication of ecological knowledge is the key to a wider public support for ocean conservation, and that this endeavour has to be driven by scientists in their own interest as major deep-sea stakeholders.}, }
@article {pmid25048896, year = {2014}, author = {Olawoyin, R and Heidrich, B and Oyewole, S and Okareh, OT and McGlothlin, CW}, title = {Chemometric analysis of ecological toxicants in petrochemical and industrial environments.}, journal = {Chemosphere}, volume = {112}, number = {}, pages = {114-119}, doi = {10.1016/j.chemosphere.2014.03.107}, pmid = {25048896}, issn = {1879-1298}, mesh = {*Chemical Industry ; Ecotoxicology/*methods ; Environmental Monitoring/*methods ; Humans ; Informatics/*methods ; Metals, Heavy/analysis ; Nigeria ; Petroleum/*analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Risk Assessment ; Statistics as Topic ; }, abstract = {The application of chemometrics in the assessment of toxicants, such as heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) potentially derived from petrochemical activities in the microenvironment, is vital in providing safeguards for human health of children and adults residing around petrochemical industrial regions. Several multivariate statistical methods are used in geosciences and environmental protection studies to classify, identify and group prevalent pollutants with regard to exhibited trends. Chemometrics can be applied for toxicant source identification, estimation of contaminants contributions to the toxicity of sites of interest, the assessment of the integral risk index of an area and provision of mitigating measures that limit or eliminate the contaminants identified. In this study, the principal component analysis (PCA) was used for dimensionality reduction of both organic and inorganic substances data in the environment, which are potentially hazardous. The high molecular weight (HMW) PAHs correlated positively with stronger impact on the model than the lower molecular weight (LMW) PAHs, the total petroleum hydrocarbons (TPHs), PAHs and BTEX correlate positively in the F1 vs F2 plot indicating similar source contributions of these pollutants in the environmental material. Cu, Cr, Cd, Fe, Zn and Pb all show positive correlation in the same space indicating similar source of contamination. Analytical processes involving environmental assessment data obtained in the Niger Delta area of Nigeria, confirmed the usefulness of chemometrics for comprehensive ecological evaluation.}, }
@article {pmid25046685, year = {2014}, author = {Osborne, CP and Salomaa, A and Kluyver, TA and Visser, V and Kellogg, EA and Morrone, O and Vorontsova, MS and Clayton, WD and Simpson, DA}, title = {A global database of C4 photosynthesis in grasses.}, journal = {The New phytologist}, volume = {204}, number = {3}, pages = {441-446}, doi = {10.1111/nph.12942}, pmid = {25046685}, issn = {1469-8137}, mesh = {Biological Evolution ; *Databases, Factual ; Ecosystem ; Photosynthesis/*physiology ; Poaceae/classification/genetics/*physiology ; }, }
@article {pmid25044053, year = {2014}, author = {Burton, GA and Basu, N and Ellis, BR and Kapo, KE and Entrekin, S and Nadelhoffer, K}, title = {Hydraulic &quot;fracking&quot;: are surface water impacts an ecological concern?.}, journal = {Environmental toxicology and chemistry}, volume = {33}, number = {8}, pages = {1679-1689}, doi = {10.1002/etc.2619}, pmid = {25044053}, issn = {1552-8618}, mesh = {Animals ; Databases, Factual ; Ecology ; Ecosystem ; *Environmental Monitoring ; Groundwater/chemistry ; *Mechanical Phenomena ; Mining/*methods ; *Natural Gas ; North America ; Water/*chemistry ; Water Pollutants, Chemical/analysis ; }, abstract = {Use of high-volume hydraulic fracturing (HVHF) in unconventional reservoirs to recover previously inaccessible oil and natural gas is rapidly expanding in North America and elsewhere. Although hydraulic fracturing has been practiced for decades, the advent of more technologically advanced horizontal drilling coupled with improved slickwater chemical formulations has allowed extensive natural gas and oil deposits to be recovered from shale formations. Millions of liters of local groundwaters are utilized to generate extensive fracture networks within these low-permeability reservoirs, allowing extraction of the trapped hydrocarbons. Although the technology is relatively standardized, the geographies and related policies and regulations guiding these operations vary markedly. Some ecosystems are more at risk from these operations than others because of either their sensitivities or the manner in which the HVHF operations are conducted. Generally, the closer geographical proximity of the susceptible ecosystem to a drilling site or a location of related industrial processes, the higher the risk of that ecosystem being impacted by the operation. The associated construction of roads, power grids, pipelines, well pads, and water-extraction systems along with increased truck traffic are common to virtually all HVHF operations. These operations may result in increased erosion and sedimentation, increased risk to aquatic ecosystems from chemical spills or runoff, habitat fragmentation, loss of stream riparian zones, altered biogeochemical cycling, and reduction of available surface and hyporheic water volumes because of withdrawal-induced lowering of local groundwater levels. The potential risks to surface waters from HVHF operations are similar in many ways to those resulting from agriculture, silviculture, mining, and urban development. Indeed, groundwater extraction associated with agriculture is perhaps a larger concern in the long term in some regions. Understanding the ecological impacts of these anthropogenic activities provides useful information for evaluations of potential HVHF hazards. Geographic information system-based modeling combined with strategic site monitoring has provided insights into the relative importance of these and other ecoregion and land-use factors in discerning potential HVHF impacts. Recent findings suggest that proper siting and operational controls along with strategic monitoring can reduce the potential for risks to aquatic ecosystems. Nevertheless, inadequate data exist to predict ecological risk at this time. The authors suggest considering the plausibility of surface water hazards associated with the various HVHF operations in terms of the ecological context and in the context of relevant anthropogenic activities.}, }
@article {pmid25042415, year = {2015}, author = {Pascual-Aguilar, J and Andreu, V and Gimeno-García, E and Picó, Y}, title = {Current anthropogenic pressures on agro-ecological protected coastal wetlands.}, journal = {The Science of the total environment}, volume = {503-504}, number = {}, pages = {190-199}, doi = {10.1016/j.scitotenv.2014.07.007}, pmid = {25042415}, issn = {1879-1026}, mesh = {Agriculture/*statistics &amp; numerical data ; Cities/*statistics &amp; numerical data ; Conservation of Natural Resources ; Ecology ; *Environmental Monitoring ; Geographic Information Systems ; Geologic Sediments/chemistry ; Spain ; Water Pollutants, Chemical/*analysis ; *Wetlands ; }, abstract = {Coastal wetlands are areas that suffer from great pressure. Much of it is due to the rapid development of the surrounding artificial landscapes, where socio-economic factors lead to alterations in the nearby environment, affecting the quality of natural and agricultural systems. This work analyses interconnections among landscapes under the hypothesis that urban-artificial impacts could be detected on soils and waters of an agro-ecological protected area, L'Albufera de Valencia Natural Park, located in the vicinity of the City of Valencia, Spain. The methodological framework developed addresses two types of anthropogenic pressure: (1) direct, due to artificialisation of soil covers that cause soil sealing, and (2) indirect, which are related to water flows coming from urban populations through sewage and irrigation systems and which, ultimately, will be identified by the presence of emerging pharmaceutical contaminants in waters of the protected area. For soil sealing, a methodology based on temporal comparison of two digital layers for the years 1991 and 2011, applying Geographical Information Systems and landscapes metrics, was applied. To determine presence of emerging contaminants, 21 water samples within the Natural Park were analysed applying liquid chromatography tandem mass spectrometry for the detection of 17 pharmaceutical compounds. Results showed that both processes are present in the Natural Park, with a clear geographical pattern. Soil sealing and presence of pharmaceuticals are more intensive in the northern part of the study area. This is related to population density (detection of pharmaceuticals) and land cover conversion from agricultural and natural surfaces to artificial ones (soil sealing).}, }
@article {pmid25025376, year = {2014}, author = {Russell, JR and Hedley, PE and Cardle, L and Dancey, S and Morris, J and Booth, A and Odee, D and Mwaura, L and Omondi, W and Angaine, P and Machua, J and Muchugi, A and Milne, I and Kindt, R and Jamnadass, R and Dawson, IK}, title = {tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102502}, pmid = {25025376}, issn = {1932-6203}, mesh = {Base Sequence ; Crops, Agricultural/genetics ; Databases, Genetic ; Expressed Sequence Tags ; *Genes, Plant ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Sequence Analysis, DNA ; Trees/*genetics ; }, abstract = {The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.}, }
@article {pmid24923325, year = {2014}, author = {Haq, IU and Graupner, K and Nazir, R and van Elsas, JD}, title = {The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1652-1668}, pmid = {24923325}, issn = {1759-6653}, mesh = {Burkholderia/*genetics ; Computational Biology ; *Evolution, Molecular ; Fungi/*genetics ; Genome, Fungal/*genetics ; Phylogeny ; Sequence Alignment ; *Soil Microbiology ; }, abstract = {Burkholderia terrae strain BS001, obtained as an inhabitant of the mycosphere of Laccaria proxima (a close relative of Lyophyllum sp. strain Karsten), actively interacts with Lyophyllum sp. strain Karsten. We here summarize the remarkable ecological behavior of B. terrae BS001 in the mycosphere and add key data to this. Moreover, we extensively analyze the approximately 11.5-Mb five-replicon genome of B. terrae BS001 and highlight its remarkable features. Seventy-nine regions of genomic plasticity (RGP), that is, 16.48% of the total genome size, were found. One 70.42-kb RGP, RGP76, revealed a typical conjugal element structure, including a full type 4 secretion system. Comparative analyses across 24 related Burkholderia genomes revealed that 95.66% of the total BS001 genome belongs to the variable part, whereas the remaining 4.34% constitutes the core genome. Genes for biofilm formation and several secretion systems, under which a type 3 secretion system (T3SS), were found, which is consistent with the hypothesis that T3SSs play a role in the interaction with Lyophyllum sp. strain Karsten. The high number of predicted metabolic pathways and membrane transporters suggested that strain BS001 can take up and utilize a range of sugars, amino acids and organic acids. In particular, a unique glycerol uptake system was found. The BS001 genome further contains genetic systems for the degradation of complex organic compounds. Moreover, gene clusters encoding nonribosomal peptide synthetases (NRPS) and hybrid polyketide synthases/NRPS were found, highlighting the potential role of secondary metabolites in the ecology of strain BS001. The patchwork of genetic features observed in the genome is consistent with the notion that 1) horizontal gene transfer is a main driver of B. terrae BS001 adaptation and 2) the organism is very flexible in its ecological behavior in soil.}, }
@article {pmid24902875, year = {2015}, author = {Kivelä, M and Arnaud-Haond, S and Saramäki, J}, title = {EDENetworks: a user-friendly software to build and analyse networks in biogeography, ecology and population genetics.}, journal = {Molecular ecology resources}, volume = {15}, number = {1}, pages = {117-122}, doi = {10.1111/1755-0998.12290}, pmid = {24902875}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Ecology/*methods ; Genetics, Population/*methods ; Phylogeography/*methods ; *Software ; }, abstract = {The recent application of graph-based network theory analysis to biogeography, community ecology and population genetics has created a need for user-friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy-to-use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray-Curtis or Sorensen distance, or population genetic metrics such as FST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.}, }
@article {pmid24896260, year = {2014}, author = {Grimm, A and Gruber, B and Henle, K}, title = {Reliability of different mark-recapture methods for population size estimation tested against reference population sizes constructed from field data.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e98840}, pmid = {24896260}, issn = {1932-6203}, mesh = {Datasets as Topic ; Ecology/*methods ; *Models, Theoretical ; *Population Density ; Reproducibility of Results ; }, abstract = {Reliable estimates of population size are fundamental in many ecological studies and biodiversity conservation. Selecting appropriate methods to estimate abundance is often very difficult, especially if data are scarce. Most studies concerning the reliability of different estimators used simulation data based on assumptions about capture variability that do not necessarily reflect conditions in natural populations. Here, we used data from an intensively studied closed population of the arboreal gecko Gehyra variegata to construct reference population sizes for assessing twelve different population size estimators in terms of bias, precision, accuracy, and their 95%-confidence intervals. Two of the reference populations reflect natural biological entities, whereas the other reference populations reflect artificial subsets of the population. Since individual heterogeneity was assumed, we tested modifications of the Lincoln-Petersen estimator, a set of models in programs MARK and CARE-2, and a truncated geometric distribution. Ranking of methods was similar across criteria. Models accounting for individual heterogeneity performed best in all assessment criteria. For populations from heterogeneous habitats without obvious covariates explaining individual heterogeneity, we recommend using the moment estimator or the interpolated jackknife estimator (both implemented in CAPTURE/MARK). If data for capture frequencies are substantial, we recommend the sample coverage or the estimating equation (both models implemented in CARE-2). Depending on the distribution of catchabilities, our proposed multiple Lincoln-Petersen and a truncated geometric distribution obtained comparably good results. The former usually resulted in a minimum population size and the latter can be recommended when there is a long tail of low capture probabilities. Models with covariates and mixture models performed poorly. Our approach identified suitable methods and extended options to evaluate the performance of mark-recapture population size estimators under field conditions, which is essential for selecting an appropriate method and obtaining reliable results in ecology and conservation biology, and thus for sound management.}, }
@article {pmid24883050, year = {2014}, author = {Mitchell, JT and Schick, RS and Hallyburton, M and Dennis, MF and Kollins, SH and Beckham, JC and McClernon, FJ}, title = {Combined ecological momentary assessment and global positioning system tracking to assess smoking behavior: a proof of concept study.}, journal = {Journal of dual diagnosis}, volume = {10}, number = {1}, pages = {19-29}, pmid = {24883050}, issn = {1550-4271}, support = {K24 DA016388/DA/NIDA NIH HHS/United States ; R03 DA029694/DA/NIDA NIH HHS/United States ; R21 DA034471/DA/NIDA NIH HHS/United States ; K23 DA032577/DA/NIDA NIH HHS/United States ; K24 DA023464/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; Attention Deficit Disorder with Hyperactivity/*epidemiology/psychology ; Female ; Geographic Information Systems ; Humans ; Male ; Smoking/*epidemiology/psychology ; }, abstract = {OBJECTIVE: Ecological momentary assessment (EMA) methods have provided a rich assessment of the contextual factors associated with a wide range of behaviors including alcohol use, eating, physical activity, and smoking. Despite this rich database, this information has not been linked to specific locations in space. Such location information, which can now be easily acquired from global positioning system (GPS) tracking devices, could provide unique information regarding the space-time distribution of behaviors and new insights into their determinants. In a proof of concept study, we assessed the acceptability and feasibility of acquiring and combining EMA and GPS data from adult smokers with attention deficit hyperactivity disorder (ADHD).<br><br>METHODS: Participants were adults with ADHD who were enrolled in a larger EMA study on smoking and psychiatric symptoms. Among those enrolled in the latter study who were approached to participate (N = 11), 10 consented, provided daily EMA entries, and carried a GPS device with them during a 7-day assessment period to assess aspects of their smoking behavior.<br><br>RESULTS: The majority of those eligible to participate were willing to carry a GPS device and signed the consent (10 out of 11, 91%). Of the 10 who consented, 7 participants provided EMA entries and carried the GPS device with them daily for at least 70% of the sampling period. Data are presented on the spatial distribution of smoking episodes and ADHD symptoms on a subset of the sample to demonstrate applications of GPS data.<br><br>CONCLUSIONS: We conclude by discussing how EMA and GPS might be used to study the ecology of smoking and make recommendations for future research and analysis.}, }
@article {pmid24845052, year = {2014}, author = {Caira, JN and Jensen, K}, title = {A digest of elasmobranch tapeworms.}, journal = {The Journal of parasitology}, volume = {100}, number = {4}, pages = {373-391}, doi = {10.1645/14-516.1}, pmid = {24845052}, issn = {1937-2345}, mesh = {Animals ; Cestoda/anatomy &amp; histology/*classification/physiology ; Cestode Infections/parasitology/*veterinary ; Databases, Factual ; Elasmobranchii/*parasitology ; Fish Diseases/*parasitology ; Host-Parasite Interactions ; Life Cycle Stages ; }, abstract = {This review brings together decades of work on elasmobranch tapeworms. The field has advanced significantly over the past 20 yr, with an emphasis on the discovery and description of novel taxa, and the establishment of phylogenetic frameworks for individual orders and their interrelationships. Tapeworms parasitizing elasmobranchs represent 9 orders and include 977 species and 201 genera-over 250 species and 50 genera are new within the last 2 decades. The 9 orders are treated individually, highlighting recent assessments of phylogenetic relationships informed by molecular sequence data. All but the &quot;Tetraphyllidea&quot; are monophyletic. Although much remains to be learned about their interrelationships, existing phylogenetic hypotheses suggest that elasmobranch tapeworms have played a key role in the evolution of the cestodes of essentially all other vertebrate groups. The apical organ is a defining feature (i.e., a synapomorphy) of a clade consisting of acetabulate taxa and Litobothriidea. Novel hook amino acid composition data support the independent origin of hooks in the various groups of hooked tapeworms. Cestode records exist for representatives of most of the major groups of elasmobranchs, however skates (Rajiformes) and catsharks (&quot;Scyliorhinidae&quot;) are particularly neglected in terms of species sampled. The majority of tapeworm species are extremely host-specific exhibiting species-specific (i.e., oioxenous) associations with their hosts. Rapid advancements in elasmobranch taxonomy, with over 300 of the 1,200 species appearing new in the past 20 yr, signal the need for careful attention to be paid to host identifications; such identifications are best documented using a combination of specimen, photographic, and molecular data. Above the species level, many cestode taxa are restricted to host orders, families, or even genera. Documentation of these affiliations allows robust predictions to be made regarding the cestode faunas of unexplored elasmobranchs. Trypanorhynchs are the notable exceptions. Life cycles remain poorly known. Recent applications of molecular methods to larval identifications have reinvigorated this area of research. Tapeworms are more diverse in elasmobranchs of tropical and subtropical waters, but they occur globally not only at the poles and in deep waters, but also in freshwaters of South America and Southeast Asia. The cestode faunas of batoids are much more speciose and complex than those of sharks. The faunas of deeper water sharks are particularly depauperate. The tapeworms of elasmobranchs and their hosts are now among the most well documented host-parasite systems in existence. This system has not yet reached its potential as a resource for investigations of basic ecological and evolutionary principles.}, }
@article {pmid24768450, year = {2015}, author = {Ramachandra, TV and Bharath, AH and Sowmyashree, MV}, title = {Monitoring urbanization and its implications in a mega city from space: spatiotemporal patterns and its indicators.}, journal = {Journal of environmental management}, volume = {148}, number = {}, pages = {67-81}, doi = {10.1016/j.jenvman.2014.02.015}, pmid = {24768450}, issn = {1095-8630}, mesh = {*Cities ; *Conservation of Natural Resources ; Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; India ; Spatio-Temporal Analysis ; Urbanization/*trends ; }, abstract = {Rapid and invasive urbanization has been associated with depletion of natural resources (vegetation and water resources), which in turn deteriorates the landscape structure and conditions in the local environment. Rapid increase in population due to the migration from rural areas is one of the critical issues of the urban growth. Urbanisation in India is drastically changing the land cover and often resulting in the sprawl. The sprawl regions often lack basic amenities such as treated water supply, sanitation, etc. This necessitates regular monitoring and understanding of the rate of urban development in order to ensure the sustenance of natural resources .Urban sprawl is the extent of urbanization which leads to the development of urban forms with the destruction of ecology and natural landforms. The rate of change of land use and extent of urban sprawl can be efficiently visualized and modelled with the help of geoinformatics. The knowledge of urban area, especially the growth magnitude, shape geometry, and spatial pattern is essential to understand the growth and characteristics of urbanization process. Urban pattern, shape and growth can be quantified using spatial metrics. This communication quantifies the urbanisation and associated growth pattern in Delhi. Spatial data of four decades were analysed to understand land over and land use dynamics. Further the region was divided into 4 zones and into circles of 1 km incrementing radius to understand and quantify the local spatial changes. Results of the landscape metrics indicate that the urban center was highly aggregated and the outskirts and the buffer regions were in the verge of aggregating urban patches. Shannon's Entropy index clearly depicted the outgrowth of sprawl areas in different zones of Delhi.}, }
@article {pmid24690219, year = {2014}, author = {Kenall, A and Harold, S and Foote, C}, title = {An open future for ecological and evolutionary data?.}, journal = {BMC ecology}, volume = {14}, number = {}, pages = {10}, pmid = {24690219}, issn = {1472-6785}, mesh = {Biological Evolution ; *Databases, Factual ; Ecology ; Editorial Policies ; *Information Dissemination ; *Periodicals as Topic ; Research ; }, abstract = {As part of BioMed Central's open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology.}, }
@article {pmid24675669, year = {2014}, author = {Coverdale, TC and Brisson, CP and Young, EW and Yin, SF and Donnelly, JP and Bertness, MD}, title = {Indirect human impacts reverse centuries of carbon sequestration and salt marsh accretion.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e93296}, pmid = {24675669}, issn = {1932-6203}, mesh = {Animals ; Brachyura/physiology ; Carbon/*chemistry ; Carbon Sequestration/*physiology ; *Conservation of Natural Resources ; Geographic Information Systems ; Humans ; Salinity ; Salts ; Soil ; United States ; Water Movements ; *Wetlands ; }, abstract = {Direct and indirect human impacts on coastal ecosystems have increased over the last several centuries, leading to unprecedented degradation of coastal habitats and loss of ecological services. Here we document a two-century temporal disparity between salt marsh accretion and subsequent loss to indirect human impacts. Field surveys, manipulative experiments and GIS analyses reveal that crab burrowing weakens the marsh peat base and facilitates further burrowing, leading to bank calving, disruption of marsh accretion, and a loss of over two centuries of sequestered carbon from the marsh edge in only three decades. Analogous temporal disparities exist in other systems and are a largely unrecognized obstacle in attaining sustainable ecosystem services in an increasingly human impacted world. In light of the growing threat of indirect impacts worldwide and despite uncertainties in the fate of lost carbon, we suggest that estimates of carbon emissions based only on direct human impacts may significantly underestimate total anthropogenic carbon emissions.}, }
@article {pmid24658631, year = {2014}, author = {Petchey, OL and Fox, JW and Haddon, L}, title = {Imbalance in individual researcher's peer review activities quantified for four British Ecological Society journals, 2003-2010.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92896}, pmid = {24658631}, issn = {1932-6203}, mesh = {Databases, Factual ; Humans ; *Peer Review, Research ; *Periodicals as Topic ; Publishing ; *Research Personnel ; United Kingdom ; }, abstract = {Researchers contribute to the scientific peer review system by providing reviews, and &quot;withdraw&quot; from it by submitting manuscripts that are subsequently reviewed. So far as we are aware, there has been no quantification of the balance of individual's contributions and withdrawals. We compared the number of reviews provided by individual researchers (i.e., their contribution) to the number required by their submissions (i.e. their withdrawals) in a large and anonymised database provided by the British Ecological Society. The database covered the Journal of Ecology, Journal of Animal Ecology, Journal of Applied Ecology, and Functional Ecology from 2003-2010. The majority of researchers (64%) did not have balanced contributions and withdrawals. Depending on assumptions, 12% to 44% contributed more than twice as much as required; 20% to 52% contributed less than half as much as required. Balance, or lack thereof, varied little in relation to the number of years a researcher had been active (reviewing or submitting). Researchers who contributed less than required did not lack the opportunity to review. Researchers who submitted more were more likely to accept invitations to review. These finding suggest overall that peer review of the four analysed journals is not in crisis, but only due to the favourable balance of over- and under-contributing researchers. These findings are limited to the four journals analysed, and therefore cannot include researcher's other peer review activities, which if included might change the proportions reported. Relatively low effort was required to assemble, check, and analyse the data. Broader analyses of individual researcher's peer review activities would contribute to greater quality, efficiency, and fairness in the peer review system.}, }
@article {pmid24640546, year = {2014}, author = {Thorson, JT and Cope, JM and Patrick, WS}, title = {Assessing the quality of life history information in publicly available databases.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {24}, number = {1}, pages = {217-226}, pmid = {24640546}, issn = {1051-0761}, mesh = {Animals ; Bayes Theorem ; Databases, Factual/*standards ; Fishes/*physiology ; Reproduction ; }, abstract = {Single-species life history parameters are central to ecological research and management, including the fields of macro-ecology, fisheries science, and ecosystem modeling. However, there has been little independent evaluation of the precision and accuracy of the life history values in global and publicly available databases. We therefore develop a novel method based on a Bayesian errors-in-variables model that compares database entries with estimates from local experts, and we illustrate this process by assessing the accuracy and precision of entries in FishBase, one of the largest and oldest life history databases. This model distinguishes biases among seven life history parameters, two types of information available in FishBase (i.e., published values and those estimated from other parameters), and two taxa (i.e., bony and cartilaginous fishes) relative to values from regional experts in the United States, while accounting for additional variance caused by sex- and region-specific life history traits. For published values in FishBase, the model identifies a small positive bias in natural mortality and negative bias in maximum age, perhaps caused by unacknowledged mortality caused by fishing. For life history values calculated by FishBase, the model identified large and inconsistent biases. The model also demonstrates greatest precision for body size parameters, decreased precision for values derived from geographically distant populations, and greatest between-sex differences in age at maturity. We recommend that our bias and precision estimates be used in future errors-in-variables models as a prior on measurement errors. This approach is broadly applicable to global databases of life history traits and, if used, will encourage further development and improvements in these databases.}, }
@article {pmid24621524, year = {2014}, author = {Larsson, J and Celepli, N and Ininbergs, K and Dupont, CL and Yooseph, S and Bergman, B and Ekman, M}, title = {Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.}, journal = {The ISME journal}, volume = {8}, number = {9}, pages = {1892-1903}, pmid = {24621524}, issn = {1751-7370}, mesh = {Cyanobacteria/classification/*genetics/isolation &amp; purification ; Genes, Bacterial ; *Multigene Family ; Oceans and Seas ; Phycocyanin/classification/*genetics ; Phycoerythrin/classification/*genetics ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Photoautotrophic picocyanobacteria harvest light via phycobilisomes (PBS) consisting of the pigments phycocyanin (PC) and phycoerythrin (PE), encoded by genes in conserved gene clusters. The presence and arrangement of these gene clusters give picocyanobacteria characteristic light absorption properties and allow the colonization of specific ecological niches. To date, a full understanding of the evolution and distribution of the PBS gene cluster in picocyanobacteria has been hampered by the scarcity of genome sequences from fresh- and brackish water-adapted strains. To remediate this, we analysed genomes assembled from metagenomic samples collected along a natural salinity gradient, and over the course of a growth season, in the Baltic Sea. We found that while PBS gene clusters in picocyanobacteria sampled in marine habitats were highly similar to known references, brackish-adapted genotypes harboured a novel type not seen in previously sequenced genomes. Phylogenetic analyses showed that the novel gene cluster belonged to a clade of uncultivated picocyanobacteria that dominate the brackish Baltic Sea throughout the summer season, but are uncommon in other examined aquatic ecosystems. Further, our data suggest that the PE genes were lost in the ancestor of PC-containing coastal picocyanobacteria and that multiple horizontal gene transfer events have re-introduced PE genes into brackish-adapted strains, including the novel clade discovered here.}, }
@article {pmid24595056, year = {2014}, author = {Walls, RL and Deck, J and Guralnick, R and Baskauf, S and Beaman, R and Blum, S and Bowers, S and Buttigieg, PL and Davies, N and Endresen, D and Gandolfo, MA and Hanner, R and Janning, A and Krishtalka, L and Matsunaga, A and Midford, P and Morrison, N and Ó Tuama, É and Schildhauer, M and Smith, B and Stucky, BJ and Thomer, A and Wieczorek, J and Whitacre, J and Wooley, J}, title = {Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e89606}, pmid = {24595056}, issn = {1932-6203}, support = {U54 HG004028/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biodiversity ; *Knowledge ; *Semantics ; }, abstract = {The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.}, }
@article {pmid24590051, year = {2014}, author = {Xie, H and Yao, G and Wang, P}, title = {Identifying regional key eco-space to maintain ecological security using GIS.}, journal = {International journal of environmental research and public health}, volume = {11}, number = {3}, pages = {2550-2568}, pmid = {24590051}, issn = {1660-4601}, mesh = {China ; Conservation of Natural Resources/*methods ; Ecology/*methods ; *Ecosystem ; *Geographic Information Systems ; }, abstract = {Ecological security and environmental sustainability are the foundations of sustainable development. With the acceleration of urbanization, increasing human activities have promoted greater impacts on the eco-spaces that maintain ecological security. Regional key eco-space has become the primary need to maintain environmental sustainability and can offer society with continued ecosystem services. In this paper, considering the security of water resources, biodiversity conservation, disaster avoidance and protection and natural recreation, an integrated index of eco-space importance was established and a method for identifying key eco-space was created using GIS, with Lanzhou City, China as a case study. The results show that the area of core eco-space in the Lanzhou City is approximately 50,908.7 hm(2), accounting for 40% of the region's total area. These areas mainly consist of geological hazard protection zones and the core zones of regional river systems, wetlands, nature reserves, forest parks and scenic spots. The results of this study provide some guidance for the management of ecological security, ecological restoration and environmental sustainability.}, }
@article {pmid24587149, year = {2014}, author = {Ducatez, S and Lefebvre, L}, title = {Patterns of research effort in birds.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e89955}, pmid = {24587149}, issn = {1932-6203}, mesh = {*Animal Distribution ; Animals ; Birds/*genetics/*physiology ; Databases, Factual ; Geography ; History, 20th Century ; History, 21st Century ; *Phylogeny ; Physiology, Comparative/*methods ; Research/*history ; Research Design/*trends ; Species Specificity ; }, abstract = {Between species differences in research effort can lead to biases in our global view of evolution, ecology and conservation. The increase in meta-taxonomic comparative analyses on birds underlines the need to better address how research effort is distributed in this class. Methods have been developed to choose which species should be studied to obtain unbiased comparative data sets, but a precise and global knowledge of research effort is required to be able to properly apply them. We address this issue by providing a data set of research effort (number of papers from 1978 to 2008 in the Zoological Record database) estimates for the 10,064 species of birds. We then test whether research effort is associated with phylogeny, geography and eleven different life history and ecological traits. We show that phylogeny accounts for a large proportion of the variance, while geographic range and all the tested traits are also significant contributors to research effort variance. We identify avian taxa that are under- and overstudied and address the importance of research effort biases in evaluating vulnerability to extinction, with non-threatened species studied twice as much as threatened ones. Our research effort data set covering the entire class Aves provides a tool for researchers to incorporate this potential confounding variable in comparative analyses.}, }
@article {pmid24586306, year = {2014}, author = {Schweingruber, FH and Ríha, P and Doležal, J}, title = {Variation in stem anatomical characteristics of Campanuloideae species in relation to evolutionary history and ecological preferences.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e88199}, pmid = {24586306}, issn = {1932-6203}, mesh = {Adaptation, Biological/genetics/*physiology ; Bayes Theorem ; *Biological Evolution ; Campanulaceae/*anatomy &amp; histology ; Computational Biology ; *Ecosystem ; Models, Genetic ; *Phylogeny ; Plant Stems/*anatomy &amp; histology ; Species Specificity ; }, abstract = {BACKGROUND: The detailed knowledge of plant anatomical characters and their variation among closely related taxa is key to understanding their evolution and function. We examined anatomical variation in 46 herbaceous taxa from the subfamily Campanuloideae (Campanulaceae) to link this information with their phylogeny, ecology and comparative material of 56 woody tropical taxa from the subfamily Lobelioideae. The species studied covered major environmental gradients from Mediterranean to Arctic zones, allowing us to test hypotheses on the evolution of anatomical structure in relation to plant competitive ability and ecological preferences.<br><br>To understand the evolution of anatomical diversity, we reconstructed the phylogeny of studied species from nucleotide sequences and examined the distribution of anatomical characters on the resulting phylogenetic tree. Redundancy analysis, with phylogenetic corrections, was used to separate the evolutionary inertia from the adaptation to the environment. A large anatomical diversity exists within the Campanuloideae. Traits connected with the quality of fibres were the most congruent with phylogeny, and the Rapunculus 2 (&quot;phyteumoid&quot;) clade was especially distinguished by a number of characters (absence of fibres, pervasive parenchyma, type of rays) from two other clades (Campanula s. str. and Rapunculus 1) characterized by the dominance of fibres and the absence of parenchyma. Septate fibres are an exclusive trait in the Lobelioideae, separating it clearly from the Campanuloideae where annual rings, pervasive parenchyma and crystals in the phellem are characteristic features.<br><br>CONCLUSIONS/SIGNIFICANCE: Despite clear phylogenetic inertia in the anatomical features studied, the ecological attributes and plant height had a significant effect on anatomical divergence. From all three evolutionary clades, the taller species converged towards similar anatomical structure, characterized by a smaller number of early wood vessels of large diameter, thinner cell-walls and alternate intervessel pits, while the opposite trend was found in small Arctic and alpine taxa. This supports the existing generalization that narrower vessels allow plants to grow in colder places where they can avoid freezing-induced embolism, while taller plants have wider vessels to minimize hydraulic resistance with their greater path lengths.}, }
@article {pmid24550506, year = {2014}, author = {Barribeau, SM and Sadd, BM and du Plessis, L and Schmid-Hempel, P}, title = {Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {9}, pages = {3496-3501}, pmid = {24550506}, issn = {1091-6490}, support = {268853//European Research Council/International ; }, mesh = {Analysis of Variance ; Animals ; Base Sequence ; Bees/immunology/*parasitology ; *Biological Evolution ; Computational Biology ; Crithidia/*physiology ; DNA Primers/genetics ; Gene Expression Profiling ; Gene Expression Regulation/genetics/*immunology ; Gene Ontology ; Genotype ; Host-Parasite Interactions/genetics/*immunology ; Molecular Sequence Data ; Sequence Analysis, RNA ; Species Specificity ; Switzerland ; }, abstract = {In many systems, host-parasite evolutionary dynamics have led to the emergence and maintenance of diverse parasite and host genotypes within the same population. Genotypes vary in key attributes: Parasite genotypes vary in ability to infect, host genotypes vary in susceptibility, and infection outcome is frequently the result of both parties' genotypic identities. These host-parasite genotype-by-genotype (GH × GP) interactions influence evolutionary and ecological dynamics in important ways. Interactions can be produced through genetic variation; however, here, we assess the role of variable gene expression as an additional source of GH × GP interactions. The bumblebee Bombus terrestris and its trypanosome gut parasite Crithidia bombi are a model system for host-parasite matching. Full-transcriptome sequencing of the bumblebee host revealed that different parasite genotypes indeed induce fundamentally different host expression responses and host genotypes vary in their responses to the infecting parasite genotype. It appears that broadly and successfully infecting parasite genotypes lead to reduced host immune gene expression relative to unexposed bees but induce the expression of genes responsible for controlling gene expression. Contrastingly, a poorly infecting parasite genotype induced the expression of immunologically important genes, including antimicrobial peptides. A targeted expression assay confirmed the transcriptome results and also revealed strong host genotype effects. In all, the expression of a number of genes depends on the host genotype and the parasite genotype and the interaction between both host and parasite genotypes. These results suggest that alongside sequence variation in coding immunological genes, variation that controls immune gene expression can also produce patterns of host-parasite specificity.}, }
@article {pmid24499424, year = {2014}, author = {Cizauskas, CA and Bellan, SE and Turner, WC and Vance, RE and Getz, WM}, title = {Frequent and seasonally variable sublethal anthrax infections are accompanied by short-lived immunity in an endemic system.}, journal = {The Journal of animal ecology}, volume = {83}, number = {5}, pages = {1078-1090}, pmid = {24499424}, issn = {1365-2656}, support = {R01 GM083863/GM/NIGMS NIH HHS/United States ; GM083863/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptive Immunity ; Animals ; Antelopes/*immunology/*microbiology ; Anthrax/*immunology/*veterinary ; Antibodies, Bacterial/blood ; Elephants/*immunology/*microbiology ; Equidae/*immunology/*microbiology ; *Host-Pathogen Interactions ; Namibia/epidemiology ; *Seasons ; }, abstract = {Few studies have examined host-pathogen interactions in wildlife from an immunological perspective, particularly in the context of seasonal and longitudinal dynamics. In addition, though most ecological immunology studies employ serological antibody assays, endpoint titre determination is usually based on subjective criteria and needs to be made more objective. Despite the fact that anthrax is an ancient and emerging zoonotic infectious disease found world-wide, its natural ecology is not well understood. In particular, little is known about the adaptive immune responses of wild herbivore hosts against Bacillus anthracis. Working in the natural anthrax system of Etosha National Park, Namibia, we collected 154 serum samples from plains zebra (Equus quagga), 21 from springbok (Antidorcas marsupialis) and 45 from African elephants (Loxodonta africana) over 2-3 years, resampling individuals when possible for seasonal and longitudinal comparisons. We used enzyme-linked immunosorbent assays to measure anti-anthrax antibody titres and developed three increasingly conservative models to determine endpoint titres with more rigourous, objective mensuration. Between 52 and 87% of zebra, 0-15% of springbok and 3-52% of elephants had measurable anti-anthrax antibody titres, depending on the model used. While the ability of elephants and springbok to mount anti-anthrax adaptive immune responses is still equivocal, our results indicate that zebra in ENP often survive sublethal anthrax infections, encounter most B. anthracis in the wet season and can partially booster their immunity to B. anthracis. Thus, rather than being solely a lethal disease, anthrax often occurs as a sublethal infection in some susceptible hosts. Though we found that adaptive immunity to anthrax wanes rapidly, subsequent and frequent sublethal B. anthracis infections cause maturation of anti-anthrax immunity. By triggering host immune responses, these common sublethal infections may act as immunomodulators and affect population dynamics through indirect immunological and co-infection effects. In addition, with our three endpoint titre models, we introduce more mensuration rigour into serological antibody assays, even under the often-restrictive conditions that come with adapting laboratory immunology methods to wild systems. With these methods, we identified significantly more zebras responding immunologically to anthrax than have previous studies using less comprehensive titre analyses.}, }
@article {pmid24494694, year = {2014}, author = {Kuester, A and Conner, JK and Culley, T and Baucom, RS}, title = {How weeds emerge: a taxonomic and trait-based examination using United States data.}, journal = {The New phytologist}, volume = {202}, number = {3}, pages = {1055-1068}, pmid = {24494694}, issn = {1469-8137}, mesh = {Adaptation, Physiological ; *Databases as Topic ; Genome Size ; Genome, Plant/genetics ; Herbicide Resistance ; Introduced Species ; Logistic Models ; Phenotype ; Plant Weeds/*classification/genetics/*growth &amp; development ; *Quantitative Trait, Heritable ; Reproduction ; Species Specificity ; United States ; }, abstract = {Weeds can cause great economic and ecological harm to ecosystems. Despite their importance, comparisons of the taxonomy and traits of successful weeds often focus on a few specific comparisons - for example, introduced versus native weeds. We used publicly available inventories of US plant species to make comprehensive comparisons of the factors that underlie weediness. We quantitatively examined taxonomy to determine if certain genera are overrepresented by introduced, weedy or herbicide-resistant species, and we compared phenotypic traits of weeds to those of nonweeds, whether introduced or native. We uncovered genera that have more weeds and introduced species than expected by chance and plant families that have more herbicide-resistant species than expected by chance. Certain traits, generally related to fast reproduction, were more likely to be associated with weedy plants regardless of species' origins. We also found stress tolerance traits associated with either native or introduced weeds compared with native or introduced nonweeds. Weeds and introduced species have significantly smaller genomes than nonweeds and native species. These results support trends for weedy plants reported from other floras, suggest that native and introduced weeds have different stress adaptations, and provide a comprehensive survey of trends across weeds within the USA.}, }
@article {pmid24486469, year = {2014}, author = {Hanewinkel, M and Cullmann, DA and Michiels, HG and Kändler, G}, title = {Converting probabilistic tree species range shift projections into meaningful classes for management.}, journal = {Journal of environmental management}, volume = {134}, number = {}, pages = {153-165}, doi = {10.1016/j.jenvman.2014.01.010}, pmid = {24486469}, issn = {1095-8630}, mesh = {*Algorithms ; *Climate Change ; Decision Making ; Europe ; Fagus ; Humans ; Linear Models ; Models, Theoretical ; Picea ; Trees/*classification ; Uncertainty ; }, abstract = {The paper deals with the management problem how to decide on tree species suitability under changing environmental conditions. It presents an algorithm that classifies the output of a range shift model for major tree species in Europe into multiple classes that can be linked to qualities characterizing the ecological niche of the species. The classes: i) Core distribution area, ii) Extended distribution area, iii) Occasional occurrence area, and iv) No occurrence area are first theoretically developed and then statistically described. The classes are interpreted from an ecological point of view using criteria like population structure, competitive strength, site spectrum and vulnerability to biotic hazards. The functioning of the algorithm is demonstrated using the example of a generalized linear model that was fitted to a pan-European dataset of presence/absence of major tree species with downscaled climate data from a General Circulation Model (GCM). Applications of the algorithm to tree species suitability classification on a European and regional level are shown. The thresholds that are used by the algorithm are precision-based and include Cohen's Kappa. A validation of the algorithm using an independent dataset of the German National Forest Inventory shows good accordance of the statistically derived classes with ecological traits for Norway spruce, while the differentiation especially between core and extended distribution for European beech that is in the centre of its natural range in this area is less accurate. We hypothesize that for species in the core of their range regional factors like forest history superimpose climatic factors. Problems of uncertainty issued from potentially applying a multitude of modelling approaches and/or climate realizations within the range shift model are discussed and a way to deal with the uncertainty by revealing the underlying attitude towards risk of the decision maker is proposed.}, }
@article {pmid24473682, year = {2014}, author = {Nestlerode, JA and Hansen, VD and Teague, A and Harwell, MC}, title = {Application of a three-tier framework to assess ecological condition of Gulf of Mexico coastal wetlands.}, journal = {Environmental monitoring and assessment}, volume = {186}, number = {6}, pages = {3477-3493}, pmid = {24473682}, issn = {1573-2959}, mesh = {Conservation of Natural Resources/legislation &amp; jurisprudence ; Ecology ; Environmental Monitoring/legislation &amp; jurisprudence/*methods ; Geographic Information Systems ; Gulf of Mexico ; Hydrology ; Seawater/chemistry ; Soil/chemistry ; United States ; United States Environmental Protection Agency ; *Wetlands ; }, abstract = {A multi-level coastal wetland assessment strategy was applied to wetlands in the northern Gulf of Mexico (GOM) to evaluate the feasibility of this approach for a broad national scale wetland condition assessment (US Environmental Protection Agency's National Wetlands Condition Assessment). Landscape-scale assessment indicators (tier 1) were developed and applied at the sub-watershed (12-digit hydrologic unit code (HUC)) level within the GOM coastal wetland sample frame with scores calculated using land-use maps and geographic information system. Rapid assessment protocols (tier 2), using a combination of data analysis and field work, evaluated metrics associated with landscape context, hydrology, physical structure, and biological structure. Intensive site monitoring (tier 3) included measures of soil chemistry and composition, water column and pore-water chemistry, and dominant macrophyte community composition and tissue chemistry. Relationships within and among assessment levels were evaluated using multivariate analyses with few significant correlations found. More detailed measures of hydrology, soils, and macrophyte species composition from sites across a known condition gradient, in conjunction with validation of standardized rapid assessment method, may be necessary to fully characterize coastal wetlands across the region.}, }
@article {pmid24473680, year = {2014}, author = {Saranya, KR and Reddy, CS and Rao, PV and Jha, CS}, title = {Decadal time-scale monitoring of forest fires in Similipal Biosphere Reserve, India using remote sensing and GIS.}, journal = {Environmental monitoring and assessment}, volume = {186}, number = {5}, pages = {3283-3296}, pmid = {24473680}, issn = {1573-2959}, mesh = {Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Environmental Monitoring/*methods ; *Fires ; *Geographic Information Systems ; India ; *Remote Sensing Technology ; *Trees ; }, abstract = {Analyzing the spatial extent and distribution of forest fires is essential for sustainable forest resource management. There is no comprehensive data existing on forest fires on a regular basis in Biosphere Reserves of India. The present work have been carried out to locate and estimate the spatial extent of forest burnt areas using Resourcesat-1 data and fire frequency covering decadal fire events (2004-2013) in Similipal Biosphere Reserve. The anomalous quantity of forest burnt area was recorded during 2009 as 1,014.7 km(2). There was inconsistency in the fire susceptibility across the different vegetation types. The spatial analysis of burnt area shows that an area of 34.2 % of dry deciduous forests, followed by tree savannah, shrub savannah, and grasslands affected by fires in 2013. The analysis based on decadal time scale satellite data reveals that an area of 2,175.9 km(2) (59.6 % of total vegetation cover) has been affected by varied rate of frequency of forest fires. Fire density pattern indicates low count of burnt area patches in 2013 estimated at 1,017 and high count at 1,916 in 2004. An estimate of fire risk area over a decade identifies 12.2 km(2) is experiencing an annual fire damage. Summing the fire frequency data across the grids (each 1 km(2)) indicates 1,211 (26 %) grids are having very high disturbance regimes due to repeated fires in all the 10 years, followed by 711 grids in 9 years and 418 in 8 years and 382 in 7 years. The spatial database offers excellent opportunities to understand the ecological impact of fires on biodiversity and is helpful in formulating conservation action plans.}, }
@article {pmid24454840, year = {2014}, author = {Kalwij, JM and Robertson, MP and Ronk, A and Zobel, M and Pärtel, M}, title = {Spatially-explicit estimation of geographical representation in large-scale species distribution datasets.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85306}, pmid = {24454840}, issn = {1932-6203}, mesh = {*Biodiversity ; Datasets as Topic ; Europe ; *Geography ; Plants/*classification ; }, abstract = {Much ecological research relies on existing multispecies distribution datasets. Such datasets, however, can vary considerably in quality, extent, resolution or taxonomic coverage. We provide a framework for a spatially-explicit evaluation of geographical representation within large-scale species distribution datasets, using the comparison of an occurrence atlas with a range atlas dataset as a working example. Specifically, we compared occurrence maps for 3773 taxa from the widely-used Atlas Florae Europaeae (AFE) with digitised range maps for 2049 taxa of the lesser-known Atlas of North European Vascular Plants. We calculated the level of agreement at a 50-km spatial resolution using average latitudinal and longitudinal species range, and area of occupancy. Agreement in species distribution was calculated and mapped using Jaccard similarity index and a reduced major axis (RMA) regression analysis of species richness between the entire atlases (5221 taxa in total) and between co-occurring species (601 taxa). We found no difference in distribution ranges or in the area of occupancy frequency distribution, indicating that atlases were sufficiently overlapping for a valid comparison. The similarity index map showed high levels of agreement for central, western, and northern Europe. The RMA regression confirmed that geographical representation of AFE was low in areas with a sparse data recording history (e.g., Russia, Belarus and the Ukraine). For co-occurring species in south-eastern Europe, however, the Atlas of North European Vascular Plants showed remarkably higher richness estimations. Geographical representation of atlas data can be much more heterogeneous than often assumed. Level of agreement between datasets can be used to evaluate geographical representation within datasets. Merging atlases into a single dataset is worthwhile in spite of methodological differences, and helps to fill gaps in our knowledge of species distribution ranges. Species distribution dataset mergers, such as the one exemplified here, can serve as a baseline towards comprehensive species distribution datasets.}, }
@article {pmid24447661, year = {2014}, author = {Zhang, Z and Sheppard, JK and Swaisgood, RR and Wang, G and Nie, Y and Wei, W and Zhao, N and Wei, F}, title = {Ecological scale and seasonal heterogeneity in the spatial behaviors of giant pandas.}, journal = {Integrative zoology}, volume = {9}, number = {1}, pages = {46-60}, doi = {10.1111/1749-4877.12030}, pmid = {24447661}, issn = {1749-4877}, mesh = {*Altitude ; Animals ; China ; Female ; Geographic Information Systems ; Homing Behavior/*physiology ; Male ; *Seasons ; Spatial Behavior/*physiology ; Telemetry ; Ursidae/*physiology ; }, abstract = {We report on the first study to track the spatial behaviors of wild giant pandas (Ailuropoda melanoleuca) using high-resolution global positioning system (GPS) telemetry. Between 2008 and 2009, 4 pandas (2 male and 2 female) were tracked in Foping Reserve, China for an average of 305 days (± 54.8 SE). Panda home ranges were larger than those of previous very high frequency tracking studies, with a bimodal distribution of space-use and distinct winter and summer centers of activity. Home range sizes were larger in winter than in summer, although there was considerable individual variability. All tracked pandas exhibited individualistic, unoriented and multiphasic movement paths, with a high level of tortuosity within seasonal core habitats and directed, linear, large-scale movements between habitats. Pandas moved from low elevation winter habitats to high elevation (>2000 m) summer habitats in May, when temperatures averaged 17.5 °C (± 0.3 SE), and these large-scale movements took <1 month to complete. The peak in panda mean elevation occurred in Jul, after which they began slow, large-scale movements back to winter habitats that were completed in Nov. An adult female panda made 2 longdistance movements during the mating season. Pandas remain close to rivers and streams during winter, possibly reflecting the elevated water requirements to digest their high-fiber food. Panda movement path tortuosity and first-passage-time as a function of spatial scale indicated a mean peak in habitat search effort and patch use of approximately 700 m. Despite a high degree of spatial overlap between panda home ranges, particularly in winter, we detected neither avoidance nor attraction behavior between conspecifics.}, }
@article {pmid24416350, year = {2014}, author = {Baruch-Mordo, S and Wilson, KR and Lewis, DL and Broderick, J and Mao, JS and Breck, SW}, title = {Stochasticity in natural forage production affects use of urban areas by black bears: implications to management of human-bear conflicts.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85122}, pmid = {24416350}, issn = {1932-6203}, mesh = {Animals ; Colorado ; *Conservation of Natural Resources ; Ecosystem ; Female ; Food ; Geographic Information Systems ; Humans ; Male ; *Models, Statistical ; Population Dynamics ; Reproduction/*physiology ; Stochastic Processes ; Urban Renewal/*statistics &amp; numerical data ; Ursidae/*physiology ; }, abstract = {The rapid expansion of global urban development is increasing opportunities for wildlife to forage and become dependent on anthropogenic resources. Wildlife using urban areas are often perceived dichotomously as urban or not, with some individuals removed in the belief that dependency on anthropogenic resources is irreversible and can lead to increased human-wildlife conflict. For American black bears (Ursus americanus), little is known about the degree of bear urbanization and its ecological mechanisms to guide the management of human-bear conflicts. Using 6 years of GPS location and activity data from bears in Aspen, Colorado, USA, we evaluated the degree of bear urbanization and the factors that best explained its variations. We estimated space use, activity patterns, survival, and reproduction and modeled their relationship with ecological covariates related to bear characteristics and natural food availability. Space use and activity patterns were dependent on natural food availability (good or poor food years), where bears used higher human density areas and became more nocturnal in poor food years. Patterns were reversible, i.e., individuals using urban areas in poor food years used wildland areas in subsequent good food years. While reproductive output was similar across years, survival was lower in poor food years when bears used urban areas to a greater extent. Our findings suggest that bear use of urban areas is reversible and fluctuates with the availability of natural food resources, and that removal of urban individuals in times of food failures has the potential to negatively affect bear populations. Given that under current predictions urbanization is expected to increase by 11% across American black bear range, and that natural food failure years are expected to increase in frequency with global climate change, alternative methods of reducing urban human-bear conflict are required if the goal is to prevent urban areas from becoming population sinks.}, }
@article {pmid24398621, year = {2014}, author = {Christens, BD and Inzeo, PT and Faust, V}, title = {Channeling power across ecological systems: social regularities in community organizing.}, journal = {American journal of community psychology}, volume = {53}, number = {3-4}, pages = {419-431}, doi = {10.1007/s10464-013-9620-4}, pmid = {24398621}, issn = {1573-2770}, mesh = {Community Networks/*organization &amp; administration ; Humans ; *Interpersonal Relations ; Organizational Case Studies ; *Power (Psychology) ; Wisconsin ; }, abstract = {Relational and social network perspectives provide opportunities for more holistic conceptualizations of phenomena of interest in community psychology, including power and empowerment. In this article, we apply these tools to build on multilevel frameworks of empowerment by proposing that networks of relationships between individuals constitute the connective spaces between ecological systems. Drawing on an example of a model for grassroots community organizing practiced by WISDOM—a statewide federation supporting local community organizing initiatives in Wisconsin—we identify social regularities (i.e., relational and temporal patterns) that promote empowerment and the development and exercise of social power through building and altering relational ties. Through an emphasis on listening-focused one-to-one meetings, reflection, and social analysis, WISDOM organizing initiatives construct and reinforce social regularities that develop social power in the organizing initiatives and advance psychological empowerment among participant leaders in organizing. These patterns are established by organizationally driven brokerage and mobilization of interpersonal ties, some of which span ecological systems.Hence, elements of these power-focused social regularities can be conceptualized as cross-system channels through which micro-level empowerment processes feed into macro-level exercise of social power, and vice versa. We describe examples of these channels in action, and offer recommendations for theory and design of future action research [corrected] .}, }
@article {pmid24391791, year = {2013}, author = {Peng, G and Bing, W and Guangpo, G and Guangcan, Z}, title = {Spatial distribution of soil organic carbon and total nitrogen based on GIS and geostatistics in a small watershed in a hilly area of northern China.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83592}, pmid = {24391791}, issn = {1932-6203}, mesh = {Carbon/*analysis ; Carbon Cycle ; China ; Climate Change ; Environmental Monitoring ; Geographic Information Systems ; Groundwater ; Nitrogen/*analysis ; Regression Analysis ; Soil/*chemistry ; Spatial Analysis ; }, abstract = {The spatial variability of soil organic carbon (SOC) and total nitrogen (STN) levels is important in both global carbon-nitrogen cycle and climate change research. There has been little research on the spatial distribution of SOC and STN at the watershed scale based on geographic information systems (GIS) and geostatistics. Ninety-seven soil samples taken at depths of 0-20 cm were collected during October 2010 and 2011 from the Matiyu small watershed (4.2 km(2)) of a hilly area in Shandong Province, northern China. The impacts of different land use types, elevation, vegetation coverage and other factors on SOC and STN spatial distributions were examined using GIS and a geostatistical method, regression-kriging. The results show that the concentration variations of SOC and STN in the Matiyu small watershed were moderate variation based on the mean, median, minimum and maximum, and the coefficients of variation (CV). Residual values of SOC and STN had moderate spatial autocorrelations, and the Nugget/Sill were 0.2% and 0.1%, respectively. Distribution maps of regression-kriging revealed that both SOC and STN concentrations in the Matiyu watershed decreased from southeast to northwest. This result was similar to the watershed DEM trend and significantly correlated with land use type, elevation and aspect. SOC and STN predictions with the regression-kriging method were more accurate than those obtained using ordinary kriging. This research indicates that geostatistical characteristics of SOC and STN concentrations in the watershed were closely related to both land-use type and spatial topographic structure and that regression-kriging is suitable for investigating the spatial distributions of SOC and STN in the complex topography of the watershed.}, }
@article {pmid24378926, year = {2014}, author = {van Dijk, A and Mount, R and Gibbons, P and Vardon, M and Canadell, P}, title = {Environmental reporting and accounting in Australia: progress, prospects and research priorities.}, journal = {The Science of the total environment}, volume = {473-474}, number = {}, pages = {338-349}, doi = {10.1016/j.scitotenv.2013.12.053}, pmid = {24378926}, issn = {1879-1026}, mesh = {Australia ; *Conservation of Natural Resources ; Data Collection ; Environmental Monitoring/*methods/standards ; }, abstract = {Despite strong demand for information to support the sustainable use of Australia's natural resources and conserve environmental values and despite considerable effort and investment, nation-wide environmental data collection and analysis remains a substantially unmet challenge. We review progress in producing national environmental reports and accounts, identify challenges and opportunities, and analyse the potential role of research in addressing these. Australia's low and concentrated population density and the short history since European settlement contribute to the lack of environmental data. There are additional factors: highly diverse data requirements and standards, disagreement on information priorities, poorly measurable management objectives, lack of coordination, over-reliance on researchers and businesses for data collection, lack of business engagement, and short-term, project-based activities. New opportunities have arisen to overcome some of these challenges: enhanced monitoring networks, standardisation, data management and modelling, greater commitment to share and integrate data, community monitoring, increasing acceptance of environmental and sustainability indicators, and progress in environmental accounting practices. Successes in generating climate, water and greenhouse gas information appear to be attributable to an unambiguous data requirement, considerable investment, and legislative instruments that enhance data sharing and create a clearly defined role for operational agencies. Based on the analysis presented, we suggest six priorities for research: (1) common definitions and standards for information that address management objectives, (2) ecological measures that are scalable from local to national level, (3) promotion of long-term data collection and reporting by researchers, (4) efficient satellite and sensor network technologies and data analysis methods, (5) environmental modelling approaches that can reconcile multiple data sources, and (6) experimental accounting to pursue consistent, credible and relevant information structures and to identify new data requirements. Opportunities exist to make progress in each of these areas and help secure a more sustainable future.}, }
@article {pmid25977753, year = {2014}, author = {Ahmed, Z and Zeeshan, S and Fleischmann, P and Rössler, W and Dandekar, T}, title = {Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies.}, journal = {F1000Research}, volume = {3}, number = {}, pages = {311}, pmid = {25977753}, issn = {2046-1402}, abstract = {Field studies on arthropod ecology and behaviour require simple and robust monitoring tools, preferably with direct access to an integrated database. We have developed and here present a database tool allowing smart-phone based monitoring of arthropods. This smart phone application provides an easy solution to collect, manage and process the data in the field which has been a very difficult task for field biologists using traditional methods. To monitor our example species, the desert ant Cataglyphis fortis, we considered behavior, nest search runs, feeding habits and path segmentations including detailed information on solar position and azimuth calculation, ant orientation and time of day. For this we established a user friendly database system integrating the Ant-App-DB with a smart phone and tablet application, combining experimental data manipulation with data management and providing solar position and timing estimations without any GPS or GIS system. Moreover, the new desktop application Dataplus allows efficient data extraction and conversion from smart phone application to personal computers, for further ecological data analysis and sharing. All features, software code and database as well as Dataplus application are made available completely free of charge and sufficiently generic to be easily adapted to other field monitoring studies on arthropods or other migratory organisms. The software applications Ant-App-DB and Dataplus described here are developed using the Android SDK, Java, XML, C# and SQLite Database.}, }
@article {pmid24284892, year = {2014}, author = {Cazelles, B and Cazelles, K and Chavez, M}, title = {Wavelet analysis in ecology and epidemiology: impact of statistical tests.}, journal = {Journal of the Royal Society, Interface}, volume = {11}, number = {91}, pages = {20130585}, pmid = {24284892}, issn = {1742-5662}, mesh = {Algorithms ; Data Interpretation, Statistical ; Dengue/epidemiology ; *Ecology ; *Epidemiology ; Fourier Analysis ; Humans ; Markov Chains ; Models, Statistical ; Normal Distribution ; Thailand/epidemiology ; Time Factors ; *Wavelet Analysis ; }, abstract = {Wavelet analysis is now frequently used to extract information from ecological and epidemiological time series. Statistical hypothesis tests are conducted on associated wavelet quantities to assess the likelihood that they are due to a random process. Such random processes represent null models and are generally based on synthetic data that share some statistical characteristics with the original time series. This allows the comparison of null statistics with those obtained from original time series. When creating synthetic datasets, different techniques of resampling result in different characteristics shared by the synthetic time series. Therefore, it becomes crucial to consider the impact of the resampling method on the results. We have addressed this point by comparing seven different statistical testing methods applied with different real and simulated data. Our results show that statistical assessment of periodic patterns is strongly affected by the choice of the resampling method, so two different resampling techniques could lead to two different conclusions about the same time series. Moreover, our results clearly show the inadequacy of resampling series generated by white noise and red noise that are nevertheless the methods currently used in the wide majority of wavelets applications. Our results highlight that the characteristics of a time series, namely its Fourier spectrum and autocorrelation, are important to consider when choosing the resampling technique. Results suggest that data-driven resampling methods should be used such as the hidden Markov model algorithm and the 'beta-surrogate' method.}, }
@article {pmid24214839, year = {2014}, author = {Awkerman, JA and Raimondo, S and Jackson, CR and Barron, MG}, title = {Augmenting aquatic species sensitivity distributions with interspecies toxicity estimation models.}, journal = {Environmental toxicology and chemistry}, volume = {33}, number = {3}, pages = {688-695}, doi = {10.1002/etc.2456}, pmid = {24214839}, issn = {1552-8618}, mesh = {Aquatic Organisms/*drug effects ; Databases, Factual ; *Models, Biological ; Models, Statistical ; Risk Assessment ; Species Specificity ; Uncertainty ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Species sensitivity distributions (SSDs) are cumulative distribution functions of species toxicity values. The SSD approach is being used increasingly in ecological risk assessment but is often limited by available toxicity data needed for diverse species representation. In the present study, the authors evaluate augmenting aquatic species databases limited to standard test species using toxicity values extrapolated from interspecies correlation estimation (ICE) models for SSD development. The authors compared hazard concentrations at the 5th centile (HC5) of SSDs developed using limited measured data augmented with ICE toxicity values (augmented SSDs) with those estimated using larger measured toxicity datasets of diverse species (reference SSDs). When SSDs had similar species composition to the reference SSDs, 0.76 of the HC5 estimates were closer to the reference HC5; however, the proportion of augmented HC5s that were within 5-fold of the reference HC5s was 0.94, compared with 0.96 when predicted SSDs had random species assemblages. The range of toxicity values among represented species in all SSDs also depended on a chemical's mode of action. Predicted HC5 estimations for acetylcholinesterase inhibitors showed the greatest discrepancies from the reference HC5 when SSDs were limited to commonly tested species. The results of the present study indicate that ICE models used to augment datasets for SSDs do not greatly affect HC5 uncertainty. Uncertainty analysis of risk assessments using SSD hazard concentrations should address species composition, especially for chemicals with known taxa-specific differences in toxicological effects. This article is a US Government work and is in the public domain in the USA.}, }
@article {pmid24115604, year = {2013}, author = {Liberles, DA and Teufel, AI and Liu, L and Stadler, T}, title = {On the need for mechanistic models in computational genomics and metagenomics.}, journal = {Genome biology and evolution}, volume = {5}, number = {10}, pages = {2008-2018}, pmid = {24115604}, issn = {1759-6653}, mesh = {Bacteria/genetics ; *Computational Biology ; DNA-Binding Proteins/*genetics ; Ecology ; *Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation ; Gene Regulatory Networks/genetics ; *Metagenomics ; Models, Theoretical ; }, abstract = {Computational genomics is now generating very large volumes of data that have the potential to be used to address important questions in both basic biology and biomedicine. Addressing these important biological questions becomes possible when mechanistic models rooted in biochemistry and evolutionary/population genetic processes are developed, instead of fitting data to off-the-shelf statistical distributions that do not enable mechanistic inference. Three examples are presented, the first involving ecological processes inferred from metagenomic data, the second involving mechanisms of gene regulation rooted in protein-DNA interactions with consideration of DNA structure, and the third involving existing models for the retention of duplicate genes that enables prediction of evolutionary mechanisms. This description of mechanistic models is generalized toward future developments in computational genomics and the need for biological mechanisms and processes in biological models.}, }
@article {pmid24112409, year = {2013}, author = {Kõljalg, U and Nilsson, RH and Abarenkov, K and Tedersoo, L and Taylor, AF and Bahram, M and Bates, ST and Bruns, TD and Bengtsson-Palme, J and Callaghan, TM and Douglas, B and Drenkhan, T and Eberhardt, U and Dueñas, M and Grebenc, T and Griffith, GW and Hartmann, M and Kirk, PM and Kohout, P and Larsson, E and Lindahl, BD and Lücking, R and Martín, MP and Matheny, PB and Nguyen, NH and Niskanen, T and Oja, J and Peay, KG and Peintner, U and Peterson, M and Põldmaa, K and Saag, L and Saar, I and Schüßler, A and Scott, JA and Senés, C and Smith, ME and Suija, A and Taylor, DL and Telleria, MT and Weiss, M and Larsson, KH}, title = {Towards a unified paradigm for sequence-based identification of fungi.}, journal = {Molecular ecology}, volume = {22}, number = {21}, pages = {5271-5277}, doi = {10.1111/mec.12481}, pmid = {24112409}, issn = {1365-294X}, mesh = {DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Databases, Nucleic Acid ; Fungi/*classification/genetics ; Internet ; *Phylogeny ; }, abstract = {The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.}, }
@article {pmid24102517, year = {2014}, author = {Loozen, G and Ozcelik, O and Boon, N and De Mol, A and Schoen, C and Quirynen, M and Teughels, W}, title = {Inter-bacterial correlations in subgingival biofilms: a large-scale survey.}, journal = {Journal of clinical periodontology}, volume = {41}, number = {1}, pages = {1-10}, doi = {10.1111/jcpe.12167}, pmid = {24102517}, issn = {1600-051X}, mesh = {Antibiosis/physiology ; Bacteria/*classification/isolation &amp; purification ; Bacterial Load ; Bacteroides/isolation &amp; purification ; *Biofilms ; Cross-Sectional Studies ; Databases as Topic ; Dental Plaque/*microbiology ; Eubacterium/isolation &amp; purification ; Gingiva/*microbiology ; Humans ; Microbial Interactions ; Periodontal Pocket/classification/*microbiology ; Periodontitis/classification/*microbiology ; Porphyromonas/isolation &amp; purification ; Porphyromonas gingivalis/isolation &amp; purification ; Prevotella intermedia/isolation &amp; purification ; Retrospective Studies ; Streptococcus/isolation &amp; purification ; Treponema denticola/isolation &amp; purification ; }, abstract = {AIM: Although the complexity of the oral ecology and the ecological differences between health and disease are well accepted, a clear view on the dynamics in relation to disease is lacking. In this study, the prevalence and abundance of 20 key oral bacteria was assessed in health and disease and more importantly a closer look was given to the inter-bacterial relationships.<br><br>MATERIALS AND METHODS: A blinded microbiological database was analysed in this cross-sectional, retrospective study. The database was constructed based on microbiological analyses of samples from 6308 patients, with gradations of periodontitis (healthy to periodontitis). Data concerning the abundance of 20 oral bacteria and probing pocket depth were provided.<br><br>RESULTS: Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Eubacterium nodatum, Porphyromonas micra and Porphyromonas intermedia showed a clear increase in abundance and prevalence with increasing pocket depth. Correlation matrices illustrated that almost all microorganisms were in one way correlated to other species and most of these correlations were significant. Several beneficial bacteria showed strong correlations with other beneficial bacteria.<br><br>CONCLUSION: Knowledge on bacterial correlations can pave the way for new treatment options focusing on restoring the shifted balance.}, }
@article {pmid24096010, year = {2013}, author = {Martins, A and Guimarães, L and Guilhermino, L}, title = {Chronic toxicity of the veterinary antibiotic florfenicol to Daphnia magna assessed at two temperatures.}, journal = {Environmental toxicology and pharmacology}, volume = {36}, number = {3}, pages = {1022-1032}, doi = {10.1016/j.etap.2013.09.001}, pmid = {24096010}, issn = {1872-7077}, mesh = {Algorithms ; Animals ; Anti-Bacterial Agents/*toxicity ; Daphnia/*physiology ; Data Interpretation, Statistical ; Reproducibility of Results ; Spectrophotometry, Ultraviolet ; Temperature ; Thiamphenicol/*analogs &amp; derivatives/toxicity ; Veterinary Drugs/*toxicity ; }, abstract = {The hypothesis that temperature variation is able to modify the chronic toxicity of the antibiotic florfenicol (FLO) to Daphnia magna was tested in the present study. Twenty-one day laboratory bioassays were carried out at 20 and 25 °C. FLO concentrations and its potential decay during the assays were checked by spectrophotometry. At 20 °C, FLO significantly reduced the D. magna somatic growth (≥1.6 mg/L) and impaired its reproduction (EC₂₀=6.9 mg/L; EC₅₀=7.6 mg/L), with the population growth rate becoming negative at 12.6 mg/L. At 25 °C, the EC values were lower (1.7 and 1.9 mg/L, respectively) than at 20 °C, as well as the lowest exposure concentration causing a negative population growth rate (3.1 mg/L). These results clearly indicate that temperature raise from 20 to 25 °C was able to modify the FLO toxicity. Therefore, more studies on the combined effects of temperature changes and environmental contaminants are needed to improve the basis for ecological risk assessment, environmental and human safety.}, }
@article {pmid24089937, year = {2013}, author = {Kramer, S and Bollt, EM}, title = {Spatially dependent parameter estimation and nonlinear data assimilation by autosynchronization of a system of partial differential equations.}, journal = {Chaos (Woodbury, N.Y.)}, volume = {23}, number = {3}, pages = {033101}, doi = {10.1063/1.4812722}, pmid = {24089937}, issn = {1089-7682}, mesh = {Algorithms ; Animals ; Data Interpretation, Statistical ; Ecology/methods ; Ecosystem ; Models, Statistical ; *Nonlinear Dynamics ; Oceans and Seas ; Phytoplankton/physiology ; Plankton ; Population Dynamics ; Predatory Behavior ; Remote Sensing Technology/methods ; Satellite Imagery ; Signal Processing, Computer-Assisted ; Species Specificity ; Zooplankton/physiology ; }, abstract = {Given multiple images that describe chaotic reaction-diffusion dynamics, parameters of a partial differential equation (PDE) model are estimated using autosynchronization, where parameters are controlled by synchronization of the model to the observed data. A two-component system of predator-prey reaction-diffusion PDEs is used with spatially dependent parameters to benchmark the methods described. Applications to modeling the ecological habitat of marine plankton blooms by nonlinear data assimilation through remote sensing are discussed.}, }
@article {pmid24063811, year = {2013}, author = {Lane-deGraaf, KE and Kennedy, RC and Arifin, SM and Madey, GR and Fuentes, A and Hollocher, H}, title = {A test of agent-based models as a tool for predicting patterns of pathogen transmission in complex landscapes.}, journal = {BMC ecology}, volume = {13}, number = {}, pages = {35}, pmid = {24063811}, issn = {1472-6785}, mesh = {Animal Distribution ; Animals ; Computer Simulation ; Ecology/methods ; Entamoeba/*pathogenicity ; Entamoebiasis/*transmission ; *Environment ; Gene Flow ; Geographic Information Systems ; Macaca/genetics/*parasitology ; *Models, Biological ; }, abstract = {BACKGROUND: Landscape complexity can mitigate or facilitate host dispersal, influencing patterns of pathogen transmission. Spatial transmission of pathogens through landscapes, therefore, presents an important but not fully elucidated aspect of transmission dynamics. Using an agent-based model (LiNK) that incorporates GIS data, we examined the effects of landscape information on the spatial patterns of host movement and pathogen transmission in a system of long-tailed macaques and their gut parasites. We first examined the role of the landscape to identify any individual or additive effects on host movement. We then compared modeled dispersal distance to patterns of actual macaque gene flow to both confirm our model's predictions and to understand the role of individual land uses on dispersal. Finally, we compared the rate and the spread of two gastrointestinal parasites, Entamoeba histolytica and E. dispar, to understand how landscape complexity influences spatial patterns of pathogen transmission.<br><br>RESULTS: LiNK captured emergent properties of the landscape, finding that interaction effects between landscape layers could mitigate the rate of infection in a non-additive way. We also found that the inclusion of landscape information facilitated an accurate prediction of macaque dispersal patterns across a complex landscape, as confirmed by Mantel tests comparing genetic and simulated dispersed distances. Finally, we demonstrated that landscape heterogeneity proved a significant barrier for a highly virulent pathogen, limiting the dispersal ability of hosts and thus its own transmission into distant populations.<br><br>CONCLUSIONS: Landscape complexity plays a significant role in determining the path of host dispersal and patterns of pathogen transmission. Incorporating landscape heterogeneity and host behavior into disease management decisions can be important in targeting response efforts, identifying cryptic transmission opportunities, and reducing or understanding potential for unintended ecological and evolutionary consequences. The inclusion of these data into models of pathogen transmission patterns improves our understanding of these dynamics, ultimately proving beneficial for sound public health policy.}, }
@article {pmid24045641, year = {2013}, author = {Wang, Q and Quensen, JF and Fish, JA and Lee, TK and Sun, Y and Tiedje, JM and Cole, JR}, title = {Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.}, journal = {mBio}, volume = {4}, number = {5}, pages = {e00592-13}, pmid = {24045641}, issn = {2150-7511}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; UH3DK083993/DK/NIDDK NIH HHS/United States ; }, mesh = {Alaska ; Algorithms ; Amino Acid Sequence ; Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; Ecosystem ; Florida ; Frameshift Mutation ; Hawaii ; Metagenomics/*instrumentation/methods ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Soil Microbiology ; Utah ; }, abstract = {UNLABELLED: Biological nitrogen fixation is an important component of sustainable soil fertility and a key component of the nitrogen cycle. We used targeted metagenomics to study the nitrogen fixation-capable terrestrial bacterial community by targeting the gene for nitrogenase reductase (nifH). We obtained 1.1 million nifH 454 amplicon sequences from 222 soil samples collected from 4 National Ecological Observatory Network (NEON) sites in Alaska, Hawaii, Utah, and Florida. To accurately detect and correct frameshifts caused by indel sequencing errors, we developed FrameBot, a tool for frameshift correction and nearest-neighbor classification, and compared its accuracy to that of two other rapid frameshift correction tools. We found FrameBot was, in general, more accurate as long as a reference protein sequence with 80% or greater identity to a query was available, as was the case for virtually all nifH reads for the 4 NEON sites. Frameshifts were present in 12.7% of the reads. Those nifH sequences related to the Proteobacteria phylum were most abundant, followed by those for Cyanobacteria in the Alaska and Utah sites. Predominant genera with nifH sequences similar to reads included Azospirillum, Bradyrhizobium, and Rhizobium, the latter two without obvious plant hosts at the sites. Surprisingly, 80% of the sequences had greater than 95% amino acid identity to known nifH gene sequences. These samples were grouped by site and correlated with soil environmental factors, especially drainage, light intensity, mean annual temperature, and mean annual precipitation. FrameBot was tested successfully on three ecofunctional genes but should be applicable to any.<br><br>IMPORTANCE: High-throughput phylogenetic analysis of microbial communities using rRNA-targeted sequencing is now commonplace; however, such data often allow little inference with respect to either the presence or the diversity of genes involved in most important ecological processes. To study the gene pool for these processes, it is more straightforward to assess the genes directly responsible for the ecological function (ecofunctional genes). However, analyzing these genes involves technical challenges beyond those seen for rRNA. In particular, frameshift errors cause garbled downstream protein translations. Our FrameBot tool described here both corrects frameshift errors in query reads and determines their closest matching protein sequences in a set of reference sequences. We validated this new tool with sequences from defined communities and demonstrated the tool's utility on nifH gene fragments sequenced from soils in well-characterized and major terrestrial ecosystem types.}, }
@article {pmid24007337, year = {2013}, author = {Gilbert, JD and Acquisti, C and Martinson, HM and Elser, JJ and Kumar, S and Fagan, WF}, title = {GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {599}, pmid = {24007337}, issn = {1471-2164}, support = {R01 HG002096/HG/NHGRI NIH HHS/United States ; HG002096-12/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acids/genetics ; Animals ; Computational Biology ; Diet ; Drosophila/*genetics ; Drosophila Proteins/genetics ; Ecology ; Evolution, Molecular ; Internet ; *Knowledge Bases ; Phylogeny ; Proteome/*genetics ; Proteomics/*methods ; }, abstract = {BACKGROUND: &quot;Stoichioproteomics&quot; relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels.<br><br>RESULTS: Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline.<br><br>CONCLUSIONS: The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.}, }
@article {pmid23994579, year = {2013}, author = {Volchko, Y and Norrman, J and Bergknut, M and Rosén, L and Söderqvist, T}, title = {Incorporating the soil function concept into sustainability appraisal of remediation alternatives.}, journal = {Journal of environmental management}, volume = {129}, number = {}, pages = {367-376}, doi = {10.1016/j.jenvman.2013.07.025}, pmid = {23994579}, issn = {1095-8630}, mesh = {Conservation of Natural Resources/*methods ; Decision Support Techniques ; Ecology/*methods ; *Ecosystem ; Environmental Restoration and Remediation/*methods ; Models, Theoretical ; *Soil ; Terminology as Topic ; }, abstract = {Soil functions are critical for ecosystem survival and thus for an ecosystem's provision of services to humans. This is recognized in the proposed EU Soil Framework Directive from 2006, which lists seven important soil functions and services to be considered in a soil management practice. Emerging regulatory requirements demand a holistic view on soil evaluation in remediation projects. This paper presents a multi-scale, structured and transparent approach for incorporating the soil function concept into sustainability appraisal of remediation alternatives using a set of ecological, socio-cultural and economic criteria. The basis for the presented approach is a conceptualization of the linkages between soil functions and ecosystem services connected to with the sustainability paradigm. The approach suggests using (1) soil quality indicators (i.e. physical, chemical and biological soil properties) for exploring the performance of soil functions at the site level, and (2) soil service indicators (i.e. value-related measurements) for evaluating the performance of services resulting from soil functions across all levels of the spatial scale. The suggested approach is demonstrated by application in a Multi-Criteria Decision Analysis (MCDA) framework for sustainability appraisals of remediation alternatives. Further, the possibilities of using soil quality indicators for soil function evaluation are explored by reviewing existing literature on potential negative and positive effects of remediation technologies on the functionality of the treated soil. The suggested approach for including the soil function concept in remediation projects is believed to provide a basis for better informed decisions that will facilitate efficient management of contaminated land and to meet emerging regulatory requirements on soil protection.}, }
@article {pmid23969110, year = {2014}, author = {Paparoditis, P and Västermark, A and Le, AJ and Fuerst, JA and Saier, MH}, title = {Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.}, journal = {Biochimica et biophysica acta}, volume = {1838}, number = {1 Pt B}, pages = {193-215}, pmid = {23969110}, issn = {0006-3002}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms ; Bacterial Proteins/genetics/*metabolism ; Biological Evolution ; *Computational Biology ; Databases, Genetic ; Electron Transport ; *Genome, Bacterial ; Membrane Proteins/genetics/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Phylogeny ; Planctomycetales/classification/genetics/*metabolism ; }, abstract = {Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Database (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium-dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and trimethyl-amine-oxide (TMAO) reductases, consistent with its Na(+)-rich marine environment. R. baltica also possesses a Na(+)-translocating NADH:quinone dehydrogenase (Na(+)-NDH), a Na(+) efflux decarboxylase, two Na(+)-exporting ABC pumps, two Na(+)-translocating F-type ATPases, two Na(+):H(+) antiporters and two K(+):H(+) antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H(+)-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predictions regarding the physiology, ecology and evolution of R. baltica.}, }
@article {pmid23966100, year = {2014}, author = {Hartikainen, H and Ashford, OS and Berney, C and Okamura, B and Feist, SW and Baker-Austin, C and Stentiford, GD and Bass, D}, title = {Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {177-186}, pmid = {23966100}, issn = {1751-7370}, mesh = {*Biodiversity ; Data Mining ; Ecology ; Ecosystem ; *Environmental Microbiology ; Europe ; Haplosporida/*classification/genetics/*physiology ; Molecular Probes ; *Phylogeny ; }, abstract = {Haplosporidians are rhizarian parasites of mostly marine invertebrates. They include the causative agents of diseases of commercially important molluscs, including MSX disease in oysters. Despite their importance for food security, their diversity and distributions are poorly known. We used a combination of group-specific PCR primers to probe environmental DNA samples from planktonic and benthic environments in Europe, South Africa and Panama. This revealed several highly distinct novel clades, novel lineages within known clades and seasonal (spring vs autumn) and habitat-related (brackish vs littoral) variation in assemblage composition. High frequencies of haplosporidian lineages in the water column provide the first evidence for life cycles involving planktonic hosts, host-free stages or both. The general absence of haplosporidian lineages from all large online sequence data sets emphasises the importance of lineage-specific approaches for studying these highly divergent and diverse lineages. Combined with host-based field surveys, environmental sampling for pathogens will enhance future detection of known and novel pathogens and the assessment of disease risk.}, }
@article {pmid23949660, year = {2014}, author = {Lagkouvardos, I and Weinmaier, T and Lauro, FM and Cavicchioli, R and Rattei, T and Horn, M}, title = {Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {115-125}, pmid = {23949660}, issn = {1751-7370}, support = {281633//European Research Council/International ; }, mesh = {Bacterial Proteins/genetics ; *Biodiversity ; Chlamydiaceae/*classification/*genetics ; Databases, Genetic ; Ecology ; Environmental Microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22,000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.}, }
@article {pmid23913468, year = {2014}, author = {Hill, RA and Pyper, BJ and Lawrence, GS and Mann, GS and Allard, P and Mackintosh, CE and Healey, N and Dwyer, J and Trowell, J}, title = {Using sparse dose-response data for wildlife risk assessment.}, journal = {Integrated environmental assessment and management}, volume = {10}, number = {1}, pages = {3-11}, doi = {10.1002/ieam.1477}, pmid = {23913468}, issn = {1551-3793}, mesh = {Animals ; *Animals, Wild ; Databases, Factual ; *Dose-Response Relationship, Drug ; Ecotoxicology/methods ; *Models, Theoretical ; Risk Assessment/*methods ; }, abstract = {Hazard quotients based on a point-estimate comparison of exposure to a toxicity reference value (TRV) are commonly used to characterize risks for wildlife. Quotients may be appropriate for screening-level assessments but should be avoided in detailed assessments, because they provide little insight regarding the likely magnitude of effects and associated uncertainty. To better characterize risks to wildlife and support more informed decision making, practitioners should make full use of available dose-response data. First, relevant studies should be compiled and data extracted. Data extractions are not trivial--practitioners must evaluate the potential use of each study or its components, extract numerous variables, and in some cases, calculate variables of interest. Second, plots should be used to thoroughly explore the data, especially in the range of doses relevant to a given risk assessment. Plots should be used to understand variation in dose-response among studies, species, and other factors. Finally, quantitative dose-response models should be considered if they are likely to provide an improved basis for decision making. The most common dose-response models are simple models for data from a particular study for a particular species, using generalized linear models or other models appropriate for a given endpoint. Although simple models work well in some instances, they generally do not reflect the full breadth of information in a dose-response data set, because they apply only for particular studies, species, and endpoints. More advanced models are available that explicitly account for variation among studies and species, or that standardize multiple endpoints to a common response variable. Application of these models may be useful in some cases when data are abundant, but there are challenges to implementing and interpreting such models when data are sparse.}, }
@article {pmid23898667, year = {2013}, author = {Bu, CQ and Hu, ZB and Yu, LZ and Yan, QL and Zheng, X}, title = {[Forest resources in Qungyuan County of Liaoning, Northeast China: the structure and optimal spatial allocation].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {4}, pages = {1070-1076}, pmid = {23898667}, issn = {1001-9332}, mesh = {*Biomass ; China ; Conservation of Natural Resources/*methods ; *Ecosystem ; Forestry/*economics ; Geographic Information Systems ; Remote Sensing Technology ; Spatial Analysis ; Trees/*growth &amp; development ; }, abstract = {By using RS/GIS techniques and the method of multiple objective grey situation decision, and in considering the forest economic benefits (biomass and stand productivity) and ecological benefits (water and soil conservation) , an optimal spatial allocation of the present forest types in Qingyuan County of Liaoning, Northeast China was approached in this study. After the optimization of spatial allocation, the structural proportions of different forest types in Qingyuan County changed obviously, with the area of coniferous forests reduced from 43% to 23% , the area of broadleaved forests reduced from 51% to 31% , the area of mixed coniferous-broadleaf forests increased from 3% to 43% , and the area of shrubs remained unchanged. As compared with the results before optimization, the biomass, stand productivity, and water conservation function of the forest ecosystem in Qingyuan County after optimization increased by 0.6%, 2.1% , and 31.7%, respectively, and the soil conservation function remained unchanged. It could be concluded that after the optimization of spatial allocation, the forest ecosystem of Qingyuan County could maintain its soil conservation function, and, at the time of keeping higher timber production, fully exert waler conservation function, realizing the maximization of the economic and ecological benefits of the forest ecosystem.}, }
@article {pmid23785456, year = {2013}, author = {Morris, BD and White, EP}, title = {The EcoData retriever: improving access to existing ecological data.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65848}, pmid = {23785456}, issn = {1932-6203}, mesh = {Database Management Systems ; *Databases, Factual ; *Ecology ; Humans ; Internet ; *Software ; Software Design ; User-Computer Interface ; }, abstract = {Ecological research relies increasingly on the use of previously collected data. Use of existing datasets allows questions to be addressed more quickly, more generally, and at larger scales than would otherwise be possible. As a result of large-scale data collection efforts, and an increasing emphasis on data publication by journals and funding agencies, a large and ever-increasing amount of ecological data is now publicly available via the internet. Most ecological datasets do not adhere to any agreed-upon standards in format, data structure or method of access. Some may be broken up across multiple files, stored in compressed archives, and violate basic principles of data structure. As a result acquiring and utilizing available datasets can be a time consuming and error prone process. The EcoData Retriever is an extensible software framework which automates the tasks of discovering, downloading, and reformatting ecological data files for storage in a local data file or relational database. The automation of these tasks saves significant time for researchers and substantially reduces the likelihood of errors resulting from manual data manipulation and unfamiliarity with the complexities of individual datasets.}, }
@article {pmid23763602, year = {2013}, author = {Primmer, CR and Papakostas, S and Leder, EH and Davis, MJ and Ragan, MA}, title = {Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research.}, journal = {Molecular ecology}, volume = {22}, number = {12}, pages = {3216-3241}, doi = {10.1111/mec.12309}, pmid = {23763602}, issn = {1365-294X}, mesh = {Biological Evolution ; Computational Biology ; *Databases, Genetic ; Ecology/methods ; *Gene Ontology ; *Molecular Sequence Annotation ; }, abstract = {Recent advances in molecular technologies have opened up unprecedented opportunities for molecular ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. The aim of this review is to highlight how the Gene Ontology (GO) database can be of use in resolving this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species-neutral, the GO is well suited for cross-species use, meaning that, functional annotation derived from model organisms can be transferred to inferred orthologues in newly sequenced species. In other words, the GO can provide gene annotation information for species with nonannotated genomes. In this review, we describe the GO database, how functional information is linked with genes/gene products in model organisms, and how molecular ecologists can utilize this information to annotate their own data. Then, we outline various applications of GO for enhancing the understanding of molecular basis of traits in ecologically relevant species. We also highlight potential pitfalls, provide step-by-step recommendations for conducting a sound study in nonmodel organisms, suggest avenues for future research and outline a strategy for maximizing the benefits of a more ecological and evolutionary genomics-oriented ontology by ensuring its compatibility with the GO.}, }
@article {pmid23757040, year = {2013}, author = {Delmont, TO and Simonet, P and Vogel, TM}, title = {Mastering methodological pitfalls for surviving the metagenomic jungle.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {8}, pages = {744-754}, doi = {10.1002/bies.201200155}, pmid = {23757040}, issn = {1521-1878}, mesh = {Biodiversity ; Biotechnology ; Computational Biology ; DNA/analysis ; Ecology ; Ecosystem ; Genes, Bacterial ; Genetic Variation ; Humans ; *Metagenome ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Metagenomics is a culture- and PCR-independent approach that is now widely exploited for directly studying microbial evolution, microbial ecology, and developing biotechnologies. Observations and discoveries are critically dependent on DNA extraction methods, sequencing technologies, and bioinformatics tools. The potential pitfalls need to be understood and, to some degree, mastered if the resulting data are to survive scrutiny. In particular, methodological variations appear to affect results from different ecosystems differently, thus increasing the risk of biological and ecological misinterpretation. Part of the difficulty is derived from the lack of knowledge concerning the true microbial diversity and because no approach can guarantee accessing microorganisms in the same proportion in which they exist in the environment. However, the variation between different approaches (e.g. DNA extraction techniques, sequence annotation systems) can be used to evaluate whether observations are meaningful. These methodological variations can be integrated into the error analysis before comparing microbial communities.}, }
@article {pmid23734492, year = {2013}, author = {Tracey, JA and Zhu, J and Boydston, E and Lyren, L and Fisher, RN and Crooks, KR}, title = {Mapping behavioral landscapes for animal movement: a finite mixture modeling approach.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {23}, number = {3}, pages = {654-669}, pmid = {23734492}, issn = {1051-0761}, mesh = {Animals ; Behavior, Animal/*physiology ; California ; *Ecosystem ; Female ; Geographic Information Systems ; Lynx/*physiology ; Male ; *Models, Biological ; Motor Activity/*physiology ; Telemetry ; }, abstract = {Because of its role in many ecological processes, movement of animals in response to landscape features is an important subject in ecology and conservation biology. In this paper, we develop models of animal movement in relation to objects or fields in a landscape. We took a finite mixture modeling approach in which the component densities are conceptually related to different choices for movement in response to a landscape feature, and the mixing proportions are related to the probability of selecting each response as a function of one or more covariates. We combined particle swarm optimization and an expectation-maximization (EM) algorithm to obtain maximum-likelihood estimates of the model parameters. We used this approach to analyze data for movement of three bobcats in relation to urban areas in southern California, USA. A behavioral interpretation of the models revealed similarities and differences in bobcat movement response to urbanization. All three bobcats avoided urbanization by moving either parallel to urban boundaries or toward less urban areas as the proportion of urban land cover in the surrounding area increased. However, one bobcat, a male with a dispersal-like large-scale movement pattern, avoided urbanization at lower densities and responded strictly by moving parallel to the urban edge. The other two bobcats, which were both residents and occupied similar geographic areas, avoided urban areas using a combination of movements parallel to the urban edge and movement toward areas of less urbanization. However, the resident female appeared to exhibit greater repulsion at lower levels of urbanization than the resident male, consistent with empirical observations of bobcats in southern California. Using the parameterized finite mixture models, we mapped behavioral states to geographic space, creating a representation of a behavioral landscape. This approach can provide guidance for conservation planning based on analysis of animal movement data using statistical models, thereby linking connectivity evaluations to empirical data.}, }
@article {pmid23718006, year = {2013}, author = {Dong, ZY and Liu, DW and Wang, ZM and Ren, CY and Tang, XG and Jia, MM and Wang, Y}, title = {[Wetlands of priority restoration in Northeast China based on spatial analysis].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {1}, pages = {170-176}, pmid = {23718006}, issn = {1001-9332}, mesh = {China ; Conservation of Natural Resources/*methods ; Geographic Information Systems ; Remote Sensing Technology ; *Spatial Analysis ; *Wetlands ; }, abstract = {By using GIS/RS technology, and from the aspects of landscape structure, river- and road densities, wetness index, geomorphology, and cultivated land productivity, a spatial analysis was made on the potentiality of wetland restoration in Northeast China, with the regions of priority and secondary priority restoration wetlands determined. Then, by using the coordinated development index of crop production and wetland as well as the landscape indices, the wetland restoration effect was verified. In Northeast China, the wetland area of priority restoration was 1.78 x 10(6) hm2, among which, farmland and grassland were the main types for restoration, accounting for 96.7% of the total, and mainly located in the Sanjiang Plain in the northeastern part and the Songnen Plain in the central part of Northeast China. The wetland area of secondary priority restoration was 1.03 x 10(6) hm2. After the restoration of the wetlands, the wetland area in Northeast China would be increased by 37.4%, compared with the present wetland area, and the value of the coordinated development index of crop production and wetland would increase from 0.539 before restoration to 0.733 after restoration. The landscape pattern would be more benefit to the performance of the ecological functions of the wetlands. This study revealed that the restoration scheme of the wetlands in Northeast China based on spatial analysis was practicable, which could provide data support for the implement of wetland restoration and the improvement of ecological environment in Northeast China.}, }
@article {pmid23706558, year = {2013}, author = {Karl, JW and Gillan, JK and Herrick, JE}, title = {Geographic searching for ecological studies: a new frontier.}, journal = {Trends in ecology &amp; evolution}, volume = {28}, number = {7}, pages = {383-384}, doi = {10.1016/j.tree.2013.05.001}, pmid = {23706558}, issn = {1872-8383}, mesh = {Ecology/*methods/trends ; Ecosystem ; Geographic Information Systems ; *Geographic Mapping ; Periodicals as Topic ; Research Design/trends ; }, }
@article {pmid23701397, year = {2013}, author = {Catchen, J and Hohenlohe, PA and Bassham, S and Amores, A and Cresko, WA}, title = {Stacks: an analysis tool set for population genomics.}, journal = {Molecular ecology}, volume = {22}, number = {11}, pages = {3124-3140}, pmid = {23701397}, issn = {1365-294X}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; F32 GM095213/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; R24 OD011199/OD/NIH HHS/United States ; R24 GM079486/GM/NIGMS NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; R24 RR032670/RR/NCRR NIH HHS/United States ; 1R24GM079486-01A1/GM/NIGMS NIH HHS/United States ; F32GM095213-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Databases, Nucleic Acid ; Electronic Data Processing/*methods ; Genetic Markers ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Software ; }, abstract = {Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.}, }
@article {pmid23692056, year = {2013}, author = {Pe'er, G and Matsinos, YG and Johst, K and Franz, KW and Turlure, C and Radchuk, V and Malinowska, AH and Curtis, JM and Naujokaitis-Lewis, I and Wintle, BA and Henle, K}, title = {A protocol for better design, application, and communication of population viability analyses.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {27}, number = {4}, pages = {644-656}, doi = {10.1111/cobi.12076}, pmid = {23692056}, issn = {1523-1739}, mesh = {Communication ; Conservation of Natural Resources/*methods/statistics &amp; numerical data ; Databases, Factual ; Ecology/*methods ; Guidelines as Topic ; *Models, Biological ; Population Dynamics ; Population Growth ; Statistics as Topic/*methods ; Uncertainty ; }, abstract = {Population viability analyses (PVAs) contribute to conservation theory, policy, and management. Most PVAs focus on single species within a given landscape and address a specific problem. This specificity often is reflected in the organization of published PVA descriptions. Many lack structure, making them difficult to understand, assess, repeat, or use for drawing generalizations across PVA studies. In an assessment comparing published PVAs and existing guidelines, we found that model selection was rarely justified; important parameters remained neglected or their implementation was described vaguely; limited details were given on parameter ranges, sensitivity analysis, and scenarios; and results were often reported too inconsistently to enable repeatability and comparability. Although many guidelines exist on how to design and implement reliable PVAs and standards exist for documenting and communicating ecological models in general, there is a lack of organized guidelines for designing, applying, and communicating PVAs that account for their diversity of structures and contents. To fill this gap, we integrated published guidelines and recommendations for PVA design and application, protocols for documenting ecological models in general and individual-based models in particular, and our collective experience in developing, applying, and reviewing PVAs. We devised a comprehensive protocol for the design, application, and communication of PVAs (DAC-PVA), which has 3 primary elements. The first defines what a useful PVA is; the second element provides a workflow for the design and application of a useful PVA and highlights important aspects that need to be considered during these processes; and the third element focuses on communication of PVAs to ensure clarity, comprehensiveness, repeatability, and comparability. Thereby, DAC-PVA should strengthen the credibility and relevance of PVAs for policy and management, and improve the capacity to generalize PVA findings across studies.}, }
@article {pmid23662775, year = {2013}, author = {Stecher, B and Berry, D and Loy, A}, title = {Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {5}, pages = {793-829}, doi = {10.1111/1574-6976.12024}, pmid = {23662775}, issn = {1574-6976}, mesh = {Animals ; Computational Biology ; *Germ-Free Life ; Intestines/*microbiology ; Isotope Labeling ; Mice ; *Microbiota ; *Models, Animal ; Single-Cell Analysis/*methods ; Symbiosis ; }, abstract = {The highly diverse intestinal microbiota forms a structured community engaged in constant communication with itself and its host and is characterized by extensive ecological interactions. A key benefit that the microbiota affords its host is its ability to protect against infections in a process termed colonization resistance (CR), which remains insufficiently understood. In this review, we connect basic concepts of CR with new insights from recent years and highlight key technological advances in the field of microbial ecology. We present a selection of statistical and bioinformatics tools used to generate hypotheses about synergistic and antagonistic interactions in microbial ecosystems from metagenomic datasets. We emphasize the importance of experimentally testing these hypotheses and discuss the value of gnotobiotic mouse models for investigating specific aspects related to microbiota-host-pathogen interactions in a well-defined experimental system. We further introduce new developments in the area of single-cell analysis using fluorescence in situ hybridization in combination with metabolic stable isotope labeling technologies for studying the in vivo activities of complex community members. These approaches promise to yield novel insights into the mechanisms of CR and intestinal ecophysiology in general, and give researchers the means to experimentally test hypotheses in vivo at varying levels of biological and ecological complexity.}, }
@article {pmid23624424, year = {2013}, author = {D'Antonio, A and Monz, C and Newman, P and Lawson, S and Taff, D}, title = {Enhancing the utility of visitor impact assessment in parks and protected areas: a combined social-ecological approach.}, journal = {Journal of environmental management}, volume = {124}, number = {}, pages = {72-81}, doi = {10.1016/j.jenvman.2013.03.036}, pmid = {23624424}, issn = {1095-8630}, mesh = {Colorado ; Conservation of Natural Resources ; *Ecology ; Geographic Information Systems ; Humans ; *Recreation ; }, abstract = {Understanding the ecological consequences of visitor use in parks and how visitors interact with resource conditions is essential for avoiding the impairment of park and protected area resources and visitor experiences. This study combined ecological measures of off-trail resource impacts with social science techniques to understand visitor judgments of ecological impacts and visitors' degree of exposure to impacts. Specifically, this paper reports on a novel integration of techniques that was tested in the Bear Lake Road Corridor of Rocky Mountain National Park, CO, USA in which resource change, as a result of visitor use off designated trails and sites, was assessed and combined with social science and visitor use data. Visual survey techniques were used to understand visitor judgments of ecologically important resource impacts and GPS-tracking of visitor use and behavior allowed for the determination of the degree of visitor's exposure to impaired resources. Results suggest that resource impacts are prevalent and intense throughout the area, but tended to be spatially limited in proximity to attraction sites. Visitors are interacting with resource conditions reported to be unacceptable for significant portions of their hikes. Overall, the work represents an advancement of predictive capabilities when managing park and protected area resources.}, }
@article {pmid23617735, year = {2013}, author = {Schulz, B and Eckstein, RL and Durka, W}, title = {Scoring and analysis of methylation-sensitive amplification polymorphisms for epigenetic population studies.}, journal = {Molecular ecology resources}, volume = {13}, number = {4}, pages = {642-653}, doi = {10.1111/1755-0998.12100}, pmid = {23617735}, issn = {1755-0998}, mesh = {*DNA Methylation ; *Data Interpretation, Statistical ; *Epigenesis, Genetic ; Nucleic Acid Amplification Techniques/*methods ; Viola/*genetics/metabolism ; }, abstract = {DNA methylation is an important, heritable epigenetic modification in most eukaryotic organisms that is connected with numerous biological processes. To study the impact of natural epigenetic variation in an ecological or evolutionary context, epigenetic studies are increasingly using methylation-sensitive amplification polymorphism (MSAP) for surveys at the population or species level. However, no consensus exists on how to interpret and score the multistate information obtained from the MSAP banding patterns. Here, we review the previously used scoring approaches for population epigenetic studies and develop new alternatives. To assess effects of the different approaches on parameters of epigenetic diversity and differentiation, we applied eight scoring schemes to a case study of three populations of the plant species Viola elatior. For a total number of 168 detected polymorphic MSAP fragments, the number of ultimately scored polymorphic epiloci ranged between 78 and 286 depending on the particular scoring scheme. Both, estimates of epigenetic diversity and differentiation varied strongly between scoring approaches. However, linear regression and PCoA revealed qualitatively similar patterns, suggesting that the scoring approaches are largely consistent. For single-locus analyses of MSAP data, for example the search for loci under selection, we advocate a new scoring approach that separately takes into account different methylation types and thus seems appropriate for drawing more detailed conclusions in ecological or evolutionary contexts. An R script (MSAP_score.r) for scoring and basic data analysis is provided.}, }
@article {pmid23608176, year = {2013}, author = {Garbolino, E and De Ruffray, P and Brisse, H and Grandjouan, G}, title = {[Probable flora: an expression mean of ecological gradients in France].}, journal = {Comptes rendus biologies}, volume = {336}, number = {2}, pages = {73-81}, doi = {10.1016/j.crvi.2013.02.003}, pmid = {23608176}, issn = {1768-3238}, mesh = {Algorithms ; Atlantic Ocean ; Classification ; Data Collection ; Databases, Factual ; *Environment ; France ; Mediterranean Region ; *Plants/classification/genetics ; Soil/chemistry ; }, abstract = {The application of the criterion of fidelity of plants to plants over four millions botanical observations in France is considered to characterize the ecology of 215,000 phytosociological surveys. Among those discriminant plants, some are missing of the surveys, but they can have a certain probability of occurrence: these plants are called &quot;probable plants&quot; and they represent the &quot;probable flora&quot; of a territory. The study of their geographical distribution shows ecological gradients of flora across France in a better way than only considering the botanical observations. In fact, this method mitigates the discontinuities of taxa observations whose absence may be due to historical and/or anthropogenic factors.}, }
@article {pmid23555227, year = {2013}, author = {Korolev, KS}, title = {The fate of cooperation during range expansions.}, journal = {PLoS computational biology}, volume = {9}, number = {3}, pages = {e1002994}, pmid = {23555227}, issn = {1553-7358}, mesh = {*Animal Migration ; Animals ; Biological Evolution ; Computational Biology ; *Cooperative Behavior ; Diffusion ; Ecology ; Feedback ; *Models, Biological ; Population Dynamics ; *Selection, Genetic ; Spatial Behavior ; }, abstract = {Species expand their geographical ranges following an environmental change, long range dispersal, or a new adaptation. Range expansions not only bring an ecological change, but also affect the evolution of the expanding species. Although the dynamics of deleterious, neutral, and beneficial mutations have been extensively studied in expanding populations, the fate of alleles under frequency-dependent selection remains largely unexplored. The dynamics of cooperative alleles are particularly interesting because selection can be both frequency and density dependent, resulting in a coupling between population and evolutionary dynamics. This coupling leads to an increase in the frequency of cooperators at the expansion front, and, under certain conditions, the entire front can be taken over by cooperators. Thus, a mixed population wave can split into an expansion wave of only cooperators followed by an invasion wave of defectors. After the splitting, cooperators increase in abundance by expanding into new territories faster than they are invaded by defectors. Our results not only provide an explanation for the maintenance of cooperation but also elucidate the effect of eco-evolutionary feedback on the maintenance of genetic diversity during range expansions. When cooperators do not split away, we find that defectors can spread much faster with cooperators than they would be able to on their own or by invading cooperators. This enhanced rate of expansion in mixed waves could counterbalance the loss of genetic diversity due to the founder effect for mutations under frequency-dependent selection. Although we focus on cooperator-defector interactions, our analysis could also be relevant for other systems described by reaction-diffusion equations.}, }
@article {pmid23550586, year = {2013}, author = {Díez, CM and Gaut, BS and Meca, E and Scheinvar, E and Montes-Hernandez, S and Eguiarte, LE and Tenaillon, MI}, title = {Genome size variation in wild and cultivated maize along altitudinal gradients.}, journal = {The New phytologist}, volume = {199}, number = {1}, pages = {264-276}, pmid = {23550586}, issn = {1469-8137}, support = {P50 GM076516/GM/NIGMS NIH HHS/United States ; P50GM76516/GM/NIGMS NIH HHS/United States ; }, mesh = {Altitude ; Climate ; Crops, Agricultural ; Data Interpretation, Statistical ; Genetic Variation ; Genetics, Population ; *Genome Size ; *Genome, Plant ; Mexico ; Selection, Genetic ; Zea mays/*genetics ; }, abstract = {It is still an open question as to whether genome size (GS) variation is shaped by natural selection. One approach to address this question is a population-level survey that assesses both the variation in GS and the relationship of GS to ecological variants. We assessed GS in Zea mays, a species that includes the cultivated crop, maize, and its closest wild relatives, the teosintes. We measured GS in five plants of each of 22 maize landraces and 21 teosinte populations from Mexico sampled from parallel altitudinal gradients. GS was significantly smaller in landraces than in teosintes, but the largest component of GS variation was among landraces and among populations. In maize, GS correlated negatively with altitude; more generally, the best GS predictors were linked to geography. By contrast, GS variation in teosintes was best explained by temperature and precipitation. Overall, our results further document the size flexibility of the Zea genome, but also point to a drastic shift in patterns of GS variation since domestication. We argue that such patterns may reflect the indirect action of selection on GS, through a multiplicity of phenotypes and life-history traits.}, }
@article {pmid23546798, year = {2013}, author = {Kim, KS and Sappington, TW}, title = {Microsatellite data analysis for population genetics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1006}, number = {}, pages = {271-295}, doi = {10.1007/978-1-62703-389-3_19}, pmid = {23546798}, issn = {1940-6029}, mesh = {Computational Biology/instrumentation/*methods ; Ecology ; Gene Flow ; Genetic Variation ; Genetics ; *Genetics, Population ; Genotype ; Microsatellite Repeats/*genetics ; *Software ; }, abstract = {Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.}, }
@article {pmid23533370, year = {2013}, author = {Fortuna, MA and Zaman, L and Wagner, AP and Ofria, C}, title = {Evolving digital ecological networks.}, journal = {PLoS computational biology}, volume = {9}, number = {3}, pages = {e1002928}, pmid = {23533370}, issn = {1553-7358}, mesh = {Animals ; *Biological Evolution ; *Computational Biology ; Computer Simulation ; *Ecology ; Genome ; Host-Parasite Interactions ; *Models, Biological ; Plants ; Symbiosis ; }, abstract = {&quot;It is hard to realize that the living world as we know it is just one among many possibilities&quot; [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms) that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism). Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks) that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved).}, }
@article {pmid23505408, year = {2013}, author = {Costello, MJ and Bouchet, P and Boxshall, G and Fauchald, K and Gordon, D and Hoeksema, BW and Poore, GC and van Soest, RW and Stöhr, S and Walter, TC and Vanhoorne, B and Decock, W and Appeltans, W}, title = {Global coordination and standardisation in marine biodiversity through the World Register of Marine Species (WoRMS) and related databases.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e51629}, pmid = {23505408}, issn = {1932-6203}, mesh = {Animals ; Aquatic Organisms/*classification ; *Biodiversity ; *Databases, Factual ; *Internet ; *Marine Biology ; }, abstract = {The World Register of Marine Species is an over 90% complete open-access inventory of all marine species names. Here we illustrate the scale of the problems with species names, synonyms, and their classification, and describe how WoRMS publishes online quality assured information on marine species. Within WoRMS, over 100 global, 12 regional and 4 thematic species databases are integrated with a common taxonomy. Over 240 editors from 133 institutions and 31 countries manage the content. To avoid duplication of effort, content is exchanged with 10 external databases. At present WoRMS contains 460,000 taxonomic names (from Kingdom to subspecies), 368,000 species level combinations of which 215,000 are currently accepted marine species names, and 26,000 related but non-marine species. Associated information includes 150,000 literature sources, 20,000 images, and locations of 44,000 specimens. Usage has grown linearly since its launch in 2007, with about 600,000 unique visitors to the website in 2011, and at least 90 organisations from 12 countries using WoRMS for their data management. By providing easy access to expert-validated content, WoRMS improves quality control in the use of species names, with consequent benefits to taxonomy, ecology, conservation and marine biodiversity research and management. The service manages information on species names that would otherwise be overly costly for individuals, and thus minimises errors in the application of nomenclature standards. WoRMS' content is expanding to include host-parasite relationships, additional literature sources, locations of specimens, images, distribution range, ecological, and biological data. Species are being categorised as introduced (alien, invasive), of conservation importance, and on other attributes. These developments have a multiplier effect on its potential as a resource for biodiversity research and management. As a consequence of WoRMS, we are witnessing improved communication within the scientific community, and anticipate increased taxonomic efficiency and quality control in marine biodiversity research and management.}, }
@article {pmid23487930, year = {2013}, author = {Wang, HB and Chen, WH and Li, XS and Li, SH and Yan, BL}, title = {[Isolation and identification of Marinobacter adhaerens HY-3 and its allelopathy on Skeletonema costatum].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {34}, number = {1}, pages = {145-149}, pmid = {23487930}, issn = {0250-3301}, mesh = {*Allelopathy ; Diatoms/*growth &amp; development/*physiology ; Eutrophication ; Marine Biology ; Marinobacter/*isolation &amp; purification/*physiology ; }, abstract = {UNLABELLED: The allelopathy between bacteria and algae is a very complicated physical and ecological phenomenon. A marine bacterium was isolated from the water of a shrimp and crab mix-culturing pond. By 16S rRNA analysis, it was identified as Marinobacter adhaerens HY-3. Skeletonema costatum, a common dominant species of red-tide microorganism in China, was chosen as the other research object. The allelopathic effect of Marinobacter adhaerens HY- 3 on S. costatum was studied. Using the growth mass of Skeletonema costatum and the content of chlorophyll a as the parameters, the effects of HY-3 on the growth and photosynthesis of Skeletonema costatum were studied after co-cultivation and addition of extracellular metabolites of HY-3. The results showed that the growth of S. costatum was inhibited when the concentration of the strain HY-3 was above 10(4), and the growth mass of the 10(4), 10(6) and 10(8) HY-3 group was 70%, 23% and 22% of the control group respectively on the 10th day, with the content of chlorophyll being 88%, 62% and 60% of the control group, respectively. Therefore, the suppression increased with increasing concentration of HY-3. However, addition of extracellular metabolites of HY-3 had no effect on the growth of S. costatum.<br><br>CONCLUSIONS: M. adhaerens HY-3 had certain allelopathy on S. costatum and affected its growth and photosynthesis. Moreover, interaction between M. adhaerens HY-3 and S. costatum was achieved by their direct contact and the extracellular metabolites did not contain allelopathy factors.}, }
@article {pmid23458322, year = {2013}, author = {Peterson, EE and Ver Hoef, JM and Isaak, DJ and Falke, JA and Fortin, MJ and Jordan, CE and McNyset, K and Monestiez, P and Ruesch, AS and Sengupta, A and Som, N and Steel, EA and Theobald, DM and Torgersen, CE and Wenger, SJ}, title = {Modelling dendritic ecological networks in space: an integrated network perspective.}, journal = {Ecology letters}, volume = {16}, number = {5}, pages = {707-719}, doi = {10.1111/ele.12084}, pmid = {23458322}, issn = {1461-0248}, mesh = {*Ecology/methods ; Ecosystem ; Linear Models ; *Models, Biological ; *Models, Statistical ; *Rivers ; }, abstract = {Dendritic ecological networks (DENs) are a unique form of ecological networks that exhibit a dendritic network topology (e.g. stream and cave networks or plant architecture). DENs have a dual spatial representation; as points within the network and as points in geographical space. Consequently, some analytical methods used to quantify relationships in other types of ecological networks, or in 2-D space, may be inadequate for studying the influence of structure and connectivity on ecological processes within DENs. We propose a conceptual taxonomy of network analysis methods that account for DEN characteristics to varying degrees and provide a synthesis of the different approaches within the context of stream ecology. Within this context, we summarise the key innovations of a new family of spatial statistical models that describe spatial relationships in DENs. Finally, we discuss how different network analyses may be combined to address more complex and novel research questions. While our main focus is streams, the taxonomy of network analyses is also relevant anywhere spatial patterns in both network and 2-D space can be used to explore the influence of multi-scale processes on biota and their habitat (e.g. plant morphology and pest infestation, or preferential migration along stream or road corridors).}, }
@article {pmid23431801, year = {2012}, author = {Sun, XP and Wang, TM and Wu, JG and Ge, JP}, title = {[Change trend of vegetation cover in Beijing metropolitan region before and after the 2008 Olympics].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {11}, pages = {3133-3140}, pmid = {23431801}, issn = {1001-9332}, mesh = {China ; Cities ; *Conservation of Natural Resources ; Crops, Agricultural/growth &amp; development ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Poaceae/growth &amp; development ; *Remote Sensing Technology ; Satellite Communications ; Sports ; Trees/*growth &amp; development ; }, abstract = {The MODIS-NDVI data from 2000 to 2009 were used to analyze the temporal dynamics and spatial distribution of the vegetation cover in the Beijing metropolitan region before and after the 2008 Olympics. During the study period, the proportion of the significantly increased pixels of NDVI occupied 20.7% while that of the significantly decreased pixels only occupied 4.1% of the total, and the decreasing rate of the NDVI was slightly faster than the increasing rate. The significant changes of the NDVI were mainly concentrated in the low altitude and small slope areas with intensive human activities, and two bands were formed in the plain area, i. e., the vegetation increasing band within the 5th Ring Road and the vegetation decreasing band from the 5th Ring Road to the outside areas of the 6th Ring Road. In the areas with significant vegetation change, there was an obvious transition between the high and low NDVI sections but less change in the medium NDVI section, mainly due to the conversion of land cover type. In the Capital function core area and ecological conservation zones, vegetation change represented a positive trend; while in the urban function expansion area and urban development area, vegetation change had the dual characteristics of both positive and negative trends. A series of ecological engineering projects during the preparatory period of the 2008 Olympics was the main cause of the vegetation increase in the study area.}, }
@article {pmid23387123, year = {2012}, author = {Gonzalez-Mirelis, G and Lindegarth, M}, title = {Predicting the distribution of out-of-reach biotopes with decision trees in a Swedish marine protected area.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {22}, number = {8}, pages = {2248-2264}, pmid = {23387123}, issn = {1051-0761}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Demography ; *Ecosystem ; Fishes/*physiology ; Geographic Information Systems ; *Models, Biological ; Oceans and Seas ; Sweden ; }, abstract = {Through spatially explicit predictive models, knowledge of spatial patterns of biota can be generated for out-of-reach environments, where there is a paucity of survey data. This knowledge is invaluable for conservation decisions. We used distribution modeling to predict the occurrence of benthic biotopes, or megafaunal communities of the seabed, to support the spatial planning of a marine national park. Nine biotope classes were obtained prior to modeling from multivariate species data derived from point source, underwater imagery. Five map layers relating to depth and terrain were used as predictor variables. Biotope type was predicted on a pixel-by-pixel basis, where pixel size was 15 x 15 m and total modeled area was 455 km2. To choose a suitable modeling technique we compared the performance of five common models based on recursive partitioning: two types of classification and regression trees ([1] pruned by 10-fold cross-validation and [2] pruned by minimizing complexity), random forests, conditional inference (CI) trees, and CI forests. The selected model was a CI forest (an ensemble of CI trees), a machine-learning technique whose discriminatory power (class-by-class area under the curve [AUC] ranged from 0.75 to 0.86) and classification accuracy (72%) surpassed those of the other methods tested. Conditional inference trees are virtually new to the field of ecology. The final model's overall prediction error was 28%. Model predictions were also checked against a custom-built measure of dubiousness, calculated at the polygon level. Key factors other than the choice of modeling technique include: the use of a multinomial response, accounting for the heterogeneity of observations, and spatial autocorrelation. To illustrate how the model results can be implemented in spatial planning, representation of biodiversity in the national park was described and quantified. Given a goal of maximizing classification accuracy, we conclude that conditional inference trees are a promising tool to map biota. Species distribution modeling is presented as an ecological tool that can handle a wide variety of systems (e.g., the benthic system).}, }
@article {pmid23363430, year = {2013}, author = {He, Q and Bertness, MD and Altieri, AH}, title = {Global shifts towards positive species interactions with increasing environmental stress.}, journal = {Ecology letters}, volume = {16}, number = {5}, pages = {695-706}, doi = {10.1111/ele.12080}, pmid = {23363430}, issn = {1461-0248}, mesh = {Climate ; Databases, Factual ; Ecosystem ; Environment ; Mortality ; Multifactorial Inheritance ; *Plant Physiological Phenomena ; *Stress, Physiological ; }, abstract = {The study of positive species interactions is a rapidly evolving field in ecology. Despite decades of research, controversy has emerged as to whether positive and negative interactions predictably shift with increasing environmental stress as hypothesised by the stress-gradient hypothesis (SGH). Here, we provide a synthesis of 727 tests of the SGH in plant communities across the globe to examine its generality across a variety of ecological factors. Our results show that plant interactions change with stress through an outright shift to facilitation (survival) or a reduction in competition (growth and reproduction). In a limited number of cases, plant interactions do not respond to stress, but they never shift towards competition with stress. These findings are consistent across stress types, plant growth forms, life histories, origins (invasive vs. native), climates, ecosystems and methodologies, though the magnitude of the shifts towards facilitation with stress is dependent on these factors. We suggest that future studies should employ standardised definitions and protocols to test the SGH, take a multi-factorial approach that considers variables such as plant traits in addition to stress, and apply the SGH to better understand how species and communities will respond to environmental change.}, }
@article {pmid23356610, year = {2013}, author = {Shah, P and Fitzpatrick, BM and Fordyce, JA}, title = {A parametric method for assessing diversification-rate variation in phylogenetic trees.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {2}, pages = {368-377}, doi = {10.1111/j.1558-5646.2012.01791.x}, pmid = {23356610}, issn = {1558-5646}, mesh = {Adaptation, Biological/genetics ; Algorithms ; Animals ; Data Interpretation, Statistical ; Evolution, Molecular ; *Genetic Variation ; *Models, Genetic ; *Models, Statistical ; *Phylogeny ; Urodela/genetics ; }, abstract = {Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here, we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data, which showed that PRC has acceptable false-positive rates and statistical power to detect rate variation. We apply the PRC method to the well-studied radiation of North American Plethodon salamanders, and support the inference that the large-bodied Plethodon glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders.}, }
@article {pmid23343858, year = {2013}, author = {de Vocht, F and Hannam, K and Buchan, I}, title = {Environmental risk factors for cancers of the brain and nervous system: the use of ecological data to generate hypotheses.}, journal = {Occupational and environmental medicine}, volume = {70}, number = {5}, pages = {349-356}, doi = {10.1136/oemed-2012-100954}, pmid = {23343858}, issn = {1470-7926}, support = {MC_PC_13042//Medical Research Council/United Kingdom ; }, mesh = {Brain/*pathology ; Brain Neoplasms/epidemiology/*etiology ; Cell Phone ; Central Nervous System Neoplasms ; Confounding Factors (Epidemiology) ; *Databases, Factual ; Ecology ; Electromagnetic Radiation ; Environmental Exposure/*adverse effects ; Epidemiologic Methods ; Global Health ; Humans ; Incidence ; Income ; Multivariate Analysis ; Risk Factors ; }, abstract = {BACKGROUND: There is a public health need to balance timely generation of hypotheses with cautious causal inference. For rare cancers this is particularly challenging because standard epidemiological study designs may not be able to elucidate causal factors in an early period of newly emerging risks. Alternative methodologies need to be considered for generating and shaping hypotheses prior to definitive investigation.<br><br>OBJECTIVES: To evaluate whether open-access databases can be used to explore links between potential risk factors and cancers at an ecological level, using the case study of brain and nervous system cancers as an example.<br><br>METHODS: National age-adjusted cancer incidence rates were obtained from the GLOBOCAN 2008 resource and combined with data from the United Nations Development Report and the World Bank list of development indicators. Data were analysed using multivariate regression models.<br><br>RESULTS: Cancer rates, potential confounders and environmental risk factors were available for 165 of 208 countries. 2008 national incidences of brain and nervous system cancers were associated with continent, gross national income in 2008 and Human Development Index Score. The only exogenous risk factor consistently associated with higher incidence was the penetration rate of mobile/cellular telecommunications subscriptions, although other factors were highlighted. According to these ecological results the latency period is at least 11-12 years, but probably more than 20 years. Missing data on cancer incidence and for other potential risk factors prohibit more detailed investigation of exposure-response associations and/or explore other hypotheses.<br><br>CONCLUSIONS: Readily available ecological data may be underused, particularly for the study of risk factors for rare diseases and those with long latencies. The results of ecological analyses in general should not be overinterpreted in causal inference, but equally they should not be ignored where alternative signals of aetiology are lacking.}, }
@article {pmid23320463, year = {2013}, author = {Orsini, L and Andrew, R and Eizaguirre, C}, title = {Evolutionary ecological genomics.}, journal = {Molecular ecology}, volume = {22}, number = {3}, pages = {527-531}, doi = {10.1111/mec.12177}, pmid = {23320463}, issn = {1365-294X}, mesh = {*Biological Evolution ; Computational Biology ; *Ecology ; Genetic Fitness ; Genetic Speciation ; *Genomics ; Hybridization, Genetic ; }, }
@article {pmid25600166, year = {2013}, author = {Unertl, KM and Johnson, KB and Gadd, CS and Lorenzi, NM}, title = {Bridging organizational divides in health care: an ecological view of health information exchange.}, journal = {JMIR medical informatics}, volume = {1}, number = {1}, pages = {e3}, pmid = {25600166}, issn = {2291-9694}, support = {T15 LM007450/LM/NLM NIH HHS/United States ; }, abstract = {BACKGROUND: The fragmented nature of health care delivery in the United States leads to fragmented health information and impedes patient care continuity and safety. Technologies to support interorganizational health information exchange (HIE) are becoming more available. Understanding how HIE technology changes health care delivery and affects people and organizations is crucial to long-term successful implementation.<br><br>OBJECTIVE: Our study investigated the impacts of HIE technology on organizations, health care providers, and patients through a new, context-aware perspective, the Regional Health Information Ecology.<br><br>METHODS: We conducted more than 180 hours of direct observation, informal interviews during observation, and 9 formal semi-structured interviews. Data collection focused on workflow and information flow among health care team members and patients and on health care provider use of HIE technology.<br><br>RESULTS: We structured the data analysis around five primary information ecology components: system, locality, diversity, keystone species, and coevolution. Our study identified three main roles, or keystone species, involved in HIE: information consumers, information exchange facilitators, and information repositories. The HIE technology impacted patient care by allowing providers direct access to health information, reducing time to obtain health information, and increasing provider awareness of patient interactions with the health care system. Developing the infrastructure needed to support HIE technology also improved connections among information technology support groups at different health care organizations. Despite the potential of this type of technology to improve continuity of patient care, HIE technology adoption by health care providers was limited.<br><br>CONCLUSIONS: To successfully build a HIE network, organizations had to shift perspectives from an ownership view of health data to a continuity of care perspective. To successfully integrate external health information into clinical work practices, health care providers had to move toward understanding potential contributions of external health information. Our study provides a foundation for future context-aware development and implementation of HIE technology. Integrating concepts from the Regional Health Information Ecology into design and implementation may lead to wider diffusion and adoption of HIE technology into clinical work.}, }
@article {pmid23239979, year = {2012}, author = {Rodríguez, A and Negro, JJ and Mulero, M and Rodríguez, C and Hernández-Pliego, J and Bustamante, J}, title = {The eye in the sky: combined use of unmanned aerial systems and GPS data loggers for ecological research and conservation of small birds.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e50336}, pmid = {23239979}, issn = {1932-6203}, mesh = {Animals ; *Behavior, Animal ; Conservation of Natural Resources ; Ecosystem ; Environment ; Environmental Monitoring ; Falconiformes/*physiology ; *Flight, Animal ; Geographic Information Systems/*instrumentation ; }, abstract = {Technological advances for wildlife monitoring have expanded our ability to study behavior and space use of many species. But biotelemetry is limited by size, weight, data memory and battery power of the attached devices, especially in animals with light body masses, such as the majority of bird species. In this study, we describe the combined use of GPS data logger information obtained from free-ranging birds, and environmental information recorded by unmanned aerial systems (UASs). As a case study, we studied habitat selection of a small raptorial bird, the lesser kestrel Falco naumanni, foraging in a highly dynamic landscape. After downloading spatio-temporal information from data loggers attached to the birds, we programmed the UASs to fly and take imagery by means of an onboard digital camera documenting the flight paths of those same birds shortly after their recorded flights. This methodology permitted us to extract environmental information at quasi-real time. We demonstrate that UASs are a useful tool for a wide variety of wildlife studies.}, }
@article {pmid23202299, year = {2013}, author = {Gomiero, A and Dagnino, A and Nasci, C and Viarengo, A}, title = {The use of protozoa in ecotoxicology: application of multiple endpoint tests of the ciliate E. crassus for the evaluation of sediment quality in coastal marine ecosystems.}, journal = {The Science of the total environment}, volume = {442}, number = {}, pages = {534-544}, doi = {10.1016/j.scitotenv.2012.10.023}, pmid = {23202299}, issn = {1879-1026}, mesh = {Biological Assay ; Data Interpretation, Statistical ; *Ecosystem ; Ecotoxicology/*methods ; Endpoint Determination ; Environmental Monitoring/*methods ; Euplotes/*drug effects/growth &amp; development ; Geologic Sediments/*chemistry ; Italy ; Oceans and Seas ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Despite an increasing number of surveys describing adverse effects of contaminated sediments on marine organisms, few studies have addressed protists. In this study, the free-crawling marine ciliate Euplotes crassus was evaluated as the test organism for the screening of sediment toxicity using sediments from both coastal and estuarine sites of the Venice Lagoon (Marghera harbour [MH], Valle Millecampi [MV], Murano island [MI] and Lido inlet [LI]). Two endpoints of high ecological value, mortality (Mry) and replication rate (RpR), were assessed in combination with the two sublethal biomarkers of stress, endocytotic rate (Ecy) and lysosomal membrane stability (NRRT). The results showed a significant inhibition of RpR, Ecy and NRRT paralleled by a small and insignificantly increased Mry of the exposed specimens. Our results thus demonstrate that only a combination of mortality and sublethal biomarkers was able to characterise an exposure-related stress syndrome. The suite of biomarkers described here was also able to detect and resolve a pollution-induced stress syndrome at an early stage of pollution. The contamination level of the sediments was assessed using chemical analysis, by estimating bioavailability and by computing a toxic pressure coefficient (TPC) to account for potential additive effects of different pollutants. The observed biological responses were consistent with the contamination levels in sediments, suggesting a high potential for using Protozoa in bioassays to assess environmental risk in coastal marine systems.}, }
@article {pmid23137142, year = {2013}, author = {Wang, IJ and Glor, RE and Losos, JB}, title = {Quantifying the roles of ecology and geography in spatial genetic divergence.}, journal = {Ecology letters}, volume = {16}, number = {2}, pages = {175-182}, doi = {10.1111/ele.12025}, pmid = {23137142}, issn = {1461-0248}, mesh = {Animals ; DNA, Mitochondrial ; *Ecology ; Gene Flow ; Genetic Speciation ; Genetic Variation ; *Genetics, Population ; Geographic Information Systems ; Lizards/*genetics ; *Models, Theoretical ; }, abstract = {Investigating the properties of ecological landscapes that influence gene flow among populations can provide key insights into the earliest stages of biological divergence. Both ecological and geographical factors can reduce gene flow, which can lead to population divergence, but we know little of the relative strengths of these phenomena in nature. Here, we use a novel application of structural equation modelling to quantify the contributions of ecological and geographical isolation to spatial genetic divergence in 17 species of Anolis lizards. Our comparative analysis shows that although both processes contributed significantly, geographical isolation explained substantially more genetic divergence than ecological isolation (36.3 vs. 17.9% of variance respectively), suggesting that despite the proposed ubiquity of ecological divergence, non-ecological factors play the dominant role in the evolution of spatial genetic divergence.}, }
@article {pmid23052472, year = {2012}, author = {Duguy, B and Alloza, JA and Baeza, MJ and De la Riva, J and Echeverría, M and Ibarra, P and Llovet, J and Cabello, FP and Rovira, P and Vallejo, RV}, title = {Modelling the ecological vulnerability to forest fires in mediterranean ecosystems using geographic information technologies.}, journal = {Environmental management}, volume = {50}, number = {6}, pages = {1012-1026}, pmid = {23052472}, issn = {1432-1009}, mesh = {Ecology ; Environmental Monitoring/*methods ; *Fires ; Geographic Information Systems ; Mediterranean Region ; *Trees ; }, abstract = {Forest fires represent a major driver of change at the ecosystem and landscape levels in the Mediterranean region. Environmental features and vegetation are key factors to estimate the ecological vulnerability to fire; defined as the degree to which an ecosystem is susceptible to, and unable to cope with, adverse effects of fire (provided a fire occurs). Given the predicted climatic changes for the region, it is urgent to validate spatially explicit tools for assessing this vulnerability in order to support the design of new fire prevention and restoration strategies. This work presents an innovative GIS-based modelling approach to evaluate the ecological vulnerability to fire of an ecosystem, considering its main components (soil and vegetation) and different time scales. The evaluation was structured in three stages: short-term (focussed on soil degradation risk), medium-term (focussed on changes in vegetation), and coupling of the short- and medium-term vulnerabilities. The model was implemented in two regions: Aragón (inland North-eastern Spain) and Valencia (eastern Spain). Maps of the ecological vulnerability to fire were produced at a regional scale. We partially validated the model in a study site combining two complementary approaches that focused on testing the adequacy of model's predictions in three ecosystems, all very common in fire-prone landscapes of eastern Spain: two shrublands and a pine forest. Both approaches were based on the comparison of model's predictions with values of NDVI (Normalized Difference Vegetation Index), which is considered a good proxy for green biomass. Both methods showed that the model's performance is satisfactory when applied to the three selected vegetation types.}, }
@article {pmid23049882, year = {2012}, author = {Topping, CJ and Dalkvist, T and Grimm, V}, title = {Post-hoc pattern-oriented testing and tuning of an existing large model: lessons from the field vole.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e45872}, pmid = {23049882}, issn = {1932-6203}, mesh = {Animals ; Arvicolinae/*physiology ; Computer Simulation ; Ecology ; *Ecosystem ; Environment ; Female ; Geographic Information Systems ; Geography ; Male ; Models, Biological ; Pattern Recognition, Automated ; Population Dynamics ; }, abstract = {Pattern-oriented modeling (POM) is a general strategy for modeling complex systems. In POM, multiple patterns observed at different scales and hierarchical levels are used to optimize model structure, to test and select sub-models of key processes, and for calibration. So far, POM has been used for developing new models and for models of low to moderate complexity. It remains unclear, though, whether the basic idea of POM to utilize multiple patterns, could also be used to test and possibly develop existing and established models of high complexity. Here, we use POM to test, calibrate, and further develop an existing agent-based model of the field vole (Microtus agrestis), which was developed and tested within the ALMaSS framework. This framework is complex because it includes a high-resolution representation of the landscape and its dynamics, of the individual's behavior, and of the interaction between landscape and individual behavior. Results of fitting to the range of patterns chosen were generally very good, but the procedure required to achieve this was long and complicated. To obtain good correspondence between model and the real world it was often necessary to model the real world environment closely. We therefore conclude that post-hoc POM is a useful and viable way to test a highly complex simulation model, but also warn against the dangers of over-fitting to real world patterns that lack details in their explanatory driving factors. To overcome some of these obstacles we suggest the adoption of open-science and open-source approaches to ecological simulation modeling.}, }
@article {pmid23039950, year = {2013}, author = {Kane, NC and Burke, JM and Marek, L and Seiler, G and Vear, F and Baute, G and Knapp, SJ and Vincourt, P and Rieseberg, LH}, title = {Sunflower genetic, genomic and ecological resources.}, journal = {Molecular ecology resources}, volume = {13}, number = {1}, pages = {10-20}, doi = {10.1111/1755-0998.12023}, pmid = {23039950}, issn = {1755-0998}, mesh = {*Biological Evolution ; *Databases, Genetic ; Ecology/*methods ; Genetic Markers/genetics ; Genome, Plant/*genetics ; Helianthus/*genetics ; Physical Chromosome Mapping ; *Seeds ; *Specimen Handling ; }, abstract = {Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here, we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experimentation and describe the numerous publicly available resources that have enabled rapid advances in ecological and evolutionary genetics. Resources include seed collections available from germplasm centres at the USDA and INRA, genomic and EST sequences, mapping populations, genetic markers, genetic and physical maps and other forward- and reverse-genetic tools. We also discuss some of the key evolutionary, genetic and ecological questions being addressed in sunflowers, as well as gaps in our knowledge and promising areas for future research.}, }
@article {pmid23002599, year = {2012}, author = {Hao, JF and Liu, HY and Hu, HB and An, J and Zhang, XH}, title = {[Responses of wetland water quality to influence the strengthness of urbanization in Nanjing, China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {33}, number = {7}, pages = {2259-2264}, pmid = {23002599}, issn = {0250-3301}, mesh = {China ; Cities ; Environmental Monitoring/*methods ; Geographic Information Systems ; Seasons ; *Urbanization ; Water Quality/*standards ; *Wetlands ; }, abstract = {28 typical wetlands were selected to monitor the contaminants in water monthly, that influenced by urbanization in different scales. On the other hand, the land use types such as impervious area and forest area in the catchments of urban wetlands were analyzed by GIS and landscape ecology. And then the effects of urbanization index (UEI) was employed to reveal the relationship between urbanization level and water quality in Xianlin New City of Nanjing. Results indicated that: (1) the seasonal variations of water quality showed that water quality in summer was worse than those in other seasons, and the water quality in winter was good. However there were no significant differences between the spring and the autumn. (2) the relationship was significant between urbanization level and water quality, and the water quality tended to be getting worse when the urbanization level was getting higher. The concentrations of TP, TN, NH(4+)-N, and Chla were 0.27, 1.07, 0.15 and 17.94 mg x L(-1) respectively in the high urbanization (HU) level wetland while the concentrations were 0.12, 0.56, 0.12 and 4.85 mg x L(-1) in the low urbanization (LW) level wetland. (3) there was a threshold between UEI and the water quality. On the whole, the water quality would get worse quickly when the value of UEI exceeded 2.2.}, }
@article {pmid22985105, year = {2013}, author = {Tannenbaum, LV and Gulsby, WD and Zobel, SS and Miller, KV}, title = {Where deer roam: chronic yet acute site exposures preclude ecological risk assessment.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {33}, number = {5}, pages = {789-799}, doi = {10.1111/j.1539-6924.2012.01890.x}, pmid = {22985105}, issn = {1539-6924}, mesh = {Animals ; *Deer ; *Ecology ; *Environmental Exposure ; Environmental Pollutants ; Geographic Information Systems ; Georgia ; *Risk Assessment ; }, abstract = {Global positioning system (GPS) technology has made possible the detailed tracking of the spatial movements of wildlife. Using GPS tracking collars placed on female white-tailed deer (Odocoileus virginianus) over a protracted period, we illustrate that this species is spatially irrelevant for consideration in ecological risk assessments (ERAs) for commonly assessed contaminated sites. Specifically, deer movements do not allow for a sufficiency of chemical exposures to occur such that toxicological endpoints would be triggered. Deer are spatially irrelevant not only because their home ranges and overall utilized areas dwarf prototypical hazardous waste sites. They are also inappropriate for assessment because they only minimally contact reasonably sized preferred locations, this while demonstrating a confounding high degree of site affinity for them. Our spatial movements analysis suggests that deer introduce the ERA novelty of a species displaying elements of both chronic and acute site exposure. We further suggest that other large commonly assessed high-profile mammals could also be found to be spatially irrelevant for ERAs were they to submit to the GPS tracking and subsequent data analysis we performed for the deer. Recognizing that certain receptors need not be considered in ERAs can help to simplify the ERA process.}, }
@article {pmid22971047, year = {2012}, author = {Pickles, BJ and Genney, DR and Anderson, IC and Alexander, IJ}, title = {Spatial analysis of ectomycorrhizal fungi reveals that root tip communities are structured by competitive interactions.}, journal = {Molecular ecology}, volume = {21}, number = {20}, pages = {5110-5123}, doi = {10.1111/j.1365-294X.2012.05739.x}, pmid = {22971047}, issn = {1365-294X}, mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Nucleic Acid ; Meristem/*microbiology ; Mycorrhizae/*genetics/physiology ; Pinus/microbiology ; Polymorphism, Restriction Fragment Length ; Soil Microbiology ; Spatial Analysis ; Stochastic Processes ; }, abstract = {Microbial ecology has made large advances over the last decade, mostly because of improvements in molecular analysis techniques that have enabled the detection and identification of progressively larger numbers of microbial species. However, determining the ecological patterns and processes taking place in communities of microbes remains a significant challenge. Are communities randomly assembled through dispersal and priority effects, or do species interact with each other leading to positive and negative associations? For mycorrhizal fungi, evidence is accumulating that stochastic and competitive interactions between species may both have a role in shaping community structure. Could the methodological approach, which is often incidence based, impact the outcomes detected? Here, we applied an incidence-based Terminal Restriction Fragment Length Polymorphism (T-RFLP) database approach to examine species diversity and ecological interactions within a community of ectomycorrhizal (ECM) fungi. Co-occurrence analysis revealed that the ECM community colonizing root tips was strongly structured by competitive interactions, or ecological processes generating a similar spatial pattern, rather than neutral processes. Analysis of β-diversity indicated that community structure was significantly more similar (spatially autocorrelated) at distances equal to or <3.41 m. The eight most frequently encountered species in the root tip community of ECM fungi displayed significant competitive interactions with at least one other species, showing that the incidence-based approach was capable of detecting this sort of ecological information.}, }
@article {pmid22934781, year = {2012}, author = {Pallmann, P and Schaarschmidt, F and Hothorn, LA and Fischer, C and Nacke, H and Priesnitz, KU and Schork, NJ}, title = {Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1068-1078}, pmid = {22934781}, issn = {1755-0998}, support = {5 UL1 RR025774/RR/NCRR NIH HHS/United States ; 5 R01 AG035020/AG/NIA NIH HHS/United States ; R01 DA030976/DA/NIDA NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; 5 P01 AG027734/AG/NIA NIH HHS/United States ; 5 R01 HL089655/HL/NHLBI NIH HHS/United States ; UL1 RR025774/RR/NCRR NIH HHS/United States ; R01 HL089655/HL/NHLBI NIH HHS/United States ; 2 U19 AI063603/AI/NIAID NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; 5 R01 DA030976/DA/NIDA NIH HHS/United States ; R01 MH093500/MH/NIMH NIH HHS/United States ; U19 AI063603/AI/NIAID NIH HHS/United States ; 2 U19 AG023122/AG/NIA NIH HHS/United States ; P01 AG027734/AG/NIA NIH HHS/United States ; R01 AG035020/AG/NIA NIH HHS/United States ; 5 U01 DA024417/DA/NIDA NIH HHS/United States ; 1 R01 MH093500/MH/NIMH NIH HHS/United States ; }, mesh = {*Biodiversity ; Biostatistics/*methods ; *Data Interpretation, Statistical ; Software ; }, abstract = {Comparing diversities between groups is a task biologists are frequently faced with, for example in ecological field trials or when dealing with metagenomics data. However, researchers often waver about which measure of diversity to choose as there is a multitude of approaches available. As Jost (2008, Molecular Ecology, 17, 4015) has pointed out, widely used measures such as the Shannon or Simpson index have undesirable properties which make them hard to compare and interpret. Many of the problems associated with the use of these 'raw' indices can be corrected by transforming them into 'true' diversity measures. We introduce a technique that allows the comparison of two or more groups of observations and simultaneously tests a user-defined selection of a number of 'true' diversity measures. This procedure yields multiplicity-adjusted P-values according to the method of Westfall and Young (1993, Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment, 49, 941), which ensures that the rate of false positives (type I error) does not rise when the number of groups and/or diversity indices is extended. Software is available in the R package 'simboot'.}, }
@article {pmid22934641, year = {2012}, author = {Roossinck, MJ}, title = {Plant virus metagenomics: biodiversity and ecology.}, journal = {Annual review of genetics}, volume = {46}, number = {}, pages = {359-369}, doi = {10.1146/annurev-genet-110711-155600}, pmid = {22934641}, issn = {1545-2948}, mesh = {Base Sequence ; Computational Biology ; *Ecosystem ; *Environmental Microbiology ; Evolution, Molecular ; *Genetic Variation ; *Genome, Viral ; Information Storage and Retrieval ; Metagenomics/methods ; Plant Diseases/virology ; Plant Viruses/*genetics ; Plants/virology ; RNA, Small Interfering/genetics ; }, abstract = {Viral metagenomics is the study of viruses in environmental samples, using next generation sequencing that produces very large data sets. For plant viruses, these studies are still relatively new, but are already indicating that our current knowledge grossly underestimates the diversity of these viruses. Some plant virus studies are using thousands of individual plants so that each sequence can be traced back to its precise host. These studies should allow for deeper ecological and evolutionary analyses. The finding of so many new plant viruses that do not cause any obvious symptoms in wild plant hosts certainly changes our perception of viruses and how they interact with their hosts. The major difficulty in these (as in all) metagenomic studies continues to be the need for better bioinformatics tools to decipher the large data sets. The implications of this new information on plant viruses for international agriculture remain to be addressed.}, }
@article {pmid22912854, year = {2012}, author = {Qiao, H and Lin, C and Ji, L and Jiang, Z}, title = {mMWeb--an online platform for employing multiple ecological niche modeling algorithms.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e43327}, pmid = {22912854}, issn = {1932-6203}, mesh = {*Algorithms ; Computational Biology/*methods ; Ecology/*methods ; *Ecosystem ; *Internet ; *Models, Biological ; *Software ; }, abstract = {BACKGROUND: Predicting the ecological niche and potential habitat distribution of a given organism is one of the central domains of ecological and biogeographical research. A wide variety of modeling techniques have been developed for this purpose. In order to implement these models, the users must prepare a specific runtime environment for each model, learn how to use multiple model platforms, and prepare data in a different format each time. Additionally, often model results are difficult to interpret, and a standardized method for comparing model results across platforms does not exist. We developed a free and open source online platform, the multi-models web-based (mMWeb) platform, to address each of these problems, providing a novel environment in which the user can implement and compare multiple ecological niche model (ENM) algorithms.<br><br>METHODOLOGY: mMWeb combines 18 existing ENMs and their corresponding algorithms and provides a uniform procedure for modeling the potential habitat niche of a species via a common web browser. mMWeb uses Java Native Interface (JNI), Java R Interface to combine the different ENMs and executes multiple tasks in parallel on a super computer. The cross-platform, user-friendly interface of mMWeb simplifies the process of building ENMs, providing an accessible and efficient environment from which to explore and compare different model algorithms.}, }
@article {pmid22808280, year = {2012}, author = {Toju, H and Tanabe, AS and Yamamoto, S and Sato, H}, title = {High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e40863}, pmid = {22808280}, issn = {1932-6203}, mesh = {Ascomycota/*classification/*genetics ; Base Pair Mismatch ; Base Sequence ; Basidiomycota/*classification/*genetics ; Cell Nucleus/genetics ; Computational Biology ; DNA Primers/*metabolism ; DNA, Fungal/*genetics ; DNA, Intergenic/*genetics ; Environmental Microbiology ; Mycological Typing Techniques ; Nucleic Acid Renaturation/genetics ; Plants/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Temperature ; }, abstract = {The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.}, }
@article {pmid22807668, year = {2012}, author = {Faust, K and Sathirapongsasuti, JF and Izard, J and Segata, N and Gevers, D and Raes, J and Huttenhower, C}, title = {Microbial co-occurrence relationships in the human microbiome.}, journal = {PLoS computational biology}, volume = {8}, number = {7}, pages = {e1002606}, pmid = {22807668}, issn = {1553-7358}, support = {U54HG004969/HG/NHGRI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R21 CA139193/CA/NCI NIH HHS/United States ; 1R01HG005969/HG/NHGRI NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; CA139193/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Computational Biology ; DNA, Bacterial/chemistry ; Ecosystem ; Female ; Gastrointestinal Tract/microbiology ; Genes, rRNA/genetics ; Humans ; Linear Models ; Male ; Metagenome/*physiology ; Microbial Interactions/physiology ; Nasal Cavity/microbiology ; Phylogeny ; Skin/microbiology ; Vagina/microbiology ; }, abstract = {The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome.}, }
@article {pmid22791706, year = {2012}, author = {Richardson, AJ and Brown, CJ and Brander, K and Bruno, JF and Buckley, L and Burrows, MT and Duarte, CM and Halpern, BS and Hoegh-Guldberg, O and Holding, J and Kappel, CV and Kiessling, W and Moore, PJ and O'Connor, MI and Pandolfi, JM and Parmesan, C and Schoeman, DS and Schwing, F and Sydeman, WJ and Poloczanska, ES}, title = {Climate change and marine life.}, journal = {Biology letters}, volume = {8}, number = {6}, pages = {907-909}, pmid = {22791706}, issn = {1744-957X}, mesh = {*Climate Change ; Data Collection ; Data Interpretation, Statistical ; *Ecosystem ; Geography ; Marine Biology/*methods/*trends ; Oceanography/methods ; Oceans and Seas ; Time Factors ; }, abstract = {A Marine Climate Impacts Workshop was held from 29 April to 3 May 2012 at the US National Center of Ecological Analysis and Synthesis in Santa Barbara. This workshop was the culmination of a series of six meetings over the past three years, which had brought together 25 experts in climate change ecology, analysis of large datasets, palaeontology, marine ecology and physical oceanography. Aims of these workshops were to produce a global synthesis of climate impacts on marine biota, to identify sensitive habitats and taxa, to inform the current Intergovernmental Panel on Climate Change (IPCC) process, and to strengthen research into ecological impacts of climate change.}, }
@article {pmid22784095, year = {2012}, author = {Balakirev, ES and Krupnova, TN and Ayala, FJ}, title = {DNA variation in the phenotypically-diverse brown alga Saccharina japonica.}, journal = {BMC plant biology}, volume = {12}, number = {}, pages = {108}, pmid = {22784095}, issn = {1471-2229}, mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Algal/*genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Genetic Markers ; Mitochondria/genetics ; Molecular Sequence Data ; Phaeophyta/*genetics ; *Phenotype ; Phylogeny ; Plastids/genetics ; *Polymorphism, Genetic ; Recombination, Genetic ; Ribulose-Bisphosphate Carboxylase/genetics ; }, abstract = {BACKGROUND: Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the &quot;longipes&quot; (LON) and &quot;shallow-water&quot; (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica.<br><br>RESULTS: The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI &quot;barcoding&quot; region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events.<br><br>CONCLUSION: Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.}, }
@article {pmid22760973, year = {2012}, author = {Perry, CK and Garside, H and Morones, S and Hayman, LL}, title = {Physical activity interventions for adolescents: an ecological perspective.}, journal = {The journal of primary prevention}, volume = {33}, number = {2-3}, pages = {111-135}, pmid = {22760973}, issn = {1573-6547}, mesh = {Adolescent ; Adolescent Behavior/*psychology ; Child ; Databases, Bibliographic ; Ecology ; Female ; Humans ; Male ; Models, Psychological ; *Motor Activity ; Self Efficacy ; }, abstract = {Many factors contribute to the decline in physical activity (PA) observed during adolescence. We used an ecological framework to review 30 publications of PA interventions published between 1977 and 2009 targeting youth aged 12-18 years (19 PA interventions). We included studies that measured a primary outcome of PA and also examined intervening variables. Most studies targeted the intrapersonal and environmental domains. The body of literature on PA interventions in youth suggests the importance of targeting ecological domains beyond the individual level. Future investigations should be theory-based and include analysis of mediators across ecological domains in order to identify the most effective combination of factors to promote PA in youth.}, }
@article {pmid22744689, year = {2012}, author = {Tevi, G and Tevi, A}, title = {Remote sensing and GIS techniques for assessment of the soil water content in order to improve agricultural practice and reduce the negative impact on groundwater: case study, agricultural area Ştefan cel Mare, Călăraşi County.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {66}, number = {3}, pages = {580-587}, doi = {10.2166/wst.2012.209}, pmid = {22744689}, issn = {0273-1223}, mesh = {Agriculture/*methods ; *Geographic Information Systems ; Geography ; Groundwater/*analysis ; Remote Sensing Technology/*methods ; Romania ; Soil/*analysis ; Spectrum Analysis ; }, abstract = {Traditional agricultural practices based on non-customized irrigation and soil fertilization are harmful for the environment, and may pose a risk for human health. By continuing the use of these practices, it is not possible to ensure effective land management, which might be acquired by using advanced satellite technology configured for modern agricultural development. The paper presents a methodology based on the correlation between remote sensing data and field observations, aiming to identify the key features and to establish an interpretation pattern for the inhomogeneity highlighted by the remote sensing data. Instead of using classical methods for the evaluation of land features (field analysis, measurements and mapping), the approach is to use high resolution multispectral and hyperspectral methods, in correlation with data processing and geographic information systems (GIS), in order to improve the agricultural practices and mitigate their environmental impact (soil and shallow aquifer).}, }
@article {pmid22705880, year = {2012}, author = {Sikhakolli, UR and López-Giráldez, F and Li, N and Common, R and Townsend, JP and Trail, F}, title = {Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {49}, number = {8}, pages = {663-673}, doi = {10.1016/j.fgb.2012.05.009}, pmid = {22705880}, issn = {1096-0937}, mesh = {Apoptosis/genetics ; Cluster Analysis ; Computational Biology/methods ; *Ecosystem ; Fruiting Bodies, Fungal/*genetics/*growth &amp; development/ultrastructure ; Fusarium/*genetics/*growth &amp; development/ultrastructure ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Lipid Metabolism/genetics ; Mating Factor ; Peptides/genetics ; Phenotype ; *Transcriptome ; }, abstract = {Fusarium graminearum and F. verticillioides are devastating cereal pathogens with very different life history and ecological characteristics. F. graminearum is homothallic, and sexual spores are an important component of its life cycle, responsible for disease initiation. F. verticilloides is heterothallic, and produces only modest numbers of fruiting bodies, which are not a significant source of inoculum. To identify corresponding differences in the transcriptional program underlying fruiting body development in the two species, comparative expression was performed, analyzing six developmental stages. To accompany the transcriptional analysis, detailed morphological characterization of F. verticillioides development was performed and compared to a previous morphological analysis of F. graminearum. Morphological development was similar between the two species, except for the observation of possible trichogynes in F. verticillioides ascogonia, which have not been previously reported for any Fusarium species. Expression of over 9000 orthologous genes were measured for the two species. Functional assignments of highly expressed orthologous genes at each time-point revealed the majority of highly expressed genes fell into the &quot;unclassified proteins&quot; category, reflecting the lack of characterization of genes for sexual development in both species. Simultaneous examination of morphological development and stage-specific gene expression suggests that degeneration of the paraphyses during sexual development is an apoptotic process. Expression of mating type genes in the two species differed, possibly reflecting the divergent roles they play in sexual development. Overall, the differences in gene expression reflect the greater role of fruiting bodies in the life cycle and ecology of F. graminearum versus F. verticillioides.}, }
@article {pmid22702658, year = {2012}, author = {Büchel, K and McDowell, E and Nelson, W and Descour, A and Gershenzon, J and Hilker, M and Soderlund, C and Gang, DR and Fenning, T and Meiners, T}, title = {An elm EST database for identifying leaf beetle egg-induced defense genes.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {242}, pmid = {22702658}, issn = {1471-2164}, mesh = {Animals ; Coleoptera/*growth &amp; development ; Computational Biology ; Cyclopentanes/metabolism ; *Databases, Genetic ; Expressed Sequence Tags ; Gene Expression Profiling ; Gene Library ; Metabolic Networks and Pathways ; Ovum/chemistry/metabolism ; Oxylipins/metabolism ; Photosynthesis/genetics ; Plant Leaves/genetics ; Ulmus/*genetics ; }, abstract = {BACKGROUND: Plants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor), egg laying by the elm leaf beetle (Xanthogaleruca luteola) activates the emission of volatiles that attract specialised egg parasitoids, which in turn kill the eggs. Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes.<br><br>RESULTS: Here we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i) untreated control elms, and elms treated with (ii) egg laying and feeding by elm leaf beetles, (iii) feeding, (iv) artificial transfer of egg clutches, and (v) methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs) were identified which clustered into 52,823 unique transcripts (Unitrans) and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant) database, particularly to those from Vitis, Ricinus, Populus and Arabidopsis. Comparative in silico analysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction, transport and primary metabolism.<br><br>CONCLUSION: Here we present a dataset for a large-scale study of the mechanisms of plant defense against insect eggs in a co-evolved, natural ecological plant-insect system. The EST database analysis provided here is a first step in elucidating the transcriptional responses of elm to elm leaf beetle infestation, and adds further to our knowledge on insect egg-induced transcriptomic changes in plants. The sequences identified in our comparative analysis give many hints about novel defense mechanisms directed towards eggs.}, }
@article {pmid22696284, year = {2012}, author = {Elbroch, LM and Wittmer, HU}, title = {Table scraps: inter-trophic food provisioning by pumas.}, journal = {Biology letters}, volume = {8}, number = {5}, pages = {776-779}, pmid = {22696284}, issn = {1744-957X}, mesh = {Animals ; Behavior, Animal ; Biodiversity ; Birds ; Chile ; Conservation of Natural Resources ; Ecology ; Environmental Monitoring/methods ; Feeding Behavior ; Female ; Geographic Information Systems ; Geography ; Male ; *Predatory Behavior ; Puma ; Species Specificity ; Time Factors ; Wolves/physiology ; }, abstract = {Large carnivores perform keystone ecological functions through direct predation, or indirectly, through food subsidies to scavengers or trophic cascades driven by their influence on the distributions of their prey. Pumas (Puma concolor) are an elusive, cryptic species difficult to study and little is known about their inter-trophic-level interactions in natural communities. Using new GPS technology, we discovered that pumas in Patagonia provided 232 ± 31 kg of edible meat/month/100 km(2) to near-threatened Andean condors (Vultur gryphus) and other members of a diverse scavenger community. This is up to 3.1 times the contributions by wolves (Canis lupus) to communities in Yellowstone National Park, USA, and highlights the keystone role large, solitary felids play in natural systems. These findings are more pertinent than ever, for managers increasingly advocate controlling pumas and other large felids to bolster prey populations and mitigate concerns over human and livestock safety, without a full understanding of the potential ecological consequences of their actions.}, }
@article {pmid22646978, year = {2012}, author = {Deng, Y and Jiang, YH and Yang, Y and He, Z and Luo, F and Zhou, J}, title = {Molecular ecological network analyses.}, journal = {BMC bioinformatics}, volume = {13}, number = {}, pages = {113}, pmid = {22646978}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; Ecology/*methods ; Ecosystem ; Genes, rRNA ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Software ; Soil/analysis ; Soil Microbiology ; Temperature ; }, abstract = {BACKGROUND: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data.<br><br>RESULTS: Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA).<br><br>CONCLUSIONS: The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.}, }
@article {pmid22645818, year = {2012}, author = {Buhle, ER and Feist, BE and Hilborn, R}, title = {Population dynamics and control of invasive Spartina alterniflora: inference and forecasting under uncertainty.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {22}, number = {3}, pages = {880-893}, pmid = {22645818}, issn = {1051-0761}, mesh = {Decision Support Techniques ; *Ecosystem ; *Introduced Species ; Models, Biological ; Poaceae/*physiology ; Population Dynamics ; Washington ; }, abstract = {Managing invaded ecosystems entails making decisions about control strategies in the face of scientific uncertainty and ecological stochasticity. Statistical tools such as model selection and Bayesian decision analysis can guide decision-making by estimating probabilities of outcomes under alternative management scenarios, but these tools have seldom been applied in invasion ecology. We illustrate the use of model selection and Bayesian methods in a case study of smooth cordgrass (Spartina alterniflora) invading Willapa Bay, Washington. To address uncertainty in model structure, we quantified the weight of evidence for two previously proposed hypotheses, that S. alterniflora recruitment varies with climatic conditions (represented by sea surface temperature) and that recruitment is subject to an Allee effect due to pollen limitation. By fitting models to time series data, we found strong support for climate effects, with higher per capita seedling production in warmer years, but no evidence for an Allee effect based on either the total area invaded or the mean distance between neighboring clones. We used the best-supported model to compare alternative control strategies, incorporating uncertainty in parameter estimates and population dynamics. For a fixed annual removal effort, the probability of eradication in 10 years was highest, and final invaded area lowest, if removals targeted the smallest clones rather than the largest or randomly selected clones. The relationship between removal effort and probability of eradication was highly nonlinear, with a sharp threshold separating -0% and -100% probability of success, and this threshold was 95% lower in simulations beginning early rather than late in the invasion. This advantage of a rapid response strategy is due to density-dependent population growth, which produces alternative stable equilibria depending on the initial invasion size when control begins. Our approach could be applied to a wide range of invasive species management problems where appropriate data are available.}, }
@article {pmid22629169, year = {2012}, author = {León Ruiz, EJ and García Mozo, H and Domínguez Vilches, E and Galán, C}, title = {The use of geostatistics in the study of floral phenology of Vulpia geniculata (L.) link.}, journal = {TheScientificWorldJournal}, volume = {2012}, number = {}, pages = {624247}, pmid = {22629169}, issn = {1537-744X}, mesh = {*Data Interpretation, Statistical ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Poaceae/*growth &amp; development ; }, abstract = {Traditionally phenology studies have been focused on changes through time, but there exist many instances in ecological research where it is necessary to interpolate among spatially stratified samples. The combined use of Geographical Information Systems (GIS) and Geostatistics can be an essential tool for spatial analysis in phenological studies. Geostatistics are a family of statistics that describe correlations through space/time and they can be used for both quantifying spatial correlation and interpolating unsampled points. In the present work, estimations based upon Geostatistics and GIS mapping have enabled the construction of spatial models that reflect phenological evolution of Vulpia geniculata (L.) Link throughout the study area during sampling season. Ten sampling points, scattered throughout the city and low mountains in the &quot;Sierra de Córdoba&quot; were chosen to carry out the weekly phenological monitoring during flowering season. The phenological data were interpolated by applying the traditional geostatitical method of Kriging, which was used to elaborate weekly estimations of V. geniculata phenology in unsampled areas. Finally, the application of Geostatistics and GIS to create phenological maps could be an essential complement in pollen aerobiological studies, given the increased interest in obtaining automatic aerobiological forecasting maps.}, }
@article {pmid22628380, year = {2012}, author = {Herben, T and Suda, J and Klimesová, J and Mihulka, S and Ríha, P and Símová, I}, title = {Ecological effects of cell-level processes: genome size, functional traits and regional abundance of herbaceous plant species.}, journal = {Annals of botany}, volume = {110}, number = {7}, pages = {1357-1367}, pmid = {22628380}, issn = {1095-8290}, mesh = {Cell Division ; Cell Size ; Chromosomes, Plant/genetics ; Czech Republic ; DNA, Plant/analysis/genetics ; Databases, Nucleic Acid ; Ecology ; Genome Size/*physiology ; Genome, Plant/*genetics ; Magnoliopsida/genetics/growth &amp; development/*physiology ; Phenotype ; Phylogeny ; Plant Leaves/genetics ; Ploidies ; Seeds/genetics ; }, abstract = {BACKGROUND AND AIMS: Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate.<br><br>METHODS: Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis.<br><br>KEY RESULTS: Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R(2) = 0·145) than for perennials (R(2) = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance.<br><br>CONCLUSIONS: The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes.}, }
@article {pmid22619109, year = {2012}, author = {Hickey, GL and Craig, PS and Luttik, R and de Zwart, D}, title = {On the quantification of intertest variability in ecotoxicity data with application to species sensitivity distributions.}, journal = {Environmental toxicology and chemistry}, volume = {31}, number = {8}, pages = {1903-1910}, doi = {10.1002/etc.1891}, pmid = {22619109}, issn = {1552-8618}, mesh = {Bayes Theorem ; Ecotoxicology/instrumentation/*methods/*standards/statistics &amp; numerical data ; Environmental Monitoring/*methods/*standards ; European Union ; Lethal Dose 50 ; Models, Biological ; *Models, Statistical ; Reproducibility of Results ; Risk Assessment/methods ; Species Specificity ; Toxicity Tests, Chronic/statistics &amp; numerical data ; }, abstract = {Ecotoxicological hazard assessment relies on species effect data to estimate quantities such as the predicted no-effect concentration. While there is a concerted effort to quantify uncertainty in risk assessments, the uncertainty due to intertest variability in species effect measurements is an overlo