@article {pmid32445889, year = {2020}, author = {Guo, J and Xu, W and Hu, Y and Huang, J and Zhao, Y and Zhang, L and Huang, CH and Ma, H}, title = {Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations.}, journal = {Molecular plant}, volume = {13}, number = {8}, pages = {1117-1133}, doi = {10.1016/j.molp.2020.05.011}, pmid = {32445889}, issn = {1752-9867}, abstract = {The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering plants. Most members of the Cucurbitaceae, a family containing ∼1000 species and many important crops, are climbers and have characteristic tendrils and pepo fruits. Here, we present 127 newly sequenced transcriptomes and genomes along with other datasets for a total of 136 cucurbits representing all tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major clades. We analyzed whole-genome duplication, diversification dynamics, and ancestral morphologies, and found that after early genome duplication event(s), a burst of diversification and morphological innovations in flower, fruit, and root characters occurred under the climate optimum in the Early Eocene. Species radiation during the Mid-Eocene Climatic Optimum also coincided with several morphological changes shared by 80% of cucurbits. We found that the cucurbit-specific tendril identity gene TEN originated from a paleo-polyploidization event at the origin of the family. Our results support the hypothesis that cucurbit diversifications were probably driven by increased genetic diversity following polyploidizations and by trait morphological innovations under paleo-climate upheavals. Our study provides a phylogenetic framework and new insights into morphological and genomic changes underlying the adaptive evolution of Cucurbitaceae.}, }
@article {pmid33846912, year = {2021}, author = {Liu, H and Jiang, Y and Misa, R and Gao, J and Xia, M and Preusse, A and Sroka, A and Jiang, Y}, title = {Ecological environment changes of mining areas around Nansi lake with remote sensing monitoring.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {33846912}, issn = {1614-7499}, support = {CHN/1101176STP//Alexander von Humboldt-Stiftung/ ; 2016YFC0501105//National Research and Development Project/ ; 2018-TD-MS052//China Coal Technology & Engineering Group Project/ ; }, abstract = {Underground mining activity has existed for more than 100 years in Nansi lake. Coal mining not only plays a supporting role in local social and economic development but also has a significant impact on the ecological environment in the region. Landsat series remote sensing data (1988~2019) are used to research the impact of coal mining on the ecological environment in Nansi lake. Then support vector machine (SVM) classifier is applied to extract the water area of the upstream lake from 1988 to 2019, and ecological environment and spatiotemporal variation characteristics are analyzed by Remote Sensing Ecology Index (RSEI). The results illustrate that the water area change is associated with annual precipitation. In terms of ecological quality, the area of poor ecological quality areas increased by 101.782 km2, while the area of good and excellent quality areas decreased by 218.988 km2 from 2009 to 2019. So compared with 2009, the ecological quality of the lake is worse in 2019, and then the reason for this change is due to large-scale underground mining. Therefore, the coal mines from the natural reserve may be closed or limited to the mining boundary for protecting the lake's ecological environment.}, }
@article {pmid33808463, year = {2021}, author = {Pushkareva, E and Sommer, V and Barrantes, I and Karsten, U}, title = {Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, doi = {10.3390/microorganisms9040714}, pmid = {33808463}, issn = {2076-2607}, support = {20016/462//Deutsche Bundesstiftung Umwelt/ ; }, abstract = {Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples.}, }
@article {pmid33793560, year = {2021}, author = {Burthe, SJ and Schäfer, SM and Asaaga, FA and Balakrishnan, N and Chanda, MM and Darshan, N and Hoti, SL and Kiran, SK and Seshadri, T and Srinivas, PN and Vanak, AT and Purse, BV}, title = {Reviewing the ecological evidence base for management of emerging tropical zoonoses: Kyasanur Forest Disease in India as a case study.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {4}, pages = {e0009243}, doi = {10.1371/journal.pntd.0009243}, pmid = {33793560}, issn = {1935-2735}, abstract = {Zoonoses disproportionately affect tropical communities and are associated with human modification and use of ecosystems. Effective management is hampered by poor ecological understanding of disease transmission and often focuses on human vaccination or treatment. Better ecological understanding of multi-vector and multi-host transmission, social and environmental factors altering human exposure, might enable a broader suite of management options. Options may include "ecological interventions" that target vectors or hosts and require good knowledge of underlying transmission processes, which may be more effective, economical, and long lasting than conventional approaches. New frameworks identify the hierarchical series of barriers that a pathogen needs to overcome before human spillover occurs and demonstrate how ecological interventions may strengthen these barriers and complement human-focused disease control. We extend these frameworks for vector-borne zoonoses, focusing on Kyasanur Forest Disease Virus (KFDV), a tick-borne, neglected zoonosis affecting poor forest communities in India, involving complex communities of tick and host species. We identify the hierarchical barriers to pathogen transmission targeted by existing management. We show that existing interventions mainly focus on human barriers (via personal protection and vaccination) or at barriers relating to Kyasanur Forest Disease (KFD) vectors (tick control on cattle and at the sites of host (monkey) deaths). We review the validity of existing management guidance for KFD through literature review and interviews with disease managers. Efficacy of interventions was difficult to quantify due to poor empirical understanding of KFDV-vector-host ecology, particularly the role of cattle and monkeys in the disease transmission cycle. Cattle are hypothesised to amplify tick populations. Monkeys may act as sentinels of human infection or are hypothesised to act as amplifying hosts for KFDV, but the spatial scale of risk arising from ticks infected via monkeys versus small mammal reservoirs is unclear. We identified 19 urgent research priorities for refinement of current management strategies or development of ecological interventions targeting vectors and host barriers to prevent disease spillover in the future.}, }
@article {pmid33784860, year = {2021}, author = {Todorov, OS and Blomberg, SP and Goswami, A and Sears, K and Drhlík, P and Peters, J and Weisbecker, V}, title = {Testing hypotheses of marsupial brain size variation using phylogenetic multiple imputations and a Bayesian comparative framework.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1947}, pages = {20210394}, doi = {10.1098/rspb.2021.0394}, pmid = {33784860}, issn = {1471-2954}, abstract = {Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets of 16 predictor variables, to model the prevalent hypotheses explaining brain size evolution using phylogenetically corrected Bayesian generalized linear mixed-effects modelling. Despite this comprehensive analysis, litter size emerges as the only significant predictor. Marsupials differ from the more frequently studied placentals in displaying a much lower diversity of reproductive traits, which are known to interact extensively with many behavioural and ecological predictors of brain size. Our results therefore suggest that studies of relative brain size evolution in placental mammals may require targeted co-analysis or adjustment of reproductive parameters like litter size, weaning age or gestation length. This supports suggestions that significant associations between behavioural or ecological variables with relative brain size may be due to a confounding influence of the extensive reproductive diversity of placental mammals.}, }
@article {pmid33480058, year = {2021}, author = {Marconi, S and Graves, SJ and Weinstein, BG and Bohlman, S and White, EP}, title = {Estimating individual-level plant traits at scale.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {}, number = {}, pages = {e02300}, doi = {10.1002/eap.2300}, pmid = {33480058}, issn = {1051-0761}, support = {GBMF4563//Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative/ ; 1926542//National Science Foundation/ ; DEB-1442280//NSF Dimension of Biodiversity program/ ; FLA-FOR-005470//USDA/NIFA McIntire-Stennis program/ ; //University of Florida Biodiversity Institute (UFBI)/ ; //Informatics Institute (UFII) Graduate Fellowship/ ; }, abstract = {Functional ecology has increasingly focused on describing ecological communities based on their traits (measurable features affecting individuals' fitness and performance). Analyzing trait distributions within and among forests could significantly improve understanding of community composition and ecosystem function. Historically, data on trait distributions are generated by (1) collecting a small number of leaves from a small number of trees, which suffers from limited sampling but produces information at the fundamental ecological unit (the individual), or (2) using remote-sensing images to infer traits, producing information continuously across large regions, but as plots (containing multiple trees of different species) or pixels, not individuals. Remote-sensing methods that identify individual trees and estimate their traits would provide the benefits of both approaches, producing continuous large-scale data linked to biological individuals. We used data from the National Ecological Observatory Network (NEON) to develop a method to scale up functional traits from 160 trees to the millions of trees within the spatial extent of two NEON sites. The pipeline consists of three stages: (1) image segmentation, to identify individual trees and estimate structural traits; (2) an ensemble of models to infer leaf mass area (LMA), nitrogen, carbon, and phosphorus content using hyperspectral signatures, and DBH from allometry; and (3) predictions for segmented crowns for the full remote-sensing footprint at the NEON sites. The R2 values on held-out test data ranged from 0.41 to 0.75 on held-out test data. The ensemble approach performed better than single partial least-squares models. Carbon performed poorly compared to other traits (R2 of 0.41). The crown segmentation step contributed the most uncertainty in the pipeline, due to over-segmentation. The pipeline produced good estimates of DBH (R2 of 0.62 on held-out data). Trait predictions for crowns performed significantly better than comparable predictions on pixels, resulting in improvement of R2 on test data of between 0.07 and 0.26. We used the pipeline to produce individual-level trait data for ~5 million individual crowns, covering a total extent of ~360 km2 . This large data set allows testing ecological questions on landscape scales, revealing that foliar traits are correlated with structural traits and environmental conditions.}, }
@article {pmid33764467, year = {2021}, author = {Modica, MV and Ahmad, R and Ainsworth, S and Anderluh, G and Antunes, A and Beis, D and Caliskan, F and Serra, MD and Dutertre, S and Moran, Y and Nalbantsoy, A and Oukkache, N and Pekar, S and Remm, M and von Reumont, BM and Sarigiannis, Y and Tarallo, A and Tytgat, J and Undheim, EAB and Utkin, Y and Verdes, A and Violette, A and Zancolli, G}, title = {The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics.}, journal = {GigaScience}, volume = {10}, number = {3}, pages = {}, doi = {10.1093/gigascience/giab019}, pmid = {33764467}, issn = {2047-217X}, abstract = {Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging and pursued by different teams lacking connection with each other. This lack of coordination hampers the full development of venom investigation and applications. The COST Action CA19144-European Venom Network was recently launched to promote synergistic interactions among different stakeholders and foster venom research at the European level.}, }
@article {pmid32746696, year = {2021}, author = {Baker, BJ and Appler, KE and Gong, X}, title = {New Microbial Biodiversity in Marine Sediments.}, journal = {Annual review of marine science}, volume = {13}, number = {}, pages = {161-175}, doi = {10.1146/annurev-marine-032020-014552}, pmid = {32746696}, issn = {1941-0611}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Datasets as Topic ; Geologic Sediments/*microbiology ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.}, }
@article {pmid33184309, year = {2020}, author = {García-Jiménez, R and Margalida, A and Pérez-García, JM}, title = {Influence of individual biological traits on GPS fix-loss errors in wild bird tracking.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19621}, pmid = {33184309}, issn = {2045-2322}, mesh = {*Animal Migration ; Animals ; Animals, Wild/*physiology ; Birds/*physiology ; Breeding ; Ecosystem ; Female ; France ; *Geographic Information Systems ; Humans ; Male ; Spain ; Telemetry ; Territoriality ; }, abstract = {In recent decades, global positioning system (GPS) location data and satellite telemetry systems for data transmission have become fundamental in the study of basic ecological traits in wildlife biology. Evaluating GPS location errors is essential in assessing detailed information about the behaviour of an animal species such as migration, habitat selection, species distribution or foraging strategy. While many studies of the influence of environmental and technical factors on the fix errors of solar-powered GPS transmitters have been published, few studies have focussed on the performance of GPS systems in relation to a species' biological traits. Here, we evaluate the possible effects of the biological traits of a large raptor on the frequency of lost fixes-the fix-loss rate (FLR). We analysed 95,686 records obtained from 20 Bearded Vultures Gypaetus barbatus tracked with 17 solar-powered satellite transmitters in the Pyrenees (Spain, France and Andorra), between 2006 and 2019 to evaluate the influence of biological, technical, and environmental factors on the fix-loss rate of transmitters. We show that combined effects of technical factors and the biological traits of birds explained 23% of the deviance observed. As expected, the transmitter usage time significantly increased errors in the fix-loss rate, although the flight activity of birds revealed an unexpected trade-off: the greater the proportion of fixes recorded from perched birds, the lower the FLR. This finding seems related with the fact that territorial and breeding birds spend significantly more time flying than non-territorial individuals. The fix success rate is apparently due to the interactions between a complex of factors. Non-territorial adults and subadults, males, and breeding individuals showed a significantly lower FLR than juveniles-immatures females, territorial birds or non-breeding individuals. Animal telemetry tracking studies should include error analyses before reaching any ecological conclusions or hypotheses about spatial distribution.}, }
@article {pmid33742448, year = {2021}, author = {Soria, CD and Pacifici, M and Di Marco, M and Stephen, SM and Rondinini, C}, title = {COMBINE: a coalesced mammal database of intrinsic and extrinsic traits.}, journal = {Ecology}, volume = {}, number = {}, pages = {e03344}, doi = {10.1002/ecy.3344}, pmid = {33742448}, issn = {1939-9170}, abstract = {The use of species' traits in macroecological analyses has gained popularity in the last decade, becoming an important tool to understand global biodiversity patterns. Currently, trait data can be found across a wide variety of data sets included in websites, articles, and books, each one with its own taxonomic classification, set of traits and data management methodology. Mammals, in particular, are among the most studied taxa, with large sources of trait information readily available. To facilitate the use of these data, we did an extensive review of published mammal trait data sources between 1999 and May 2020 and produced COMBINE: a COalesced Mammal dataBase of INtrinsic and Extrinsic traits. Our aim was to create a taxonomically integrated database of mammal traits that maximized trait number and coverage without compromising data quality. COMBINE contains information on 54 traits for 6,234 extant and recently extinct mammal species, including information on morphology, reproduction, diet, biogeography, life-habit, phenology, behavior, home range and density. Additionally, we calculated other relevant traits such as habitat and altitudinal breadths for all species and dispersal for terrestrial non-volant species. All data are compatible with the taxonomies of the IUCN Red List v. 2020-2 and PHYLACINE v. 1.2. Missing data were adequately flagged and imputed for non-biogeographical traits with 20% or more data available. We obtained full data sets for 21 traits such as female maturity, litter size, maximum longevity, trophic level, and dispersal, providing imputation performance statistics for all. This data set will be especially useful for those interested in including species' traits in large-scale ecological and conservation analyses. There are no copyright or proprietary restrictions; we request citation of this publication and all relevant underlying data sources (found in Data S1: trait_data_sources.csv), upon using these data.}, }
@article {pmid33485207, year = {2021}, author = {Kang, A and Ren, L and Hua, C and Song, H and Dong, M and Fang, Z and Zhu, M}, title = {Environmental management strategy in response to COVID-19 in China: Based on text mining of government open information.}, journal = {The Science of the total environment}, volume = {769}, number = {}, pages = {145158}, doi = {10.1016/j.scitotenv.2021.145158}, pmid = {33485207}, issn = {1879-1026}, mesh = {*COVID-19 ; China/epidemiology ; Conservation of Natural Resources ; Data Mining ; Government ; Humans ; *Pandemics ; Retrospective Studies ; SARS-CoV-2 ; }, abstract = {Coronavirus disease 2019 (COVID-19) is a global pandemic and a major health emergency. In the process of fighting against COVID-19, the China Ministry of Ecology and Environment (MEE) responded quickly and set up a working group as soon as possible. This article uses text mining to retrospectively analyze the government's public information on the website of MEE during the epidemic, sort out the timeline of MEE's response to COVID-19. We find that MEE's work during the COVID-19 pandemic is focused on medical waste and wastewater treatment, environment emergency monitoring, pollution prevention, and other environmental management for supporting economic recovery. It drafted three main medical waste management plans, an emergency environmental monitoring plan, and formulated "two lists" - a Positive checklist for Environmental impact assessment (EIA) approval and a positive checklist for supervision and enforcement, to promote the resumption of work and production. 2020 is the final year of China's "three years of fighting pollution prevention and control". In the case of the sudden COVID-19 epidemic, the Chinese environment department has ensured that the quality of the ecological environment has not been affected by the epidemic prevention and control while ensuring the smooth progress of the fight against pollution. China's medical waste disposal capacity has also been greatly improved during this epidemic. The review of China's environmental management strategy in response to COVID-19 can provide a reference for countries in the world that are still in the critical period of epidemic control; it can provide action guidelines for the ecological environment system to respond to sudden pandemic events in the future.}, }
@article {pmid33639712, year = {2021}, author = {Lei, J and Booth, DT and Rusli, MU and Zhang, Z}, title = {Spatial Ecology of Asian Water Monitors Adjacent to a Sea Turtle Nesting Beach.}, journal = {Zoological science}, volume = {38}, number = {1}, pages = {1-7}, doi = {10.2108/zs200071}, pmid = {33639712}, issn = {0289-0003}, mesh = {*Animal Distribution ; Animals ; *Ecosystem ; Female ; Geographic Information Systems ; Homing Behavior ; Lizards/*physiology ; Malaysia ; Male ; Nesting Behavior ; Predatory Behavior ; Turtles ; }, abstract = {Nest predation is the main cause of hatching failure for many turtle populations. For green turtles (Chelonia mydas) nesting at Chagar Hutang in Redang Island, Malaysia, Asian water monitors (Varanus salvator) are a potential nest predator. However, no studies have documented the space use of this species in coastal habitat adjacent to a sea turtle nesting beach to assess its potential impact on turtle nests. Here, we used Global Positioning System (GPS) data loggers to quantify space use of Asian water monitors in order to establish the extent to which they use sea turtle nesting areas. Asian water monitors had a diurnal activity pattern and spent most of their time in rain forest habitat behind the sea turtle nesting beach. The home range occupied by Asian water monitors varied between 0.015 and 0.198 km2 calculated by the Kernel Brownian Bridge method. The space use patterns of individual Asian water monitors varied between individuals. Two males had relatively small home ranges, whereas one male and the female had a relatively large home range. Because tracked Asian water monitors in this study rarely visited the sea turtle nesting areas, it is probable that only a few individuals are responsible for opening nests.}, }
@article {pmid33199911, year = {2021}, author = {Tripathi, A and Vázquez-Baeza, Y and Gauglitz, JM and Wang, M and Dührkop, K and Nothias-Esposito, M and Acharya, DD and Ernst, M and van der Hooft, JJJ and Zhu, Q and McDonald, D and Brejnrod, AD and Gonzalez, A and Handelsman, J and Fleischauer, M and Ludwig, M and Böcker, S and Nothias, LF and Knight, R and Dorrestein, PC}, title = {Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.}, journal = {Nature chemical biology}, volume = {17}, number = {2}, pages = {146-151}, pmid = {33199911}, issn = {1552-4469}, support = {U19 AG063744/AG/NIA NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; DNA/chemistry ; DNA Fingerprinting ; Databases, Factual ; Ecology ; Food Analysis ; Mass Spectrometry/*methods ; *Metabolomics ; Microbiota ; Multivariate Analysis ; Software ; Tandem Mass Spectrometry ; Workflow ; }, abstract = {Untargeted mass spectrometry is employed to detect small molecules in complex biospecimens, generating data that are difficult to interpret. We developed Qemistree, a data exploration strategy based on the hierarchical organization of molecular fingerprints predicted from fragmentation spectra. Qemistree allows mass spectrometry data to be represented in the context of sample metadata and chemical ontologies. By expressing molecular relationships as a tree, we can apply ecological tools that are designed to analyze and visualize the relatedness of DNA sequences to metabolomics data. Here we demonstrate the use of tree-guided data exploration tools to compare metabolomics samples across different experimental conditions such as chromatographic shifts. Additionally, we leverage a tree representation to visualize chemical diversity in a heterogeneous collection of samples. The Qemistree software pipeline is freely available to the microbiome and metabolomics communities in the form of a QIIME2 plugin, and a global natural products social molecular networking workflow.}, }
@article {pmid33654452, year = {2021}, author = {Kim, HW and Yoon, S and Kim, M and Shin, M and Yoon, H and Kim, K}, title = {EcoBank: A flexible database platform for sharing ecological data.}, journal = {Biodiversity data journal}, volume = {9}, number = {}, pages = {e61866}, doi = {10.3897/BDJ.9.e61866}, pmid = {33654452}, issn = {1314-2828}, abstract = {Background: Environmental crisis challenges the human race harder than ever before. Ecologists have produced a massive amount of data to cope with the crisis. Accordingly, many national scale ecological database systems have been developed worldwide to manage and analyse these datasets. However, in Korea, ecological datasets produced by different research institutes for different purposes have not been integrated or serviced due to poorly designed information infrastructure. To address this obstacle, we present EcoBank (www.nie-ecobank.kr), an open, web-based ecological database platform designed to play an important role in ecosystem analysis, not only in Korea, but also worldwide.<br><br>New information: The architecture of EcoBank comprises core technologies of WebGIS, Application Programming Interface (API), responsive web and open-source software (OSS). Comprehensive ecological datasets from three different sources, including the National Institute of Ecology (NIE) in Korea, related national and international platforms and repositories, enter the three conceptual modules in EcoBank: data management, analysis and service. Diverse potential stakeholders of EcoBank can be classified into three groups: researchers, policy-makers and public users. EcoBank aims to expand its horizons through mutual communication amongst these stakeholders. We opened and launched the EcoBank service in December 2019 and have now begun to broaden its network by linking it to other data platforms and repositories over the globe to find possible solutions to ecological issues in Korea.}, }
@article {pmid33605211, year = {2021}, author = {Weinstein, BG and Marconi, S and Bohlman, SA and Zare, A and Singh, A and Graves, SJ and White, EP}, title = {A remote sensing derived data set of 100 million individual tree crowns for the National Ecological Observatory Network.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, doi = {10.7554/eLife.62922}, pmid = {33605211}, issn = {2050-084X}, support = {GBMF4563//Gordon and Betty Moore Foundation/ ; 1926542//National Science Foundation/ ; McIntire Stennis projects #1007080//National Institute of Food and Agriculture/ ; }, abstract = {Forests provide biodiversity, ecosystem, and economic services. Information on individual trees is important for understanding forest ecosystems but obtaining individual-level data at broad scales is challenging due to the costs and logistics of data collection. While advances in remote sensing techniques allow surveys of individual trees at unprecedented extents, there remain technical challenges in turning sensor data into tangible information. Using deep learning methods, we produced an open-source data set of individual-level crown estimates for 100 million trees at 37 sites across the United States surveyed by the National Ecological Observatory Network's Airborne Observation Platform. Each canopy tree crown is represented by a rectangular bounding box and includes information on the height, crown area, and spatial location of the tree. These data have the potential to drive significant expansion of individual-level research on trees by facilitating both regional analyses and cross-region comparisons encompassing forest types from most of the United States.}, }
@article {pmid33592451, year = {2021}, author = {Boori, MS and Choudhary, K and Paringer, R and Kupriyanov, A}, title = {Spatiotemporal ecological vulnerability analysis with statistical correlation based on satellite remote sensing in Samara, Russia.}, journal = {Journal of environmental management}, volume = {285}, number = {}, pages = {112138}, doi = {10.1016/j.jenvman.2021.112138}, pmid = {33592451}, issn = {1095-8630}, abstract = {In the present global situation, when everywhere ecology is degraded due to the extreme exhaustion of natural resources. Therefore spatiotemporal ecological vulnerability analysis is necessary for the current situation for sustainable development with protection of fragile eco-environment. Remote sensing is a unique tool to provide complete and continuous land surface information at different scales, which can use for eco-environment analysis. A methodology constructed on the principal component analysis (PCA) to identify satellite remote sensing ecological index (RSEI) for ecological vulnerability analysis and distribution based on four land surface parameters (dryness, greenness, temperature and moisture) by using Landsat TM/ETM+/OLI/TIRS data in the Samara region Russia. The results were verified by the following four methods: location-based, categorization-based, correlation-based and city center to outwards distance-based comparisons. Results indicate that ecological condition was improved from 2010 to 2015 as RSEI increased from 0.79 to 0.98 and from 2015 to 2020 the ecological condition was degraded as RSEI decreased from 0.98 to 0.82 but overall it was improved in this decade. RSEI distribution curve shows moderate to good and excellent ecological conditions and degraded ecological condition was basically characterized by high human interference and socioeconomic activities in the study area. Such a technique is a baseline for highly accurate ecological conditions mapping, monitoring and can use for decision making, management and sustainable development.}, }
@article {pmid33462369, year = {2021}, author = {Khataee, H and Scheuring, I and Czirok, A and Neufeld, Z}, title = {Effects of social distancing on the spreading of COVID-19 inferred from mobile phone data.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1661}, pmid = {33462369}, issn = {2045-2322}, mesh = {COVID-19/epidemiology/pathology/*transmission/virology ; Cell Phone ; Europe/epidemiology ; Geographic Information Systems ; Humans ; Pandemics ; *Physical Distancing ; Quarantine ; SARS-CoV-2/isolation &amp; purification ; Travel/statistics &amp; numerical data ; }, abstract = {A better understanding of how the COVID-19 pandemic responds to social distancing efforts is required for the control of future outbreaks and to calibrate partial lock-downs. We present quantitative relationships between key parameters characterizing the COVID-19 epidemiology and social distancing efforts of nine selected European countries. Epidemiological parameters were extracted from the number of daily deaths data, while mitigation efforts are estimated from mobile phone tracking data. The decrease of the basic reproductive number ([Formula: see text]) as well as the duration of the initial exponential expansion phase of the epidemic strongly correlates with the magnitude of mobility reduction. Utilizing these relationships we decipher the relative impact of the timing and the extent of social distancing on the total death burden of the pandemic.}, }
@article {pmid33493157, year = {2021}, author = {Wieters, B and Steige, KA and He, F and Koch, EM and Ramos-Onsins, SE and Gu, H and Guo, YL and Sunyaev, S and de Meaux, J}, title = {Polygenic adaptation of rosette growth in Arabidopsis thaliana.}, journal = {PLoS genetics}, volume = {17}, number = {1}, pages = {e1008748}, doi = {10.1371/journal.pgen.1008748}, pmid = {33493157}, issn = {1553-7404}, abstract = {The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution.}, }
@article {pmid33460060, year = {2020}, author = {Pinkert, S and Friess, N and Zeuss, D and Gossner, MM and Brandl, R and Brunzel, S}, title = {Mobility costs and energy uptake mediate the effects of morphological traits on species' distribution and abundance.}, journal = {Ecology}, volume = {101}, number = {10}, pages = {e03121}, doi = {10.1002/ecy.3121}, pmid = {33460060}, issn = {1939-9170}, support = {//Stifterverband/ ; //Google/ ; //Federal Office for the Environment/ ; }, abstract = {Individuals of large or dark-colored ectothermic species often have a higher reproduction and activity than small or light-colored ones. However, investments into body size or darker colors should negatively affect the fitness of individuals as they increase their growth and maintenance costs. Thus, it is unlikely that morphological traits directly affect species' distribution and abundance. Yet, this simplification is frequently made in trait-based ecological analyses. Here, we integrated the energy allocation strategies of species into an ecophysiological framework to explore the mechanisms that link species' morphological traits and population dynamics. We hypothesized that the effects of morphological traits on species' distribution and abundance are not direct but mediated by components of the energy budget and that species can allocate more energy towards dispersal and reproduction if they compensate their energetic costs by reducing mobility costs or increasing energy uptake. To classify species' energy allocation strategies, we used easily measured proxies for the mobility costs and energy uptake of butterflies that can be also applied to other taxa. We demonstrated that contrasting effects of morphological traits on distribution and abundance of butterfly species offset each other when species' energy allocation strategies are not taken into account. Larger and darker butterfly species had wider distributions and were more abundant if they compensated the investment into body size and color darkness (i.e., melanin) by reducing their mobility costs or increasing energy uptake. Adults of darker species were more mobile and foraged less compared to lighter colored ones, if an investment into melanin was indirectly compensated via a size-dependent reduction of mobility costs or increase of energy uptake. Our results indicate that differences in the energy allocations strategies of species account for a considerable part of the variation in species' distribution and abundance that is left unexplained by morphological traits alone and ignoring these differences can lead to false mechanistic conclusions. Therefore, our findings highlight the potential of integrating proxies for species' energy allocation strategies into trait-based models not only for understanding the physiological mechanisms underlying variation in species' distribution and abundance, but also for improving predictions of the population dynamics of species.}, }
@article {pmid31953819, year = {2020}, author = {Ludwig, M and Fleischauer, M and Dührkop, K and Hoffmann, MA and Böcker, S}, title = {De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2104}, number = {}, pages = {185-207}, doi = {10.1007/978-1-0716-0239-3_11}, pmid = {31953819}, issn = {1940-6029}, mesh = {Chromatography, Liquid ; *Computational Biology/methods ; *Databases, Factual ; Humans ; *Metabolomics/methods ; Molecular Structure ; *Software ; Spectrometry, Mass, Electrospray Ionization ; Structure-Activity Relationship ; Tandem Mass Spectrometry ; User-Computer Interface ; Workflow ; }, abstract = {SIRIUS 4 is the best-in-class computational tool for metabolite identification from high-resolution tandem mass spectrometry data. It offers de novo molecular formula annotation with outstanding accuracy. When searching fragmentation spectra in a structure database, it reaches over 70% correct identifications. A predicted fingerprint, which indicates the presence or absence of thousands of molecular properties, helps to deduce information about the compound of interest even if it is not contained in any structure database. Here, we present best practices and describe how to leverage the full potential of SIRIUS 4, how to incorporate it into your own workflow, and how it adds value to the analysis of mass spectrometry data beyond spectral library search.}, }
@article {pmid33060594, year = {2020}, author = {Middleton-Welling, J and Dapporto, L and García-Barros, E and Wiemers, M and Nowicki, P and Plazio, E and Bonelli, S and Zaccagno, M and Šašić, M and Liparova, J and Schweiger, O and Harpke, A and Musche, M and Settele, J and Schmucki, R and Shreeve, T}, title = {A new comprehensive trait database of European and Maghreb butterflies, Papilionoidea.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {351}, pmid = {33060594}, issn = {2052-4463}, mesh = {Africa, Northern ; Animals ; Biological Evolution ; Butterflies/*classification ; Conservation of Natural Resources ; Databases, Factual ; Ecology ; Europe ; Phylogeny ; }, abstract = {Trait-based analyses explaining the different responses of species and communities to environmental changes are increasing in frequency. European butterflies are an indicator group that responds rapidly to environmental changes with extensive citizen science contributions to documenting changes of abundance and distribution. Species traits have been used to explain long- and short-term responses to climate, land-use and vegetation changes. Studies are often characterised by limited trait sets being used, with risks that the relative roles of different traits are not fully explored. Butterfly trait information is dispersed amongst various sources and descriptions sometimes differ between sources. We have therefore drawn together multiple information sets to provide a comprehensive trait database covering 542 taxa and 25 traits described by 217 variables and sub-states of the butterflies of Europe and Maghreb (northwest Africa) which should serve for improved trait-based ecological, conservation-related, phylogeographic and evolutionary studies of this group of insects. We provide this data in two forms; the basic data and as processed continuous and multinomial data, to enhance its potential usage.}, }
@article {pmid32737307, year = {2020}, author = {Uzun, M and Alekseeva, L and Krutkina, M and Koziaeva, V and Grouzdev, D}, title = {Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {252}, pmid = {32737307}, issn = {2052-4463}, support = {18-34-01005//Russian Foundation for Basic Research (RFBR)/International ; 18-34-01005//Russian Foundation for Basic Research (RFBR)/International ; }, mesh = {Bacteria/*classification/genetics ; Datasets as Topic ; *Genome, Bacterial ; Genomics ; Iron ; Magnetosomes/*genetics ; Phylogeny ; Sulfides ; }, abstract = {Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.}, }
@article {pmid31763752, year = {2020}, author = {Zanne, AE and Abarenkov, K and Afkhami, ME and Aguilar-Trigueros, CA and Bates, S and Bhatnagar, JM and Busby, PE and Christian, N and Cornwell, WK and Crowther, TW and Flores-Moreno, H and Floudas, D and Gazis, R and Hibbett, D and Kennedy, P and Lindner, DL and Maynard, DS and Milo, AM and Nilsson, RH and Powell, J and Schildhauer, M and Schilling, J and Treseder, KK}, title = {Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {95}, number = {2}, pages = {409-433}, doi = {10.1111/brv.12570}, pmid = {31763752}, issn = {1469-185X}, mesh = {Animals ; Databases, Factual ; Ecosystem ; Fungi/genetics/*physiology ; Plants/*microbiology ; }, abstract = {Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.}, }
@article {pmid33408411, year = {2021}, author = {Zhou, Y and Shearwin-Whyatt, L and Li, J and Song, Z and Hayakawa, T and Stevens, D and Fenelon, JC and Peel, E and Cheng, Y and Pajpach, F and Bradley, N and Suzuki, H and Nikaido, M and Damas, J and Daish, T and Perry, T and Zhu, Z and Geng, Y and Rhie, A and Sims, Y and Wood, J and Haase, B and Mountcastle, J and Fedrigo, O and Li, Q and Yang, H and Wang, J and Johnston, SD and Phillippy, AM and Howe, K and Jarvis, ED and Ryder, OA and Kaessmann, H and Donnelly, P and Korlach, J and Lewin, HA and Graves, J and Belov, K and Renfree, MB and Grutzner, F and Zhou, Q and Zhang, G}, title = {Platypus and echidna genomes reveal mammalian biology and evolution.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {33408411}, issn = {1476-4687}, abstract = {Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.}, }
@article {pmid32333771, year = {2020}, author = {Machac, A}, title = {The Dynamics of Bird Diversity in the New World.}, journal = {Systematic biology}, volume = {69}, number = {6}, pages = {1180-1199}, pmid = {32333771}, issn = {1076-836X}, mesh = {Americas ; Animals ; *Biodiversity ; Birds/*classification ; Geographic Information Systems ; *Models, Biological ; }, abstract = {Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient.].}, }
@article {pmid33372367, year = {2020}, author = {Lemm, JU and Venohr, M and Globevnik, L and Stefanidis, K and Panagopoulos, Y and van Gils, J and Posthuma, L and Kristensen, P and Feld, CK and Mahnkopf, J and Hering, D and Birk, S}, title = {Multiple stressors determine river ecological status at the European scale: Towards an integrated understanding of river status deterioration.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.15504}, pmid = {33372367}, issn = {1365-2486}, abstract = {The biota of European rivers are affected by a wide range of stressors impairing water quality and hydro-morphology. Only about 40% of Europe's rivers reach 'good ecological status', a target set by the European Water Framework Directive (WFD) and indicated by the biota. It is yet unknown how the different stressors in concert impact ecological status and how the relationship between stressors and status differs between river types. We linked the intensity of seven stressors to recently measured ecological status data for more than 50,000 sub-catchment units (covering almost 80% of Europe's surface area), which were distributed among twelve broad river types. Stressor data were either derived from remote sensing data (extent of urban and agricultural land use in the riparian zone) or modelled (alteration of mean annual flow and of base flow, total phosphorous load, total nitrogen load and mixture toxic pressure, a composite metric for toxic substances), while data on ecological status were taken from national statutory reporting of the second WFD River Basin Management Plans for the years 2010 to 2015. We used Boosted Regression Trees to link ecological status to stressor intensities. The stressors explained on average 61% of deviance in ecological status for the twelve individual river types, with all seven stressors contributing considerably to this explanation. On average 39.4% of the deviance was explained by altered hydro-morphology (morphology: 23.2%; hydrology: 16.2%), 34.4% by nutrient enrichment and 26.2% by toxic substances. More than half of the total deviance was explained by stressor interaction, with nutrient enrichment and toxic substances interacting most frequently and strongly. Our results underline that the biota of all European river types are determined by co-occurring and interacting multiple stressors, lending support to the conclusion that fundamental management strategies at the catchment-scale are required to reach the ambitious objective of good ecological status of surface waters.}, }
@article {pmid33365126, year = {2020}, author = {Allen, DC and Datry, T and Boersma, KS and Bogan, MT and Boulton, AJ and Bruno, D and Busch, MH and Costigan, KH and Dodds, WK and Fritz, KM and Godsey, SE and Jones, JB and Kaletova, T and Kampf, SK and Mims, MC and Neeson, TM and Olden, JD and Pastor, AV and Poff, NL and Ruddell, BL and Ruhi, A and Singer, G and Vezza, P and Ward, AS and Zimmer, M}, title = {River ecosystem conceptual models and non-perennial rivers: A critical review.}, journal = {WIREs. Water}, volume = {7}, number = {5}, pages = {}, pmid = {33365126}, issn = {2049-1948}, abstract = {Conceptual models underpin river ecosystem research. However, current models focus on continuously flowing rivers and few explicitly address characteristics such as flow cessation and drying. The applicability of existing conceptual models to nonperennial rivers that cease to flow (intermittent rivers and ephemeral streams, IRES) has not been evaluated. We reviewed 18 models, finding that they collectively describe main drivers of biogeochemical and ecological patterns and processes longitudinally (upstream-downstream), laterally (channel-riparian-floodplain), vertically (surface water-groundwater), and temporally across local and landscape scales. However, perennial rivers are longitudinally continuous while IRES are longitudinally discontinuous. Whereas perennial rivers have bidirectional lateral connections between aquatic and terrestrial ecosystems, in IRES, this connection is unidirectional for much of the time, from terrestrial-to-aquatic only. Vertical connectivity between surface and subsurface water occurs bidirectionally and is temporally consistent in perennial rivers. However, in IRES, this exchange is temporally variable, and can become unidirectional during drying or rewetting phases. Finally, drying adds another dimension of flow variation to be considered across temporal and spatial scales in IRES, much as flooding is considered as a temporally and spatially dynamic process in perennial rivers. Here, we focus on ways in which existing models could be modified to accommodate drying as a fundamental process that can alter these patterns and processes across spatial and temporal dimensions in streams. This perspective is needed to support river science and management in our era of rapid global change, including increasing duration, frequency, and occurrence of drying.}, }
@article {pmid33293507, year = {2020}, author = {Grantham, HS and Duncan, A and Evans, TD and Jones, KR and Beyer, HL and Schuster, R and Walston, J and Ray, JC and Robinson, JG and Callow, M and Clements, T and Costa, HM and DeGemmis, A and Elsen, PR and Ervin, J and Franco, P and Goldman, E and Goetz, S and Hansen, A and Hofsvang, E and Jantz, P and Jupiter, S and Kang, A and Langhammer, P and Laurance, WF and Lieberman, S and Linkie, M and Malhi, Y and Maxwell, S and Mendez, M and Mittermeier, R and Murray, NJ and Possingham, H and Radachowsky, J and Saatchi, S and Samper, C and Silverman, J and Shapiro, A and Strassburg, B and Stevens, T and Stokes, E and Taylor, R and Tear, T and Tizard, R and Venter, O and Visconti, P and Wang, S and Watson, JEM}, title = {Anthropogenic modification of forests means only 40% of remaining forests have high ecosystem integrity.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5978}, pmid = {33293507}, issn = {2041-1723}, abstract = {Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remain poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate a globally consistent, continuous index of forest condition as determined by the degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) has high landscape-level integrity (mostly found in Canada, Russia, the Amazon, Central Africa, and New Guinea) and only 27% of this area is found in nationally designated protected areas. Of the forest inside protected areas, only 56% has high landscape-level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally.}, }
@article {pmid33263214, year = {2020}, author = {Hassell, JM and Bettridge, JM and Ward, MJ and Ogendo, A and Imboma, T and Muloi, D and Fava, F and Robinson, TP and Begon, M and Fèvre, EM}, title = {Socio-ecological drivers of vertebrate biodiversity and human-animal interfaces across an urban landscape.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.15412}, pmid = {33263214}, issn = {1365-2486}, support = {NA//CGIAR Research Program on Agriculture for Nutrition and Health/ ; /MRC_/Medical Research Council/United Kingdom ; //Biotechnology and Biological Science Research Council/ ; //Economic and Social Research Council/ ; G1100783/1//Natural Environment Research Council/ ; WT103953MA/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Urbanization can have profound impacts on the distributional ecology of wildlife and livestock, with implications for biodiversity conservation, ecosystem services and human health. A wealth of studies have assessed biotic responses to urbanization in North America and Europe, but there is little empirical evidence that directly links human activities to urban biodiversity in the tropics. Results from a large-scale field study conducted in Nairobi, Kenya, are used to explore the impact of human activities on the biodiversity of wildlife and livestock with which humans co-exist across the city. The structure of sympatric wildlife, livestock and human populations are characterized using unsupervised machine learning, and statistical modelling is used to relate compositional variation in these communities to socio-ecological drivers occurring across the city. By characterizing landscape-scale drivers acting on these interfaces, we demonstrate that socioeconomics, elevation and subsequent changes in habitat have measurable impacts upon the diversity, density and species assemblage of wildlife, livestock and humans. Restructuring of wildlife and livestock assemblages (both in terms of species diversity and composition) has important implications for the emergence of novel diseases at urban interfaces, and we therefore use our results to generate a set of testable hypotheses that explore the influence of urban change on microbial communities. These results provide novel insight into the impact of urbanization on biodiversity in the tropics. An understanding of associations between urban processes and the structure of human and animal populations is required to link urban development to conservation efforts and risks posed by disease emergence to human health, ultimately informing sustainable urban development policy.}, }
@article {pmid33226631, year = {2020}, author = {McLean, BS and Guralnick, RP}, title = {Digital biodiversity data sets reveal breeding phenology and its drivers in a widespread North American mammal.}, journal = {Ecology}, volume = {}, number = {}, pages = {e03258}, doi = {10.1002/ecy.3258}, pmid = {33226631}, issn = {1939-9170}, abstract = {Shifts in reproductive timing are among the most commonly documented responses of organisms to global climate change. However, our knowledge of these responses is biased towards taxa that are easily observable and abundant in existing biodiversity data sets. Mammals are common subjects in reproductive biology, but mammalian phenology and its drivers in the wild remain poorly understood because many species are small, secretive, or labor-intensive to monitor. We took an informatics-based approach to reconstructing breeding phenology in the widespread North American deer mouse (Peromyscus maniculatus) using individual-level reproductive observations from digitized museum specimens and field censuses spanning >100 years and >45 degrees of latitude. We reconstructed female phenology in different regions and tested the importance of three environmental variables (photoperiod, temperature, precipitation) as breeding cues. Photoperiod and temperature were strong positive and negative breeding cues, respectively, while precipitation was not a significant predictor of breeding phenology. However, phenologies and the use of environmental cues varied substantially among regions, and we found evidence that these cueing repertoires are tuned to ecosystem-specific limiting conditions. Our results reiterate the importance of ecological context in optimizing reproduction and demonstrate how harmonization across biodiversity data resources allows new insight into phenology and its drivers in wild mammals.}, }
@article {pmid33208098, year = {2020}, author = {Wu, X and Li, X and Wang, W and Shan, Y and Wang, C and Zhu, M and La, Q and Zhong, Y and Xu, Y and Nan, P and Li, X}, title = {Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients.}, journal = {BMC genomics}, volume = {21}, number = {Suppl 10}, pages = {697}, pmid = {33208098}, issn = {1471-2164}, abstract = {BACKGROUND: Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is one of the most common herbs widely used in South and East Asia, to enhance people's health and reinforce vital energy. Despite its prevalence, however, the knowledge about phytochemical compositions and metabolite biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is very limited.<br><br>RESULTS: An integrated metabolomics and transcriptomics analysis using state-of-the-art UPLC-Q-Orbitrap mass spectrometer and advanced bioinformatics pipeline were conducted to study global metabolic profiles and phytochemical ingredients/biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. A total of 5435 metabolites were detected, from which 2190 were annotated, representing an order of magnitude increase over previously known. Metabolic profiling of Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao tissues found contents and synthetic enzymes for phytochemicals were significantly higher in leaf and stem in general, whereas the contents of the main bioactive ingredients were significantly enriched in root, underlying the value of root in herbal remedies. Using integrated metabolomics and transcriptomics data, we illustrated the complete pathways of phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis, in which some were first reported in the herb. More importantly, we discovered novel flavonoid derivatives using informatics method for neutral loss scan, in addition to inferring their likely synthesis pathways in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao.<br><br>CONCLUSIONS: The current study represents the most comprehensive metabolomics and transcriptomics analysis on traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. We demonstrated our integrated metabolomics and transcriptomics approach offers great potentials in discovering novel metabolite structure and associated synthesis pathways. This study provides novel insights into the phytochemical ingredients, metabolite biosynthesis, and complex metabolic network in herbs, highlighting the rich natural resource and nutritional value of traditional herbal plants.}, }
@article {pmid33205462, year = {2020}, author = {Culina, A and Adriaensen, F and Bailey, LD and Burgess, MD and Charmantier, A and Cole, EF and Eeva, T and Matthysen, E and Nater, CR and Sheldon, BC and Saether, BE and Vriend, SJG and Zajkova, Z and Adamík, P and Aplin, LM and Angulo, E and Artemyev, A and Barba, E and Barišić, S and Belda, E and Bilgin, CC and Bleu, J and Both, C and Bouwhuis, S and Branston, CJ and Broggi, J and Burke, T and Bushuev, A and Camacho, C and Campobello, D and Canal, D and Cantarero, A and Caro, SP and Cauchoix, M and Chaine, A and Cichoń, M and Ćiković, D and Cusimano, CA and Deimel, C and Dhondt, AA and Dingemanse, NJ and Doligez, B and Dominoni, DM and Doutrelant, C and Drobniak, SM and Dubiec, A and Eens, M and Einar Erikstad, K and Espín, S and Farine, DR and Figuerola, J and Kavak Gülbeyaz, P and Grégoire, A and Hartley, IR and Hau, M and Hegyi, G and Hille, S and Hinde, CA and Holtmann, B and Ilyina, T and Isaksson, C and Iserbyt, A and Ivankina, E and Kania, W and Kempenaers, B and Kerimov, A and Komdeur, J and Korsten, P and Král, M and Krist, M and Lambrechts, M and Lara, CE and Leivits, A and Liker, A and Lodjak, J and Mägi, M and Mainwaring, MC and Mänd, R and Massa, B and Massemin, S and Martínez-Padilla, J and Mazgajski, TD and Mennerat, A and Moreno, J and Mouchet, A and Nakagawa, S and Nilsson, JÅ and Nilsson, JF and Cláudia Norte, A and van Oers, K and Orell, M and Potti, J and Quinn, JL and Réale, D and Kristin Reiertsen, T and Rosivall, B and Russell, AF and Rytkönen, S and Sánchez-Virosta, P and Santos, ESA and Schroeder, J and Senar, JC and Seress, G and Slagsvold, T and Szulkin, M and Teplitsky, C and Tilgar, V and Tolstoguzov, A and Török, J and Valcu, M and Vatka, E and Verhulst, S and Watson, H and Yuta, T and Zamora-Marín, JM and Visser, ME}, title = {Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.13388}, pmid = {33205462}, issn = {1365-2656}, support = {223257//Research Council of Norway/ ; 267511//Research Council of Norway/ ; 016.Veni.181.054//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.}, }
@article {pmid33193120, year = {2020}, author = {Rosen, GL and Hammrich, P}, title = {Teaching Microbiome Analysis: From Design to Computation Through Inquiry.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {528051}, pmid = {33193120}, issn = {1664-302X}, abstract = {In this article, we present our three-class course sequence to educate students about microbiome analysis and metagenomics through experiential learning by taking them from inquiry to analysis of the microbiome: Molecular Ecology Lab, Bioinformatics, and Computational Microbiome Analysis. Students developed hypotheses, designed lab experiments, sequenced the DNA from microbiomes, learned basic python/R scripting, became proficient in at least one microbiome analysis software, and were able to analyze data generated from the microbiome experiments. While over 150 students (graduate and undergraduate) were impacted by the development of the series of courses, our assessment was only on undergraduate learning, where 45 students enrolled in at least one of the three courses and 4 students took all three. Students gained skills in bioinformatics through the courses, and several positive comments were received through surveys and private correspondence. Through a summative assessment, general trends show that students became more proficient in comparative genomic techniques and had positive attitudes toward their abilities to bridge biology and bioinformatics. While most students took individual or 2 of the courses, we show that pre- and post-surveys of these individual classes still showed progress toward learning objectives. It is expected that students trained will enter the workforce with skills needed to innovate in the biotechnology, health, and environmental industries. Students are trained to maximize impact and tackle real world problems in biology and medicine with their learned knowledge of data science and machine learning. The course materials for the new microbiome analysis course are available on Github: https://github.com/EESI/Comp_Metagenomics_resources.}, }
@article {pmid33147272, year = {2020}, author = {Altamiranda-Saavedra, M and Osorio-Olvera, L and Yáñez-Arenas, C and Marín-Ortiz, JC and Parra-Henao, G}, title = {Geographic abundance patterns explained by niche centrality hypothesis in two Chagas disease vectors in Latin America.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241710}, pmid = {33147272}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Chagas Disease/epidemiology/parasitology/*pathology/transmission ; Databases, Factual ; *Ecosystem ; Humans ; Insect Vectors ; Models, Theoretical ; Population Density ; Rhodnius/*parasitology ; South America/epidemiology ; Triatoma/*parasitology ; }, abstract = {Ecoepidemiological scenarios for Chagas disease transmission are complex, so vector control measures to decrease human-vector contact and prevent infection transmission are difficult to implement in all geographic contexts. This study assessed the geographic abundance patterns of two vector species of Chagas disease: Triatoma maculata (Erichson, 1848) and Rhodnius pallescens (Barber, 1932) in Latin America. We modeled their potential distribution using the maximum entropy algorithm implemented in Maxent and calculated distances to their niche centroid by fitting a minimum-volume ellipsoid. In addition, to determine which method would accurately explain geographic abundance patterns, we compared the correlation between population abundance and the distance to the ecological niche centroid (DNC) and between population abundance and Maxent environmental suitability. The potential distribution estimated for T. maculata showed that environmental suitability covers a large area, from Panama to Northern Brazil. R. pallescens showed a more restricted potential distribution, with environmental suitability covering mostly the coastal zone of Costa Rica and some areas in Nicaragua, Honduras, Belize and the Yucatán Peninsula in Mexico, northern Colombia, Acre, and Rondônia states in Brazil, as well as a small region of the western Brazilian Amazon. We found a negative slope in the relationship between population abundance and the DNC in both species. R. pallecens has a more extensive potential latitudinal range than previously reported, and the distribution model for T. maculata corroborates previous studies. In addition, population abundance increases according to the niche centroid proximity, indicating that population abundance is limited by the set of scenopoetic variables at coarser scales (non-interactive variables) used to determine the ecological niche. These findings might be used by public health agencies in Latin America to implement actions and support programs for disease prevention and vector control, identifying areas in which to expand entomological surveillance and maintain chemical control, in order to decrease human-vector contact.}, }
@article {pmid33143227, year = {2020}, author = {Petrushin, I and Belikov, S and Chernogor, L}, title = {Cooperative Interaction of Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02 in the Diseased Sponge Lubomirskiabaicalensis.}, journal = {International journal of molecular sciences}, volume = {21}, number = {21}, pages = {}, pmid = {33143227}, issn = {1422-0067}, support = {19-14-00088//Russian Science Foundation/ ; 0345-2019-0002 (AAAA-A16-116122110066-1)//Siberian Branch, Russian Academy of Sciences/ ; }, abstract = {Endemic freshwater sponges (demosponges, Lubomirskiidae) dominate in Lake Baikal, Central Siberia, Russia. These sponges are multicellular filter-feeding animals that represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of Lubomirskia baicalensis has been a significant problem in Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria from the families Flavobacteriaceae and Oxalobacteraceae dominate the microbiomes of diseased sponges. Both species are opportunistic pathogens common in freshwater ecosystems. The aim of our study was to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. Janthinobacterium sp. SLB01 attacks other cells using a type VI secretion system and suppresses gram-positive bacteria with violacein, and regulates its own activity via quorum sensing. It produces floc and strong biofilm by exopolysaccharide biosynthesis and PEP-CTERM/XrtA protein expression. Flavobacterium sp. SLB02 utilizes the fragments of cell walls produced by polysaccharides. These two strains have a marked difference in carbohydrate acquisition. We described a possible means of joint occupation of the ecological niche in the freshwater sponge microbial community. This study expands the understanding of the symbiotic relationship of microorganisms with freshwater Baikal sponges.}, }
@article {pmid33135271, year = {2020}, author = {Yamaguchi, K and Koyanagi, M and Kuraku, S}, title = {Visual and nonvisual opsin genes of sharks and other nonosteichthyan vertebrates: Genomic exploration of underwater photoreception.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeb.13730}, pmid = {33135271}, issn = {1420-9101}, support = {//RIKEN/ ; }, abstract = {Vision of sharks embraces various biological and ecological themes ranging from predation and adaptation to deep-sea life. However, behavioural and genetic studies have been limited by their elusive lifestyles, repeatedly reported declines of wild populations, and their unique life-history traits including low fecundity and enhanced longevity. Sharks have also not been actively studied on the cellular and molecular levels, because of additional difficulties in cell culture, tissue collection and genome sequencing. A recent study circumvented some of these obstacles by means of genome informatics thereby portrayed the variation of visual opsin gene repertoires among elasmobranchs (sharks and rays) and spectral shifts of the rhodopsin pigment. Comprehensive surveys in whole-genome sequences are also revealing the repertoires of nonvisual opsins with unknown functions. This review is aimed to summarize existing studies on shark opsins with an emphasis on genomic investigation of gene repertoires and to provide insights into the better understanding of underwater ecology of marine megafauna with in vitro experimentation.}, }
@article {pmid33125392, year = {2020}, author = {Sala, C and Giampieri, E and Vitali, S and Garagnani, P and Remondini, D and Bazzani, A and Franceschi, C and Castellani, GC}, title = {Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0237207}, pmid = {33125392}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Aging/genetics/physiology ; Biodiversity ; Child ; Child, Preschool ; Databases, Nucleic Acid ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Health Status ; Healthy Aging/genetics/physiology ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Middle Aged ; *Models, Biological ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-style, and substantially contributes to the pathogenesis of age-related diseases. For these reasons, the gut microbiota is a suitable candidate for assessing and quantifying healthy aging, i.e. the capability of individuals to reach an advanced age, avoiding or postponing major age-related diseases. The importance of the gut microbiota in health and aging has been proven to be related not only to its taxonomic composition, but also to its ecological properties, namely its biodiversity. Following an ecological approach, here we intended to characterize the relationship between the gut microbiota biodiversity and healthy aging through the development a parsimonious model of gut microbiota from which biodiversity can be estimated. We analysed publicly available metagenomic data relative to subjects of different ages, countries, nutritional habits and health status and we showed that a hybrid niche-neutral model well describes the observed patterns of bacterial relative abundance. Moreover, starting from such ecological modeling, we derived an estimate of the gut microbiota biodiversity that is consistent with classical indices, while having a higher statistical power. This allowed us to unveil an increase of the gut microbiota biodiversity during aging and to provide a good predictor of health status in old age, dependent on life-style and aging disorders.}, }
@article {pmid33122629, year = {2020}, author = {Cai, W and Snyder, J and Hastings, A and D'Souza, RM}, title = {Mutualistic networks emerging from adaptive niche-based interactions.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5470}, pmid = {33122629}, issn = {2041-1723}, mesh = {Animals ; Biological Evolution ; Computational Biology ; Ecology/*methods ; Ecosystem ; *Food Chain ; *Models, Theoretical ; *Symbiosis ; }, abstract = {Mutualistic networks are vital ecological and social systems shaped by adaptation and evolution. They involve bipartite cooperation via the exchange of goods or services between actors of different types. Empirical observations of mutualistic networks across genres and geographic conditions reveal correlated nested and modular patterns. Yet, the underlying mechanism for the network assembly remains unclear. We propose a niche-based adaptive mechanism where both nestedness and modularity emerge simultaneously as complementary facets of an optimal niche structure. Key dynamical properties are revealed at different timescales. Foremost, mutualism can either enhance or reduce the network stability, depending on competition intensity. Moreover, structural adaptations are asymmetric, exhibiting strong hysteresis in response to environmental change. Finally, at the evolutionary timescale we show that the adaptive mechanism plays a crucial role in preserving the distinctive patterns of mutualism under species invasions and extinctions.}, }
@article {pmid33095844, year = {2020}, author = {Snell Taylor, S and Coyle, JR and White, EP and Hurlbert, AH}, title = {A simulation study of the use of temporal occupancy for identifying core and transient species.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0241198}, pmid = {33095844}, issn = {1932-6203}, mesh = {*Animal Distribution ; Animals ; Computer Simulation ; Ecological Parameter Monitoring/*methods ; *Ecosystem ; *Models, Biological ; Population Dynamics ; Time Factors ; }, abstract = {Transient species, which do not maintain self-sustaining populations in a system where they are observed, are ubiquitous in nature and their presence often impacts the interpretation of ecological patterns and processes. Identifying transient species from temporal occupancy, the proportion of time a species is observed at a given site over a time series, is subject to classification errors as a result of imperfect detection and source-sink dynamics. We use a simulation-based approach to assess how often errors in detection or classification occur in order to validate the use of temporal occupancy as a metric for inferring whether a species is a core or transient member of a community. We found that low detection increases error in the classification of core species, while high habitat heterogeneity and high detection increase error in classification of transient species. These findings confirm that temporal occupancy is a valid metric for inferring whether a species can maintain a self-sustaining population, but imperfect detection, low abundance, and highly heterogeneous landscapes may yield high misclassification rates.}, }
@article {pmid33087857, year = {2020}, author = {Maák, I and Tóth, E and Lenda, M and Lőrinczi, G and Kiss, A and Juhász, O and Czechowski, W and Torma, A}, title = {Behaviours indicating cannibalistic necrophagy in ants are modulated by the perception of pathogen infection level.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17906}, pmid = {33087857}, issn = {2045-2322}, abstract = {Cannibalistic necrophagy is rarely observed in social hymenopterans, although a lack of food could easily favour such behaviour. One of the main supposed reasons for the rarity of necrophagy is that eating of nestmate corpses carries the risk of rapid spread of pathogens or parasites. Here we present an experimental laboratory study on behaviour indicating consumption of nestmate corpses in the ant Formica polyctena. We examined whether starvation and the fungal infection level of the corpses affects the occurrence of cannibalistic necrophagy. Our results showed that the ants distinguished between corpses of different types and with different levels of infection risk, adjusting their behaviour accordingly. The frequency of behaviours indicating cannibalistic necrophagy increased during starvation, although these behaviours seem to be fairly common in F. polyctena even in the presence of other food sources. The occurrence and significance of cannibalistic necrophagy deserve further research because, in addition to providing additional food, it may be part of the hygienic behaviour repertoire. The ability to detect infections and handle pathogens are important behavioural adaptations for social insects, crucial for the fitness of both individual workers and the entire colony.}, }
@article {pmid33031625, year = {2020}, author = {Riginos, C and Crandall, ED and Liggins, L and Gaither, MR and Ewing, RB and Meyer, C and Andrews, KR and Euclide, PT and Titus, BM and Therkildsen, NO and Salces-Castellano, A and Stewart, LC and Toonen, RJ and Deck, J}, title = {Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.}, journal = {Molecular ecology resources}, volume = {20}, number = {6}, pages = {1458-1469}, doi = {10.1111/1755-0998.13269}, pmid = {33031625}, issn = {1755-0998}, support = {DEB-1457848//Division of Environmental Biology/ ; OISE-1243541//Division of Environmental Biology/ ; }, abstract = {Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.}, }
@article {pmid33011421, year = {2021}, author = {Sannigrahi, S and Pilla, F and Zhang, Q and Chakraborti, S and Wang, Y and Basu, B and Basu, AS and Joshi, PK and Keesstra, S and Roy, PS and Sutton, PC and Bhatt, S and Rahmat, S and Jha, S and Singh, LK}, title = {Examining the effects of green revolution led agricultural expansion on net ecosystem service values in India using multiple valuation approaches.}, journal = {Journal of environmental management}, volume = {277}, number = {}, pages = {111381}, doi = {10.1016/j.jenvman.2020.111381}, pmid = {33011421}, issn = {1095-8630}, mesh = {Agriculture ; Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; Humans ; India ; }, abstract = {Ecosystem Services (ESs) are bundles of natural processes and functions that are essential for human well-being, subsistence, and livelihoods. The 'Green Revolution' (GR) has substantial impact on the agricultural landscape and ESs in India. However, the effects of GR on ESs have not been adequately documented and analyzed. This leads to the main hypothesis of this work - 'the incremental trend of ESs in India is mainly prompted by GR led agricultural innovations that took place during 1960 - 1970'. The analysis was carried out through five successive steps. First, the spatiotemporal Ecosystem Service Values (ESVs) in Billion US$ for 1985, 1995, and 2005 were estimated using several value transfer approaches. Second, the sensitivity and elasticity of different ESs to land conversion were carried out using coefficient of sensitivity and coefficient of elasticity. Third, the Geographically Weighted Regression model was performed using five explanatory factors, i.e., total crop area, crop production, crop yield, net irrigated area, and cropping intensity, to explore the cumulative and individual effects of these driving factors on ESVs. Fourth, Multi-Layer Perceptron based Artificial Neural Network was employed to estimate the normalized importance of these explanatory factors. Fifth, simple and multiple linear regression modeling was done to assess the linear associations between the driving factors and the ESs. During the observation periods, cropland, forestland and water bodies contributed to 80%-90% of ESVs, followed by grassland, mangrove, wetland and urban built-up. In all three evaluation years, the highest estimated ESVs among the nine ES categories was provided by water regulation, followed by soil formation and soil-water retention, biodiversity maintenance, waste treatment, climate regulation, and greenhouse gas regulation. Among the five explanatory factors, total crop area, crop production, and net irrigated area showed strong positive associations with ESVs, while cropping intensity exhibited a negative association. Therefore, the study reveals a strong association between GR led agricultural expansion and ESVs in India. This study suggests that there should be an urgent need for formulation of rigorous ecosystem management strategies and policies to preserve ecological integrity and flow of uninterrupted ESs and to sustain human well-being.}, }
@article {pmid32957527, year = {2020}, author = {Juhász, O and Fürjes-Mikó, Á and Tenyér, A and Somogyi, AÁ and Aguilon, DJ and Kiss, PJ and Bátori, Z and Maák, I}, title = {Consequences of Climate Change-Induced Habitat Conversions on Red Wood Ants in a Central European Mountain: A Case Study.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {9}, pages = {}, pmid = {32957527}, issn = {2076-2615}, support = {2017-01-X-NZ8-01042//Fundacja na rzecz Nauki Polskiej/ ; NKFIH K 124796//Országos Tudományos Kutatási Alapprogramok/ ; }, abstract = {The consequences of anthropogenic climate change are one of the major concerns of conservation biology. A cascade of negative effects is expected to affect various ecosystems, one of which is Central European coniferous forests and their unique biota. These coniferous forests are the primary habitat of many forest specialist species such as red wood ants. Climate change-induced rising of temperature allows trees to skip winter hibernation, making them more vulnerable to storms that cause wind felling, and in turn, promotes bark beetle infestations that results in unscheduled clear-cuttings. Red wood ants can also be exposed to such habitat changes. We investigated the effects of bark beetle-induced clear-cutting and the absence of coniferous trees on colonies of Formica polyctena, including a mixed-coniferous forest as a reference. Our aim was to investigate how these habitat features affect the nest characteristics and nesting habits of F. polyctena. Our results indicate that, in the absence of conifers, F. polyctena tend to use different alternatives for nest material, colony structure, and food sources. However, the vitality of F. polyctena colonies significantly decreased (smaller nest mound volumes). Our study highlights the ecological flexibility of this forest specialist and its potential to survive under extreme conditions.}, }
@article {pmid32933777, year = {2020}, author = {Laubmeier, AN and Cazelles, B and Cuddington, K and Erickson, KD and Fortin, MJ and Ogle, K and Wikle, CK and Zhu, K and Zipkin, EF}, title = {Ecological Dynamics: Integrating Empirical, Statistical, and Analytical Methods.}, journal = {Trends in ecology &amp; evolution}, volume = {35}, number = {12}, pages = {1090-1099}, doi = {10.1016/j.tree.2020.08.006}, pmid = {32933777}, issn = {1872-8383}, abstract = {Understanding ecological processes and predicting long-term dynamics are ongoing challenges in ecology. To address these challenges, we suggest an approach combining mathematical analyses and Bayesian hierarchical statistical modeling with diverse data sources. Novel mathematical analysis of ecological dynamics permits a process-based understanding of conditions under which systems approach equilibrium, experience large oscillations, or persist in transient states. This understanding is improved by combining ecological models with empirical observations from a variety of sources. Bayesian hierarchical models explicitly couple process-based models and data, yielding probabilistic quantification of model parameters, system characteristics, and associated uncertainties. We outline relevant tools from dynamical analysis and hierarchical modeling and argue for their integration, demonstrating the value of this synthetic approach through a simple predator-prey example.}, }
@article {pmid32913322, year = {2020}, author = {Pârvulescu, L and Iorgu, EI and Zaharia, C and Ion, MC and Satmari, A and Krapal, AM and Popa, OP and Miok, K and Petrescu, I and Popa, LO}, title = {The future of endangered crayfish in light of protected areas and habitat fragmentation.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14870}, pmid = {32913322}, issn = {2045-2322}, abstract = {The long-term survival of a species requires, among other things, gene flow between populations. Approaches for the evaluation of fragmentation in the frame of freshwater habitats consider only a small amount of the information that combined demography and geography are currently able to provide. This study addresses two species of Austropotamobius crayfish in the light of population genetics, spatial ecology and protected areas of the Carpathians. Advancing the classical approaches, we defined ecological distances upon the rasterised river network as a surrogate of habitat resistance to migration, quantifying the deviations from the species´ suitability range for a set of relevant geospatial variables in each cell of the network. Molecular analyses revealed the populations of the two Austropotamobius crayfish species are clearly distinct, lacking hybridisation. Comparing pairs of populations, we found, in some cases, a strong disagreement regarding genetic and ecological distances, potentially due to human-mediated translocations or the geophysical phenomena of regressive erosion, which may have led to unexpected colonisation routes. Protected areas were found to offer appropriate local habitat conditions but failed to ensure connectivity. The methodology applied in this study allowed us to quantify the contribution of each geospatial (environmental) variable to the overall effect of fragmentation, and we found that water quality was the most important variable. A multilevel approach proved to reveal a better understanding of drivers behind the distribution patterns, which can lead to more adequate conservation measures.}, }
@article {pmid32899582, year = {2020}, author = {Guo, Y and Wang, H and Wu, Z and Wang, S and Sun, H and Senthilnath, J and Wang, J and Robin Bryant, C and Fu, Y}, title = {Modified Red Blue Vegetation Index for Chlorophyll Estimation and Yield Prediction of Maize from Visible Images Captured by UAV.}, journal = {Sensors (Basel, Switzerland)}, volume = {20}, number = {18}, pages = {}, pmid = {32899582}, issn = {1424-8220}, support = {Grant No. 31770516//the General Program of National Nature Science Foundation of China/ ; 2017YFA06036001//the National Key Research and Development Program of China/ ; 2018EYT05//the 111 Project (B18006) and Fundamental Research Funds for the Central Universities/ ; }, abstract = {The vegetation index (VI) has been successfully used to monitor the growth and to predict the yield of agricultural crops. In this paper, a long-term observation was conducted for the yield prediction of maize using an unmanned aerial vehicle (UAV) and estimations of chlorophyll contents using SPAD-502. A new vegetation index termed as modified red blue VI (MRBVI) was developed to monitor the growth and to predict the yields of maize by establishing relationships between MRBVI- and SPAD-502-based chlorophyll contents. The coefficients of determination (R2s) were 0.462 and 0.570 in chlorophyll contents' estimations and yield predictions using MRBVI, and the results were relatively better than the results from the seven other commonly used VI approaches. All VIs during the different growth stages of maize were calculated and compared with the measured values of chlorophyll contents directly, and the relative error (RE) of MRBVI is the lowest at 0.355. Further, machine learning (ML) methods such as the backpropagation neural network model (BP), support vector machine (SVM), random forest (RF), and extreme learning machine (ELM) were adopted for predicting the yields of maize. All VIs calculated for each image captured during important phenological stages of maize were set as independent variables and the corresponding yields of each plot were defined as dependent variables. The ML models used the leave one out method (LOO), where the root mean square errors (RMSEs) were 2.157, 1.099, 1.146, and 1.698 (g/hundred grain weight) for BP, SVM, RF, and ELM. The mean absolute errors (MAEs) were 1.739, 0.886, 0.925, and 1.356 (g/hundred grain weight) for BP, SVM, RF, and ELM, respectively. Thus, the SVM method performed better in predicting the yields of maize than the other ML methods. Therefore, it is strongly suggested that the MRBVI calculated from images acquired at different growth stages integrated with advanced ML methods should be used for agricultural- and ecological-related chlorophyll estimation and yield predictions.}, }
@article {pmid32856310, year = {2020}, author = {Nam, S and Dunton, GF and Ordway, MR and Ash, GI and Jeon, S and Vlahov, D and Whittemore, R and Nelson, LE and Sinha, R and Nunez-Smith, M and Granger, DA}, title = {Feasibility and acceptability of intensive, real-time biobehavioral data collection using ecological momentary assessment, salivary biomarkers, and accelerometers among middle-aged African Americans.}, journal = {Research in nursing &amp; health}, volume = {43}, number = {5}, pages = {453-464}, doi = {10.1002/nur.22068}, pmid = {32856310}, issn = {1098-240X}, support = {//Yale University, School of Nursing/ ; }, abstract = {Perceived racial discrimination is linked to unhealthy behaviors and stress-related morbidities. A compelling body of research indicates that perceived racial discrimination may contribute to health disparities among African Americans (AAs). The purposes of this study were to describe the study protocol including data collection procedures and study measures and to evaluate the feasibility and acceptability of intensive biobehavioral data collection using ecological momentary assessment (EMA), salivary biomarkers, and accelerometers over 7 days among middle-aged AAs with a goal of understanding the relationships between perceived racial discrimination and biobehavioral responses to stress. Twelve AA men and women participated in the feasibility/acceptability study. They completed surveys, anthropometrics, and received in-person training in EMA and saliva sample collection at baseline. Participants were asked to respond to the random prompt text message-based EMA five times a day, wear an accelerometer daily for 7 days, and to self-collect saliva samples four times a day for 4 consecutive days. The EMA surveys included perceived racial discrimination, affective states, lifestyle behaviors, and social and physical contexts. The mean EMA response rate was 82.8%. All participants collected saliva samples four times a day for 4 consecutive days. About 83% of participants wore the accelerometer on the hip 6 out of 7 days. Despite the perception that the intensive nature of assessments would result in high participant burden, the acceptability of the study procedures was uniformly favorable.}, }
@article {pmid32853270, year = {2020}, author = {Xu, J and Yin, P and Hu, W and Fu, L and Zhao, H}, title = {Assessing the ecological regime and spatial spillover effects of a reclaimed mining subsided lake: A case study of the Pan'an Lake wetland in Xuzhou.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0238243}, pmid = {32853270}, issn = {1932-6203}, mesh = {China ; Coal Mining/*methods ; Conservation of Natural Resources/*methods ; Ecology/methods ; Ecosystem ; Environmental Monitoring/methods ; Lakes ; Wetlands ; }, abstract = {In the North China Plain, coal mining subsided lakes are surface water bodies that form after the conclusion of coal mining. In China, mining subsided lakes are often transformed into artificial wetland parks for ecological restoration. While many studies have focused on evaluating coal mining subsidence lake ecosystem service value and water pollution, little attention has been paid to changes in ecological regimes and ecological spillover effects before and after the reclamation of mining areas. This paper examines the Pan'an Lake artificial wetland in Jiawang District, Xuzhou, as a case study. Changes in the ecological regime of the mining subsidence area before and after land reclamation and corresponding spatial spillover effect on land prices are assessed based on remote sensing, GIS raster calculations and geostatistical methods. The results show that the ecosystem service value and ecological storage capacity changed significantly after the mining subsided lake was transformed into an artificial wetland and the wetland ecosystem has been developing well with significantly positive spillover effects on surrounding land prices. From 2008 to 2017, service functions of the artificial wetland ecosystem of Pan'an Lake increased by 81.95%, and the system's ecological storage capacity increased from RMB 6,754 yuan/hm2 in 2008 to RMB 12,289 yuan/hm2 in 2017. The average impact of the Pan'an Lake artificial wetland on the spillover effects of surrounding residential land prices was measured at RMB 195.18 yuan/m2, and the total spillover value of planned residential land in the study area was measured at RMB 805,422,100 yuan. The present study can serve as a useful guide for evaluating the economic feasibility of land reclamation planning and ecological restoration in mining subsidence areas.}, }
@article {pmid32788594, year = {2020}, author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S}, title = {Publisher Correction: A global database of Holocene paleotemperature records.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {271}, doi = {10.1038/s41597-020-00611-1}, pmid = {32788594}, issn = {2052-4463}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32778752, year = {2020}, author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D}, title = {A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {10}, pages = {1377-1384}, pmid = {32778752}, issn = {2397-334X}, support = {80NSSC18K0338/ImNASA/Intramural NASA/United States ; }, mesh = {Biodiversity ; *Conservation of Natural Resources ; *Forests ; Humans ; Policy ; }, abstract = {Tropical forests vary in composition, structure and function such that not all forests have similar ecological value. This variability is caused by natural and anthropogenic disturbance regimes, which influence the ability of forests to support biodiversity, store carbon, mediate water yield and facilitate human well-being. While international environmental agreements mandate protecting and restoring forests, only forest extent is typically considered, while forest quality is ignored. Consequently, the locations and loss rates of forests of high ecological value are unknown and coordinated strategies for conserving these forests remain undeveloped. Here, we map locations high in forest structural integrity as a measure of ecological quality on the basis of recently developed fine-resolution maps of three-dimensional forest structure, integrated with human pressure across the global moist tropics. Our analyses reveal that tall forests with closed canopies and low human pressure typical of natural conditions comprise half of the global humid or moist tropical forest estate, largely limited to the Amazon and Congo basins. Most of these forests have no formal protection and, given recent rates of loss, are at substantial risk. With the rapid disappearance of these 'best of the last' forests at stake, we provide a policy-driven framework for their conservation and restoration, and recommend locations to maintain protections, add new protections, mitigate deleterious human impacts and restore forest structure.}, }
@article {pmid32770154, year = {2020}, author = {Cichocki, N and Hübschmann, T and Schattenberg, F and Kerckhof, FM and Overmann, J and Müller, S}, title = {Bacterial mock communities as standards for reproducible cytometric microbiome analysis.}, journal = {Nature protocols}, volume = {15}, number = {9}, pages = {2788-2812}, doi = {10.1038/s41596-020-0362-0}, pmid = {32770154}, issn = {1750-2799}, mesh = {Bacteria/*cytology ; Computational Biology ; Cytological Techniques/*standards ; *Microbiota ; Reference Standards ; Reproducibility of Results ; }, abstract = {Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.}, }
@article {pmid32760547, year = {2020}, author = {Carraro, L and Bertuzzo, E and Fronhofer, EA and Furrer, R and Gounand, I and Rinaldo, A and Altermatt, F}, title = {Generation and application of river network analogues for use in ecology and evolution.}, journal = {Ecology and evolution}, volume = {10}, number = {14}, pages = {7537-7550}, pmid = {32760547}, issn = {2045-7758}, abstract = {Several key processes in freshwater ecology are governed by the connectivity inherent to dendritic river networks. These have extensively been analyzed from a geomorphological and hydrological viewpoint, yet structures classically used in ecological modeling have been poorly representative of the structure of real river basins, often failing to capture well-known scaling features of natural rivers. Pioneering work identified optimal channel networks (OCNs) as spanning trees reproducing all scaling features characteristic of natural stream networks worldwide. While OCNs have been used to create landscapes for studies on metapopulations, biodiversity, and epidemiology, their generation has not been generally accessible.Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we provide the R-package OCNet. Owing to the stochastic process generating OCNs, multiple network replicas spanning the same surface can be built; this allows performing computational experiments whose results are irrespective of the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the package provides functions that aggregate OCNs into an arbitrary number of nodes, calculate several descriptors of river networks, and draw relevant network features.We describe the main functionalities of the package and its integration with other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.In conclusion, OCNet provides a powerful tool to generate realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems and enhances our knowledge on spatial processes in freshwater ecology in general.}, }
@article {pmid32730245, year = {2020}, author = {D'Andrea, R and Gibbs, T and O'Dwyer, JP}, title = {Emergent neutrality in consumer-resource dynamics.}, journal = {PLoS computational biology}, volume = {16}, number = {7}, pages = {e1008102}, pmid = {32730245}, issn = {1553-7358}, mesh = {*Biodiversity ; Biological Evolution ; Computational Biology ; Computer Simulation ; Ecosystem ; *Models, Biological ; Stochastic Processes ; }, abstract = {Neutral theory assumes all species and individuals in a community are ecologically equivalent. This controversial hypothesis has been tested across many taxonomic groups and environmental contexts, and successfully predicts species abundance distributions across multiple high-diversity communities. However, it has been critiqued for its failure to predict a broader range of community properties, particularly regarding community dynamics from generational to geological timescales. Moreover, it is unclear whether neutrality can ever be a true description of a community given the ubiquity of interspecific differences, which presumably lead to ecological inequivalences. Here we derive analytical predictions for when and why non-neutral communities of consumers and resources may present neutral-like outcomes, which we verify using numerical simulations. Our results, which span both static and dynamical community properties, demonstrate the limitations of summarizing distributions to detect non-neutrality, and provide a potential explanation for the successes of neutral theory as a description of macroecological pattern.}, }
@article {pmid32724218, year = {2020}, author = {Muñoz, ÁG and Chourio, X and Rivière-Cinnamond, A and Diuk-Wasser, MA and Kache, PA and Mordecai, EA and Harrington, L and Thomson, MC}, title = {AeDES: a next-generation monitoring and forecasting system for environmental suitability of Aedes-borne disease transmission.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12640}, pmid = {32724218}, issn = {2045-2322}, support = {1R35GM133439-01/NH/NIH HHS/United States ; 2018-01754//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/International ; NA18OAR4310339//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/International ; U01CK000509-01//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/International ; R35 GM133439/GM/NIGMS NIH HHS/United States ; U01 CK000509/CK/NCEZID CDC HHS/United States ; 001/WHO_/World Health Organization/International ; }, mesh = {Aedes/*virology ; Animals ; Betacoronavirus/isolation &amp; purification ; COVID-19 ; Climate ; Coronavirus Infections/pathology/transmission/virology ; Databases, Factual ; Decision Making ; *Epidemiological Monitoring/veterinary ; Humans ; Mosquito Vectors/*virology ; Pandemics ; Pneumonia, Viral/pathology/transmission/virology ; SARS-CoV-2 ; Vector Borne Diseases/epidemiology/*pathology/virology ; }, abstract = {Aedes-borne diseases, such as dengue and chikungunya, are responsible for more than 50 million infections worldwide every year, with an overall increase of 30-fold in the last 50 years, mainly due to city population growth, more frequent travels and ecological changes. In the United States of America, the vast majority of Aedes-borne infections are imported from endemic regions by travelers, who can become new sources of mosquito infection upon their return home if the exposed population is susceptible to the disease, and if suitable environmental conditions for the mosquitoes and the virus are present. Since the susceptibility of the human population can be determined via periodic monitoring campaigns, the environmental suitability for the presence of mosquitoes and viruses becomes one of the most important pieces of information for decision makers in the health sector. We present a next-generation monitoring and forecasting system for [Formula: see text]-borne diseases' environmental suitability (AeDES) of transmission in the conterminous United States and transboundary regions, using calibrated ento-epidemiological models, climate models and temperature observations. After analyzing the seasonal predictive skill of AeDES, we briefly consider the recent Zika epidemic, and the compound effects of the current Central American dengue outbreak happening during the SARS-CoV-2 pandemic, to illustrate how a combination of tailored deterministic and probabilistic forecasts can inform key prevention and control strategies .}, }
@article {pmid32678108, year = {2020}, author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S}, title = {Author Correction: A global database of Holocene paleotemperature records.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {246}, doi = {10.1038/s41597-020-00584-1}, pmid = {32678108}, issn = {2052-4463}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32671561, year = {2020}, author = {Nautiyal, S and Goswami, M and Nidamanuri, RR and Hoffmann, EM and Buerkert, A}, title = {Structure and composition of field margin vegetation in the rural-urban interface of Bengaluru, India: a case study on an unexplored dimension of agroecosystems.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {8}, pages = {520}, doi = {10.1007/s10661-020-08428-6}, pmid = {32671561}, issn = {1573-2959}, support = {BT/IN/GERMAN/DFG/14/BVCR/2016//Department of Biotechnology, Ministry of Science and Technology/ ; }, mesh = {Agriculture ; Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; *Environmental Monitoring ; Europe ; Humans ; India ; }, abstract = {Field margin vegetation (FMV) refers to the plant community in the interface between agriculture and natural environments. Substantial work has been carried out on the management of field margins in European countries with the aim of conserving field-level biodiversity and enhancing agronomic benefits. India, instead, is lagging behind in the assessment of FMV and formulating subsequent management strategies for biodiversity conservation at the field boundaries. This study is a first step to better understand the structural and functional dimensions of field margin vegetation along an agricultural transformation gradient near the megacity of Bengaluru, India. Empirical field studies along with the detection of vegetation change using remote sensing and geo-informatics technique were used to record information on field margin vegetation. The phytosociological study, revealed a total of 81 species, comprising 29 species of trees, 21 shrubs and 31 herbs at the field margins of six selected villages of northern Bengaluru. Randomly selected 355 field boundaries were delineated from high-resolution Worldview 3 images for the year 2018 and from Google Earth images for the year 2004-2005. The FMV area was around to 85.40 ha in 2004-2005 but declined to 76.69 ha in 2017-2018. The survey also indicated that local farmers have in-depth ecological knowledge on the importance of FMV in ensuring a sustainable flow of resources within the agricultural landscape. The results demonstrate that rural and transition zones of the study area have higher dominance of planted tree species on the margins, whereas urban zone exhibits comparatively uniform dominance for all species. Our study also highlights the need for conservation of FMV to ensure agroecosystem health as a prerequisite for sustainable socioecological development.}, }
@article {pmid32651419, year = {2020}, author = {Pigeon, KE and MacNearney, D and Hebblewhite, M and Musiani, M and Neufeld, L and Cranston, J and Stenhouse, G and Schmiegelow, F and Finnegan, L}, title = {The density of anthropogenic features explains seasonal and behaviour-based functional responses in selection of linear features by a social predator.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11437}, pmid = {32651419}, issn = {2045-2322}, mesh = {Animals ; Deer/*physiology ; Ecosystem ; *Geographic Information Systems ; Humans ; Predatory Behavior/*physiology ; Seasons ; Wolves/*physiology ; }, abstract = {Anthropogenic linear features facilitate access and travel efficiency for predators, and can influence predator distribution and encounter rates with prey. We used GPS collar data from eight wolf packs and characteristics of seismic lines to investigate whether ease-of-travel or access to areas presumed to be preferred by prey best explained seasonal selection patterns of wolves near seismic lines, and whether the density of anthropogenic features led to functional responses in habitat selection. At a broad scale, wolves showed evidence of habitat-driven functional responses by exhibiting greater selection for areas near low-vegetation height seismic lines in areas with low densities of anthropogenic features. We highlight the importance of considering landscape heterogeneity and habitat characteristics, and the functional response in habitat selection when investigating seasonal behaviour-based selection patterns. Our results support behaviour in line with search for primary prey during summer and fall, and ease-of-travel during spring, while patterns of selection during winter aligned best with ease-of-travel for the less-industrialized foothills landscape, and with search for primary prey in the more-industrialized boreal landscape. These results highlight that time-sensitive restoration actions on anthropogenic features can affect the probability of overlap between predators and threatened prey within different landscapes.}, }
@article {pmid32614827, year = {2020}, author = {Ferguson, AW and Muloi, D and Ngatia, DK and Kiongo, W and Kimuyu, DM and Webala, PW and Olum, MO and Muturi, M and Thumbi, SM and Woodroffe, R and Murugi, L and Fèvre, EM and Murray, S and Martins, DJ}, title = {Volunteer based approach to dog vaccination campaigns to eliminate human rabies: Lessons from Laikipia County, Kenya.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {7}, pages = {e0008260}, pmid = {32614827}, issn = {1935-2735}, support = {110330/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Community-Institutional Relations ; Costs and Cost Analysis ; Dogs ; Humans ; Kenya ; Mass Vaccination/economics/*veterinary ; Population Density ; Rabies/*prevention &amp; control ; Volunteers ; }, abstract = {BACKGROUND: An estimated 59,000 people die from rabies annually, with 99% of those deaths attributable to bites from domestic dogs (Canis lupus familiaris). This preventable Neglected Tropical Disease has a large impact across continental Africa, especially for rural populations living in close contact with livestock and wildlife. Mass vaccinations of domestic dogs are effective at eliminating rabies but require large amounts of resources, planning, and political will to implement. Grassroots campaigns provide an alternative method to successful implementation of rabies control but remain understudied in their effectiveness to eliminate the disease from larger regions.<br><br>We report on the development, implementation, and effectiveness of a grassroots mass dog rabies vaccination campaign in Kenya, the Laikipia Rabies Vaccination Campaign. During 2015-2017, a total of 13,155 domestic dogs were vaccinated against rabies in 17 communities covering approximately 1500 km2. Based on an estimated population size of 34,275 domestic dogs, percent coverages increased across years, from 2% in 2015 to 24% in 2017, with only 3 of 38 community-years of vaccination exceeding the 70% target. The average cost of vaccinating an animal was $3.44 USD with in-kind contributions and $7.44 USD without in-kind contributions.<br><br>CONCLUSIONS/SIGNIFICANCE: The evolution of the Laikipia Rabies Vaccination Campaign from a localized volunteer-effort to a large-scale program attempting to eliminate rabies at the landscape scale provides a unique opportunity to examine successes, failures, and challenges facing grassroots campaigns. Success, in the form of vaccinating more dogs across the study area, was relatively straightforward to achieve. However, lack of effective post-vaccination monitoring and education programs, limited funding, and working in diverse community types appeared to hinder achievement of 70% coverage levels. These results indicate that grassroots campaigns will inevitably be faced with a philosophical question regarding the value of local impacts versus their contributions to a larger effort to eliminate rabies at the regional, country, or global scale.}, }
@article {pmid32608729, year = {2020}, author = {Zhu, LY and Chen, YY and Liu, J and Wang, YW and Wang, CR and Wei, YS and Zhang, YX}, title = {[Spatio-temporal Evolution and Relationship of Water Environment Quality and Phytoplankton Community in Wenyu River].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {41}, number = {2}, pages = {702-712}, doi = {10.13227/j.hjkx.201906207}, pmid = {32608729}, issn = {0250-3301}, mesh = {Beijing ; China ; Phytoplankton/*classification ; *Rivers ; Seasons ; Spatio-Temporal Analysis ; Water Pollution/*analysis ; *Water Quality ; }, abstract = {The Wenyu River is an important ecological corridor of Beijing. In this study, the spatio-temporal dynamics of water quality and phytoplankton community in the Wenyu River in 2006, 2011, and 2018, as well as their relationship were thoroughly analyzed by historical data analysis and field surveys. Results show that the water quality in the Wenyu River improved significantly from serious pollution owing to pollution containment. The major water pollutant has shifted from ammonia nitrogen (NH4+-N) to total nitrogen (TN). Compared with 2011, the average multiple of NH4+-N and total nitrogen TN exceeding the national standard were reduced by factors of 0.29-0.33 and 2.77-2.39, respectively, in 2018. The average concentration of NH4+-N and TN decreased from 15.52-19.16 mg·L-1 and 20.21-19.58 mg·L-1 in 2011 to 1.93-2.66 mg·L-1 and 5.66-6.79 mg·L-1 in 2018. Moreover, dissolved oxygen (DO) and NH4+-N concentrations in the Wenyu River and its tributaries, the Qinghe River, almost met requirements of their water function zoning target. Corresponding with the water quality improvement, the phytoplankton and community species increased dramatically. Phytoplankton species increased from 6 to 8 phyla, as well as community species. The dominant species changed from Chlorophyta in 2006 to the Cyanophyta in 2011, then to Bacillariophyta in 2018. The Shannon-Wiener diversity index (H') and evenness Pielou index (J) had improved. However, the major dominant species such as Cyclotella and Melosira persisted, and the Wenyu River was still in the eutrophication state in 2018. Statistical analysis results indicated that Cyanophyta, Bacillariophyta, and other algae abundance were significantly correlated with DO, pH, NH4+-N, TN, and TP.}, }
@article {pmid32586012, year = {2020}, author = {Zhou, Y and Rodriguez, J and Fisher, N and Catullo, RA}, title = {Ecological Drivers and Sex-Based Variation in Body Size and Shape in the Queensland Fruit Fly, Bactrocera tryoni (Diptera: Tephritidae).}, journal = {Insects}, volume = {11}, number = {6}, pages = {}, pmid = {32586012}, issn = {2075-4450}, abstract = {The Queensland fruit fly (Bactrocera tryoni; Q-fly) is an Australian endemic horticultural pest species, which has caused enormous economic losses. It has the potential to expand its range to currently Q-fly-free areas and poses a serious threat to the Australian horticultural industry. A large number of studies have investigated the correlation between environmental factors and Q-fly development, reproduction, and expansion. However, it is still not clear how Q-fly morphological traits vary with the environment. Our study focused on three morphological traits (body size, wing shape, and fluctuating asymmetry) in Q-fly samples collected from 1955 to 1965. We assessed how these traits vary by sex, and in response to latitude, environmental variables, and geographic distance. First, we found sexual dimorphism in body size and wing shape, but not in fluctuating asymmetry. Females had a larger body size but shorter and wider wings than males, which may be due to reproductive and/or locomotion differences between females and males. Secondly, the body size of Q-flies varied with latitude, which conforms to Bergmann's rule. Finally, we found Q-fly wing shape was more closely related to temperature rather than aridity, and low temperature and high aridity may lead to high asymmetry in Q-fly populations.}, }
@article {pmid32572035, year = {2020}, author = {Cansler, CA and Hood, SM and Varner, JM and van Mantgem, PJ and Agne, MC and Andrus, RA and Ayres, MP and Ayres, BD and Bakker, JD and Battaglia, MA and Bentz, BJ and Breece, CR and Brown, JK and Cluck, DR and Coleman, TW and Corace, RG and Covington, WW and Cram, DS and Cronan, JB and Crouse, JE and Das, AJ and Davis, RS and Dickinson, DM and Fitzgerald, SA and Fulé, PZ and Ganio, LM and Grayson, LM and Halpern, CB and Hanula, JL and Harvey, BJ and Kevin Hiers, J and Huffman, DW and Keifer, M and Keyser, TL and Kobziar, LN and Kolb, TE and Kolden, CA and Kopper, KE and Kreitler, JR and Kreye, JK and Latimer, AM and Lerch, AP and Lombardero, MJ and McDaniel, VL and McHugh, CW and McMillin, JD and Moghaddas, JJ and O'Brien, JJ and Perrakis, DDB and Peterson, DW and Prichard, SJ and Progar, RA and Raffa, KF and Reinhardt, ED and Restaino, JC and Roccaforte, JP and Rogers, BM and Ryan, KC and Safford, HD and Santoro, AE and Shearman, TM and Shumate, AM and Sieg, CH and Smith, SL and Smith, RJ and Stephenson, NL and Stuever, M and Stevens, JT and Stoddard, MT and Thies, WG and Vaillant, NM and Weiss, SA and Westlind, DJ and Woolley, TJ and Wright, MC}, title = {The Fire and Tree Mortality Database, for empirical modeling of individual tree mortality after fire.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {194}, doi = {10.1038/s41597-020-0522-7}, pmid = {32572035}, issn = {2052-4463}, abstract = {Wildland fires have a multitude of ecological effects in forests, woodlands, and savannas across the globe. A major focus of past research has been on tree mortality from fire, as trees provide a vast range of biological services. We assembled a database of individual-tree records from prescribed fires and wildfires in the United States. The Fire and Tree Mortality (FTM) database includes records from 164,293 individual trees with records of fire injury (crown scorch, bole char, etc.), tree diameter, and either mortality or top-kill up to ten years post-fire. Data span 142 species and 62 genera, from 409 fires occurring from 1981-2016. Additional variables such as insect attack are included when available. The FTM database can be used to evaluate individual fire-caused mortality models for pre-fire planning and post-fire decision support, to develop improved models, and to explore general patterns of individual fire-induced tree death. The database can also be used to identify knowledge gaps that could be addressed in future research.}, }
@article {pmid32556537, year = {2020}, author = {Piross, IS and Siliwal, M and Kumar, RS and Palatitz, P and Solt, S and Borbáth, P and Vili, N and Magonyi, N and Vas, Z and Rózsa, L and Harnos, A and Fehérvári, P}, title = {Sex interacts with age-dependent change in the abundance of lice-infesting Amur Falcons (Falco amurensis).}, journal = {Parasitology research}, volume = {119}, number = {8}, pages = {2579-2585}, pmid = {32556537}, issn = {1432-1955}, support = {GINOP 2.3.2-15- 2016-00057//European Regional Development Fund/ ; }, mesh = {Age Factors ; Amblycera/*physiology ; Animals ; Bird Diseases/*parasitology ; Ecosystem ; Ectoparasitic Infestations/parasitology/veterinary ; Falconiformes/parasitology ; Female ; India ; Lice Infestations/parasitology/*veterinary ; Male ; Phthiraptera ; Wings, Animal/parasitology ; }, abstract = {Sex-biassed and age-biassed parasite infections are common in nature, including ectoparasites-vertebrate host systems. We investigated the effect of Amur Falcons' sex, age and body size on the abundance of their lice at a migratory stopover site, where the falcons' habitat use and behaviour are more homogeneous across sex and age categories than during the breeding season. We sampled Amur Falcons in Nagaland, India at major roosting sites in 2016. We applied generalized linear models (with negative binomial distribution and log-link) to model the abundance of their two most numerous lice (Colpocephalum subzerafae and Degeeriella rufa) using the host age category (juvenile or adult) and wing length, both in interaction with sex, as explanatory variables. The abundance of C. subzerafae was only affected by host age, being nearly four times higher on juveniles than on adults. Juveniles were also more infested with D. rufa than the adults. Additionally, the abundance of the latter species was lower on adult male Falcons as compared to adult females. A juvenile bias in ectoparasite infestations is common in nature, probably due to juveniles being immunologically naïve, more resource-limited and may be inexperienced in body maintenance behaviours like preening and grooming. On the other hand, female-biassed infestations are much rarer than male-biassed infestations. We briefly discuss the possible causes of female-biassed infestations on Amur Falcons reported here, and in the closely related Red-footed Falcon and Lesser Kestrel as reported in the literature.}, }
@article {pmid32554569, year = {2020}, author = {Anderegg, WRL and Trugman, AT and Badgley, G and Anderson, CM and Bartuska, A and Ciais, P and Cullenward, D and Field, CB and Freeman, J and Goetz, SJ and Hicke, JA and Huntzinger, D and Jackson, RB and Nickerson, J and Pacala, S and Randerson, JT}, title = {Climate-driven risks to the climate mitigation potential of forests.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6497}, pages = {}, doi = {10.1126/science.aaz7005}, pmid = {32554569}, issn = {1095-9203}, mesh = {Carbon Sequestration ; *Climate Change ; Droughts ; Fires ; *Forests ; Policy Making ; }, abstract = {Forests have considerable potential to help mitigate human-caused climate change and provide society with many cobenefits. However, climate-driven risks may fundamentally compromise forest carbon sinks in the 21st century. Here, we synthesize the current understanding of climate-driven risks to forest stability from fire, drought, biotic agents, and other disturbances. We review how efforts to use forests as natural climate solutions presently consider and could more fully embrace current scientific knowledge to account for these climate-driven risks. Recent advances in vegetation physiology, disturbance ecology, mechanistic vegetation modeling, large-scale ecological observation networks, and remote sensing are improving current estimates and forecasts of the risks to forest stability. A more holistic understanding and quantification of such risks will help policy-makers and other stakeholders effectively use forests as natural climate solutions.}, }
@article {pmid32549034, year = {2020}, author = {Duarte, ME and Vigil-Hayes, M and Littletree, S and Belarde-Lewis, M}, title = {&quot;Of Course, Data Can Never Fully Represent Reality&quot;: Assessing the Relationship between &quot;Indigenous Data&quot; and &quot;Indigenous Knowledge,&quot; &quot;Traditional Ecological Knowledge,&quot; and &quot;Traditional Knowledge&quot;.}, journal = {Human biology}, volume = {91}, number = {3}, pages = {163-178}, doi = {10.13110/humanbiology.91.3.03}, pmid = {32549034}, issn = {1534-6617}, abstract = {Multiple terms describe Indigenous peoples' creative expressions, including &quot;Indigenous knowledge&quot; (IK), &quot;traditional ecological knowledge&quot; (TEK), &quot;traditional knowledge&quot; (TK), and increasingly, &quot;Indigenous data&quot; (ID). Variation in terms contributes to disciplinary divides, challenges in organizing and finding prior studies about Indigenous peoples' creative expressions, and intellectually divergent chains of reference. The authors applied a decolonial, digital, feminist, ethics-of-care approach to citation analysis of records about Indigenous peoples knowledge and data, including network analyses of author-generated keywords and research areas, and content analysis of peer-reviewed studies about ID. Results reveal ambiguous uses of the term &quot;Indigenous data&quot;; the influence of ecology and environmental studies in research areas and topics associated with IK, TEK, and TK; and the influence of public administration and governance studies in research areas and topics associated with ID studies. Researchers of ID would benefit from applying a more nuanced and robust vocabulary, one informed by studies of IK, TEK, and TK. Researchers of TEK and TK would benefit from the more people-centered approaches of IK. Researchers and systems designers who work with data sets can practice relational accountability by centering the Indigenous peoples from whom observations are sourced, combining narrative methodologies with computational methods to sustain the holism favored by Indigenous science and the relationality of Indigenous peoples.}, }
@article {pmid32541861, year = {2020}, author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S}, title = {Publisher Correction: A global database of Holocene paleotemperature records.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {183}, doi = {10.1038/s41597-020-0515-6}, pmid = {32541861}, issn = {2052-4463}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32541802, year = {2020}, author = {Birk, S and Chapman, D and Carvalho, L and Spears, BM and Andersen, HE and Argillier, C and Auer, S and Baattrup-Pedersen, A and Banin, L and Beklioğlu, M and Bondar-Kunze, E and Borja, A and Branco, P and Bucak, T and Buijse, AD and Cardoso, AC and Couture, RM and Cremona, F and de Zwart, D and Feld, CK and Ferreira, MT and Feuchtmayr, H and Gessner, MO and Gieswein, A and Globevnik, L and Graeber, D and Graf, W and Gutiérrez-Cánovas, C and Hanganu, J and Işkın, U and Järvinen, M and Jeppesen, E and Kotamäki, N and Kuijper, M and Lemm, JU and Lu, S and Solheim, AL and Mischke, U and Moe, SJ and Nõges, P and Nõges, T and Ormerod, SJ and Panagopoulos, Y and Phillips, G and Posthuma, L and Pouso, S and Prudhomme, C and Rankinen, K and Rasmussen, JJ and Richardson, J and Sagouis, A and Santos, JM and Schäfer, RB and Schinegger, R and Schmutz, S and Schneider, SC and Schülting, L and Segurado, P and Stefanidis, K and Sures, B and Thackeray, SJ and Turunen, J and Uyarra, MC and Venohr, M and von der Ohe, PC and Willby, N and Hering, D}, title = {Impacts of multiple stressors on freshwater biota across spatial scales and ecosystems.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {8}, pages = {1060-1068}, doi = {10.1038/s41559-020-1216-4}, pmid = {32541802}, issn = {2397-334X}, mesh = {Biota ; *Ecosystem ; Europe ; *Fresh Water ; Rivers ; }, abstract = {Climate and land-use change drive a suite of stressors that shape ecosystems and interact to yield complex ecological responses (that is, additive, antagonistic and synergistic effects). We know little about the spatial scales relevant for the outcomes of such interactions and little about effect sizes. These knowledge gaps need to be filled to underpin future land management decisions or climate mitigation interventions for protecting and restoring freshwater ecosystems. This study combines data across scales from 33 mesocosm experiments with those from 14 river basins and 22 cross-basin studies in Europe, producing 174 combinations of paired-stressor effects on a biological response variable. Generalized linear models showed that only one of the two stressors had a significant effect in 39% of the analysed cases, 28% of the paired-stressor combinations resulted in additive effects and 33% resulted in interactive (antagonistic, synergistic, opposing or reversal) effects. For lakes, the frequencies of additive and interactive effects were similar for all spatial scales addressed, while for rivers these frequencies increased with scale. Nutrient enrichment was the overriding stressor for lakes, with effects generally exceeding those of secondary stressors. For rivers, the effects of nutrient enrichment were dependent on the specific stressor combination and biological response variable. These results vindicate the traditional focus of lake restoration and management on nutrient stress, while highlighting that river management requires more bespoke management solutions.}, }
@article {pmid32518318, year = {2020}, author = {Wang, E and Zhang, D and Braun, MS and Hotz-Wagenblatt, A and Pärt, T and Arlt, D and Schmaljohann, H and Bairlein, F and Lei, F and Wink, M}, title = {Can Mitogenomes of the Northern Wheatear (Oenanthe oenanthe) Reconstruct Its Phylogeography and Reveal the Origin of Migrant Birds?.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9290}, doi = {10.1038/s41598-020-66287-0}, pmid = {32518318}, issn = {2045-2322}, mesh = {Animal Migration ; Evolution, Molecular ; *Genetic Speciation ; Genome, Mitochondrial/*genetics ; Germany ; Greece ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Songbirds/*classification/*genetics ; }, abstract = {The Northern Wheatear (Oenanthe oenanthe, including the nominate and the two subspecies O. o. leucorhoa and O. o. libanotica) and the Seebohm's Wheatear (Oenanthe seebohmi) are today regarded as two distinct species. Before, all four taxa were regarded as four subspecies of the Northern Wheatear. Their classification has exclusively been based on ecological and morphological traits, while their molecular characterization is still missing. With this study, we used next-generation sequencing to assemble 117 complete mitochondrial genomes covering O. o. oenanthe, O. o. leucorhoa and O. seebohmi. We compared the resolution power of each individual mitochondrial marker and concatenated marker sets to reconstruct the phylogeny and estimate speciation times of three taxa. Moreover, we tried to identify the origin of migratory wheatears caught on Helgoland (Germany) and on Crete (Greece). Mitogenome analysis revealed two different ancient lineages that separated around 400,000 years ago. Both lineages consisted of a mix of subspecies and species. The phylogenetic trees, as well as haplotype networks are incongruent with the present morphology-based classification. Mitogenome could not distinguish these presumed species. The genetic panmixia among present populations and taxa might be the consequence of mitochondrial introgression between ancient wheatear populations.}, }
@article {pmid32512194, year = {2020}, author = {Pirani, RM and Peloso, PLV and Prado, JR and Polo, ÉM and Knowles, LL and Ron, SR and Rodrigues, MT and Sturaro, MJ and Werneck, FP}, title = {Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group).}, journal = {Molecular phylogenetics and evolution}, volume = {150}, number = {}, pages = {106877}, doi = {10.1016/j.ympev.2020.106877}, pmid = {32512194}, issn = {1095-9513}, mesh = {Animals ; Anura/*classification/genetics ; Biodiversity ; Databases, Genetic ; Phylogeny ; Rainforest ; South America ; Species Specificity ; }, abstract = {General consensus emphasizes that no single biological process can explain the patterns of species' distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA (ddRADseq), we inferred phylogenetic relationships, species limits, and temporal and geographic patterns of diversification relative to the history of these biomes. Our results indicate that the D. leucophyllatus species group includes at least 14 independent lineages, which are currently arranged into ten described species. Therefore, a significant portion of species in the group are still unnamed. Different processes were associated to the group diversification history. For instance, the Andes uplift likely caused allopatric speciation for Cis-Andean species, whereas it may also be responsible for changes in the Amazonian landscape triggering parapatric speciation by local adaptation to ecological factors. Meanwhile, Atlantic Forest ancestors unable to cross the dry diagonal biomes after rainforest's retraction, evolved in isolation into different species. Diversification in the group began in the early Miocene, when connections between Atlantic Forest and the Andes (Pacific Dominion) by way of a south corridor were possible. The historical scenario in Amazonia, characterized by several speciation events and habitat heterogeneity, helped promoting diversification, resulting in the highest species diversity for the group. This marked species diversification did not happen in Atlantic Forest, where speciation is very recent (late Pliocene and Pleistocene), despite its remarkable climatic heterogeneity.}, }
@article {pmid32441459, year = {2020}, author = {Han, BA and O'Regan, SM and Paul Schmidt, J and Drake, JM}, title = {Integrating data mining and transmission theory in the ecology of infectious diseases.}, journal = {Ecology letters}, volume = {23}, number = {8}, pages = {1178-1188}, pmid = {32441459}, issn = {1461-0248}, support = {1717282//Division of Environmental Biology/ ; //NIMBioS/ ; }, mesh = {Animals ; Data Mining ; Disease Outbreaks ; Humans ; Models, Theoretical ; *Rodentia ; Zoonoses/*epidemiology ; }, abstract = {Our understanding of ecological processes is built on patterns inferred from data. Applying modern analytical tools such as machine learning to increasingly high dimensional data offers the potential to expand our perspectives on these processes, shedding new light on complex ecological phenomena such as pathogen transmission in wild populations. Here, we propose a novel approach that combines data mining with theoretical models of disease dynamics. Using rodents as an example, we incorporate statistical differences in the life history features of zoonotic reservoir hosts into pathogen transmission models, enabling us to bound the range of dynamical phenomena associated with hosts, based on their traits. We then test for associations between equilibrium prevalence, a key epidemiological metric and data on human outbreaks of rodent-borne zoonoses, identifying matches between empirical evidence and theoretical predictions of transmission dynamics. We show how this framework can be generalized to other systems through a rubric of disease models and parameters that can be derived from empirical data. By linking life history components directly to their effects on disease dynamics, our mining-modelling approach integrates machine learning and theoretical models to explore mechanisms in the macroecology of pathogen transmission and their consequences for spillover infection to humans.}, }
@article {pmid32409662, year = {2020}, author = {Cooney, CR and Sheard, C and Clark, AD and Healy, SD and Liker, A and Street, SE and Troisi, CA and Thomas, GH and Székely, T and Hemmings, N and Wright, AE}, title = {Ecology and allometry predict the evolution of avian developmental durations.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2383}, pmid = {32409662}, issn = {2041-1723}, mesh = {Animals ; Birds/*physiology ; Body Size/physiology ; Datasets as Topic ; Ecology/methods ; Embryo, Nonmammalian ; Embryonic Development/*physiology ; Female ; *Life History Traits ; Male ; *Models, Biological ; Nesting Behavior/physiology ; Time Factors ; }, abstract = {The duration of the developmental period represents a fundamental axis of life-history variation, yet broad insights regarding the drivers of this diversity are currently lacking. Here, we test mechanistic and ecological explanations for the evolution of developmental duration using embryological data and information on incubation and fledging for 3096 avian species. Developmental phases associated primarily with growth are the longest and most variable, consistent with a role for allometric constraint in determining the duration of development. In addition, developmental durations retain a strong imprint of deep evolutionary history and body size differences among species explain less variation than previously thought. Finally, we reveal ecological correlates of developmental durations, including variables associated with the relative safety of the developmental environment and pressures of breeding phenology. Overall, our results provide broad-scale insight into the relative importance of mechanistic, ecological and evolutionary constraints in shaping the diversification of this key life-history trait.}, }
@article {pmid32396806, year = {2020}, author = {Herren, CM}, title = {Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1927}, pages = {20192945}, pmid = {32396806}, issn = {1471-2954}, mesh = {Biota ; *Ecosystem ; *Introduced Species ; *Microbiota ; }, abstract = {The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this 'critical' level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.}, }
@article {pmid32368363, year = {2019}, author = {Boyce, HB and Mallick, P}, title = {Geostatistical visualization of ecological interactions in tumors.}, journal = {Proceedings. IEEE International Conference on Bioinformatics and Biomedicine}, volume = {2019}, number = {}, pages = {2741-2749}, pmid = {32368363}, issn = {2156-1125}, support = {T15 LM007033/LM/NLM NIH HHS/United States ; }, abstract = {Recent advances in our understanding of cancer progression have highlighted the roles played by molecular heterogeneity and by the tumor microenvironment in driving drug resistance and metastasis. The coupling of single-cell measurement technologies with algorithms, such as t-sne and SPADE, have enabled deep investigation of tumor heterogeneity. However, such techniques only capture molecular heterogeneity and do not enable the quantification nor visualization of intercellular interactions. They additionally do not allow the visualization of ecological niches that are critical to understanding tumor behavior. Novel computational tools to quantify and visualize spatial patterns in the tumor microenvironment are critically needed. Here, we take a tumor ecology perspective to examine how predation, mutualism, commensalism, and parasitism may impact tumor development and spatial patterning. We additionally quantify local spatial heterogeneity and the emergent global spatial behavior of the models using geostatistics. By visualizing emergent spatial patterns we demonstrate the potential utility of a geostatistical analysis in differentiating amongst cell-cell interactions in the tumor microenvironment. These studies introduce both an ecological framework for characterizing intercellular interactions in cancer and a novel way of quantifying and visualizing spatial patterns in cancer.}, }
@article {pmid32358490, year = {2020}, author = {Hale, KRS and Valdovinos, FS and Martinez, ND}, title = {Mutualism increases diversity, stability, and function of multiplex networks that integrate pollinators into food webs.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2182}, pmid = {32358490}, issn = {2041-1723}, mesh = {Animals ; Biodiversity ; Biomass ; Computer Simulation ; Ecological and Environmental Phenomena ; *Food Chain ; Models, Biological ; Plants ; *Pollination ; *Symbiosis ; }, abstract = {Ecosystems are composed of complex networks of many species interacting in different ways. While ecologists have long studied food webs of feeding interactions, recent studies increasingly focus on mutualistic networks including plants that exchange food for reproductive services provided by animals such as pollinators. Here, we synthesize both types of consumer-resource interactions to better understand the controversial effects of mutualism on ecosystems at the species, guild, and whole-community levels. We find that consumer-resource mechanisms underlying plant-pollinator mutualisms can increase persistence, productivity, abundance, and temporal stability of both mutualists and non-mutualists in food webs. These effects strongly increase with floral reward productivity and are qualitatively robust to variation in the prevalence of mutualism and pollinators feeding upon resources in addition to rewards. This work advances the ability of mechanistic network theory to synthesize different types of interactions and illustrates how mutualism can enhance the diversity, stability, and function of complex ecosystems.}, }
@article {pmid32320389, year = {2020}, author = {Wu, SL and Sánchez C, HM and Henry, JM and Citron, DT and Zhang, Q and Compton, K and Liang, B and Verma, A and Cummings, DAT and Le Menach, A and Scott, TW and Wilson, AL and Lindsay, SW and Moyes, CL and Hancock, PA and Russell, TL and Burkot, TR and Marshall, JM and Kiware, S and Reiner, RC and Smith, DL}, title = {Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology.}, journal = {PLoS computational biology}, volume = {16}, number = {4}, pages = {e1007446}, pmid = {32320389}, issn = {1553-7358}, support = {U19 AI089674/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; *Behavior, Animal ; Computational Biology ; Computer Simulation ; Culicidae/*physiology ; Disease Vectors ; Ecology ; Ecosystem ; Feeding Behavior ; Female ; Humans ; Malaria/*transmission ; Male ; Models, Theoretical ; Monte Carlo Method ; *Mosquito Vectors ; Oviposition ; Probability ; }, abstract = {Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed a new framework for individual-based simulation models called MBITES (Mosquito Bout-based and Individual-based Transmission Ecology Simulator). In MBITES, it is possible to build models that simulate the behavior and ecology of adult mosquitoes in exquisite detail on complex resource landscapes generated by spatial point processes. We also developed an ordinary differential equation model which is the Kolmogorov forward equations for models developed in MBITES under a specific set of simplifying assumptions. While mosquito infection and pathogen development are one possible part of a mosquito's state, that is not our main focus. Using extensive simulation using some models developed in MBITES, we show that vectorial capacity can be understood as an emergent property of simple behavioral algorithms interacting with complex resource landscapes, and that relative density or sparsity of resources and the need to search can have profound consequences for mosquito populations' capacity to transmit pathogens.}, }
@article {pmid32286335, year = {2020}, author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S}, title = {A global database of Holocene paleotemperature records.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {115}, doi = {10.1038/s41597-020-0445-3}, pmid = {32286335}, issn = {2052-4463}, support = {AGS-1602105//National Science Foundation (NSF)/International ; AGS-1903548//National Science Foundation (NSF)/International ; AGS-1602105//National Science Foundation (NSF)/International ; AGS-1903548//National Science Foundation (NSF)/International ; AGS-1602301//National Science Foundation (NSF)/International ; }, abstract = {A comprehensive database of paleoclimate records is needed to place recent warming into the longer-term context of natural climate variability. We present a global compilation of quality-controlled, published, temperature-sensitive proxy records extending back 12,000 years through the Holocene. Data were compiled from 679 sites where time series cover at least 4000 years, are resolved at sub-millennial scale (median spacing of 400 years or finer) and have at least one age control point every 3000 years, with cut-off values slackened in data-sparse regions. The data derive from lake sediment (51%), marine sediment (31%), peat (11%), glacier ice (3%), and other natural archives. The database contains 1319 records, including 157 from the Southern Hemisphere. The multi-proxy database comprises paleotemperature time series based on ecological assemblages, as well as biophysical and geochemical indicators that reflect mean annual or seasonal temperatures, as encoded in the database. This database can be used to reconstruct the spatiotemporal evolution of Holocene temperature at global to regional scales, and is publicly available in Linked Paleo Data (LiPD) format.}, }
@article {pmid32255797, year = {2020}, author = {Purse, BV and Darshan, N and Kasabi, GS and Gerard, F and Samrat, A and George, C and Vanak, AT and Oommen, M and Rahman, M and Burthe, SJ and Young, JC and Srinivas, PN and Schäfer, SM and Henrys, PA and Sandhya, VK and Chanda, MM and Murhekar, MV and Hoti, SL and Kiran, SK}, title = {Predicting disease risk areas through co-production of spatial models: The example of Kyasanur Forest Disease in India's forest landscapes.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {4}, pages = {e0008179}, pmid = {32255797}, issn = {1935-2735}, support = {IA/CPHI/16/1/502648/WTDBT_/DBT-Wellcome Trust India Alliance/India ; MR/P024335/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animal Distribution ; Animals ; Biodiversity ; *Disease Outbreaks ; Disease Susceptibility ; Forests ; Humans ; India/epidemiology ; Kyasanur Forest Disease/*epidemiology ; Population Density ; Risk Factors ; Spatial Regression ; Zoonoses/*epidemiology ; }, abstract = {Zoonotic diseases affect resource-poor tropical communities disproportionately, and are linked to human use and modification of ecosystems. Disentangling the socio-ecological mechanisms by which ecosystem change precipitates impacts of pathogens is critical for predicting disease risk and designing effective intervention strategies. Despite the global &quot;One Health&quot; initiative, predictive models for tropical zoonotic diseases often focus on narrow ranges of risk factors and are rarely scaled to intervention programs and ecosystem use. This study uses a participatory, co-production approach to address this disconnect between science, policy and implementation, by developing more informative disease models for a fatal tick-borne viral haemorrhagic disease, Kyasanur Forest Disease (KFD), that is spreading across degraded forest ecosystems in India. We integrated knowledge across disciplines to identify key risk factors and needs with actors and beneficiaries across the relevant policy sectors, to understand disease patterns and develop decision support tools. Human case locations (2014-2018) and spatial machine learning quantified the relative role of risk factors, including forest cover and loss, host densities and public health access, in driving landscape-scale disease patterns in a long-affected district (Shivamogga, Karnataka State). Models combining forest metrics, livestock densities and elevation accurately predicted spatial patterns in human KFD cases (2014-2018). Consistent with suggestions that KFD is an &quot;ecotonal&quot; disease, landscapes at higher risk for human KFD contained diverse forest-plantation mosaics with high coverage of moist evergreen forest and plantation, high indigenous cattle density, and low coverage of dry deciduous forest. Models predicted new hotspots of outbreaks in 2019, indicating their value for spatial targeting of intervention. Co-production was vital for: gathering outbreak data that reflected locations of exposure in the landscape; better understanding contextual socio-ecological risk factors; and tailoring the spatial grain and outputs to the scale of forest use, and public health interventions. We argue this inter-disciplinary approach to risk prediction is applicable across zoonotic diseases in tropical settings.}, }
@article {pmid32234481, year = {2020}, author = {Tournière, O and Dolan, D and Richards, GS and Sunagar, K and Columbus-Shenkar, YY and Moran, Y and Rentzsch, F}, title = {NvPOU4/Brain3 Functions as a Terminal Selector Gene in the Nervous System of the Cnidarian Nematostella vectensis.}, journal = {Cell reports}, volume = {30}, number = {13}, pages = {4473-4489.e5}, doi = {10.1016/j.celrep.2020.03.031}, pmid = {32234481}, issn = {2211-1247}, abstract = {Terminal selectors are transcription factors that control the morphological, physiological, and molecular features that characterize distinct cell types. Here, we show that, in the sea anemone Nematostella vectensis, NvPOU4 is expressed in post-mitotic cells that give rise to a diverse set of neural cell types, including cnidocytes and NvElav1-expressing neurons. Morphological analyses of NvPOU4 mutants crossed to transgenic reporter lines show that the loss of NvPOU4 does not affect the initial specification of neural cells. Transcriptomes derived from the mutants and from different neural cell populations reveal that NvPOU4 is required for the execution of the terminal differentiation program of these neural cells. These findings suggest that POU4 genes have ancient functions as terminal selectors for morphologically and functionally disparate types of neurons and they provide experimental support for the relevance of terminal selectors for understanding the evolution of cell types.}, }
@article {pmid32213967, year = {2020}, author = {Zhu, C and Zhang, Z and Wang, H and Wang, J and Yang, S}, title = {Assessing Soil Organic Matter Content in a Coal Mining Area through Spectral Variables of Different Numbers of Dimensions.}, journal = {Sensors (Basel, Switzerland)}, volume = {20}, number = {6}, pages = {}, pmid = {32213967}, issn = {1424-8220}, support = {41861037//National Natural Science Foundation of China/ ; U1603241//National Natural Science Foundation of China/ ; }, abstract = {Soil organic matter (SOM) is a crucial indicator for evaluating soil quality and an important component of soil carbon pools, which play a vital role in terrestrial ecosystems. Rapid, non-destructive and accurate monitoring of SOM content is of great significance for the environmental management and ecological restoration of mining areas. Visible-near-infrared (Vis-NIR) spectroscopy has proven its applicability in estimating SOM over the years. In this study, 168 soil samples were collected from the Zhundong coal field of Xinjiang Province, Northwest China. The SOM content (g kg-1) was determined by the potassium dichromate external heating method and the soil reflectance spectra were measured by the spectrometer. Two spectral feature extraction strategies, namely, principal component analysis (PCA) and the optimal band combination algorithm, were introduced to choose spectral variables. Linear models and random forests (RF) were used for predictive models. The coefficient of determination (R2), root mean square error (RMSE), and the ratio of the performance to the interquartile distance (RPIQ) were used to evaluate the predictive performance of the model. The results indicated that the variables (2DI and 3DI) derived from the optimal band combination algorithm outperformed the PCA variables (1DV) regardless of whether linear or RF models were used. An inherent gap exists between 2DI and 3DI, and the performance of 2DI is significantly poorer than that of 3DI. The accuracy of the prediction model increases with the increasing number of spectral variable dimensions (in the following order: 1DV < 2DI < 3DI). This study proves that the 3DI is the first choice for the optimal band combination algorithm to derive sensitive parameters related to SOM in the coal mining area. Furthermore, the optimal band combination algorithm can be applied to hyperspectral or multispectral images and to convert the spectral response into image pixels, which may be helpful for a soil property spatial distribution map.}, }
@article {pmid32204532, year = {2020}, author = {Ma, J and Lu, Y and Chen, F and Li, X and Xiao, D and Wang, H}, title = {Molecular Ecological Network Complexity Drives Stand Resilience of Soil Bacteria to Mining Disturbances among Typical Damaged Ecosystems in China.}, journal = {Microorganisms}, volume = {8}, number = {3}, pages = {}, pmid = {32204532}, issn = {2076-2607}, support = {41907405 and 51974313//National Natural Science Foundation/ ; BK20180641//Natural Science Foundation of Jiangsu Province/ ; }, abstract = {Understanding the interactions of soil microbial species and how they responded to disturbances are essential to ecological restoration and resilience in the semihumid and semiarid damaged mining areas. Information on this, however, remains unobvious and deficiently comprehended. In this study, based on the high throughput sequence and molecular ecology network analysis, we have investigated the bacterial distribution in disturbed mining areas across three provinces in China, and constructed molecular ecological networks to reveal the interactions of soil bacterial communities in diverse locations. Bacterial community diversity and composition were classified measurably between semihumid and semiarid damaged mining sites. Additionally, we distinguished key microbial populations across these mining areas, which belonged to Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. Moreover, the network modules were significantly associated with some environmental factors (e.g., annual average temperature, electrical conductivity value, and available phosphorus value). The study showed that network interactions were completely different across the different mining areas. The keystone species in different mining areas suggested that selected microbial communities, through natural successional processes, were able to resist the corresponding environment. Moreover, the results of trait-based module significances showed that several environmental factors were significantly correlated with some keystone species, such as OTU_8126 (Acidobacteria), OTU_8175 (Burkholderiales), and OTU_129 (Chloroflexi). Our study also implied that the complex network of microbial interaction might drive the stand resilience of soil bacteria in the semihumid and semiarid disturbed mining areas.}, }
@article {pmid32188863, year = {2020}, author = {Ropert-Coudert, Y and Van de Putte, AP and Reisinger, RR and Bornemann, H and Charrassin, JB and Costa, DP and Danis, B and Hückstädt, LA and Jonsen, ID and Lea, MA and Thompson, D and Torres, LG and Trathan, PN and Wotherspoon, S and Ainley, DG and Alderman, R and Andrews-Goff, V and Arthur, B and Ballard, G and Bengtson, J and Bester, MN and Blix, AS and Boehme, L and Bost, CA and Boveng, P and Cleeland, J and Constantine, R and Crawford, RJM and Dalla Rosa, L and Nico de Bruyn, PJ and Delord, K and Descamps, S and Double, M and Emmerson, L and Fedak, M and Friedlaender, A and Gales, N and Goebel, M and Goetz, KT and Guinet, C and Goldsworthy, SD and Harcourt, R and Hinke, JT and Jerosch, K and Kato, A and Kerry, KR and Kirkwood, R and Kooyman, GL and Kovacs, KM and Lawton, K and Lowther, AD and Lydersen, C and Lyver, PO and Makhado, AB and Márquez, MEI and McDonald, BI and McMahon, CR and Muelbert, M and Nachtsheim, D and Nicholls, KW and Nordøy, ES and Olmastroni, S and Phillips, RA and Pistorius, P and Plötz, J and Pütz, K and Ratcliffe, N and Ryan, PG and Santos, M and Southwell, C and Staniland, I and Takahashi, A and Tarroux, A and Trivelpiece, W and Wakefield, E and Weimerskirch, H and Wienecke, B and Xavier, JC and Raymond, B and Hindell, MA}, title = {The retrospective analysis of Antarctic tracking data project.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {94}, pmid = {32188863}, issn = {2052-4463}, abstract = {The Retrospective Analysis of Antarctic Tracking Data (RAATD) is a Scientific Committee for Antarctic Research project led jointly by the Expert Groups on Birds and Marine Mammals and Antarctic Biodiversity Informatics, and endorsed by the Commission for the Conservation of Antarctic Marine Living Resources. RAATD consolidated tracking data for multiple species of Antarctic meso- and top-predators to identify Areas of Ecological Significance. These datasets and accompanying syntheses provide a greater understanding of fundamental ecosystem processes in the Southern Ocean, support modelling of predator distributions under future climate scenarios and create inputs that can be incorporated into decision making processes by management authorities. In this data paper, we present the compiled tracking data from research groups that have worked in the Antarctic since the 1990s. The data are publicly available through biodiversity.aq and the Ocean Biogeographic Information System. The archive includes tracking data from over 70 contributors across 12 national Antarctic programs, and includes data from 17 predator species, 4060 individual animals, and over 2.9 million observed locations.}, }
@article {pmid32179987, year = {2020}, author = {Piross, IS and Solt, S and Horváth, É and Kotymán, L and Palatitz, P and Bertók, P and Szabó, K and Vili, N and Vas, Z and Rózsa, L and Harnos, A and Fehérvári, P}, title = {Sex-dependent changes in the louse abundance of red-footed falcons (Falco vespertinus).}, journal = {Parasitology research}, volume = {119}, number = {4}, pages = {1327-1335}, pmid = {32179987}, issn = {1432-1955}, mesh = {Animals ; Anoplura/*physiology ; Bird Diseases/parasitology ; Birds/parasitology ; Falconiformes/*parasitology ; Feathers ; Female ; Hungary ; Ischnocera/*physiology ; Lice Infestations/parasitology ; Male ; Phthiraptera/*physiology ; Wings, Animal/anatomy &amp; histology/parasitology ; }, abstract = {Permanent ectoparasites live in stable environments; thus, their population dynamics are mostly adapted to changes in the host life cycle. We aimed to investigate how static and dynamic traits of red-footed falcons interplay with the dynamics of their louse subpopulations during breeding and how they affect the colonisation of new hosts by lice. We sampled red-footed falcon (Falco vespertinus) nestlings (two breeding seasons) and adults (one breeding season) in southern Hungary. The mean abundance of Colpocephalum subzerafae and Degeeriella rufa lice on the nestlings was modelled with generalized linear mixed models using clutch size and host sex in interaction with wing length. For adults, we used wing length and the number of days after laying the first egg, both in interaction with sex. D. rufa abundances increased with the nestlings' wing length. In one year, this trend was steeper on females. In adult birds, both louse species exhibited higher abundances on females at the beginning, but it decreased subsequently through the breeding season. Contrarily, abundances were constantly low on adult males. Apparently, D. rufa postpones transmission until nestlings develop juvenile plumage and choose the more feathered individual among siblings. The sexual difference in the observed abundance could either be caused by the different plumage, or by the females' preference for less parasitized males. Moreover, females likely have more time to preen during the incubation period, lowering their louse burdens. Thus, sex-biased infestation levels likely arise due to parasite preferences in the nestlings and host behavioural processes in the adult falcons.}, }
@article {pmid32165619, year = {2020}, author = {Thomas, HJD and Bjorkman, AD and Myers-Smith, IH and Elmendorf, SC and Kattge, J and Diaz, S and Vellend, M and Blok, D and Cornelissen, JHC and Forbes, BC and Henry, GHR and Hollister, RD and Normand, S and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Wilmking, M and Wipf, S and Cornwell, WK and Beck, PSA and Georges, D and Goetz, SJ and Guay, KC and Rüger, N and Soudzilovskaia, NA and Spasojevic, MJ and Alatalo, JM and Alexander, HD and Anadon-Rosell, A and Angers-Blondin, S and Te Beest, M and Berner, LT and Björk, RG and Buchwal, A and Buras, A and Carbognani, M and Christie, KS and Collier, LS and Cooper, EJ and Elberling, B and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Heijmans, MMPD and Hermanutz, L and Hudson, JMG and Johnstone, JF and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Kaarlejarvi, E and Kulonen, A and Lamarque, LJ and Lantz, TC and Lévesque, E and Little, CJ 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 Petraglia, A and Rumpf, SB and Shetti, R and Speed, JDM and Suding, KN and Tape, KD and Tomaselli, M and Trant, AJ and Treier, UA and Tremblay, M and Venn, SE and Vowles, T and Weijers, S and Wookey, PA and Zamin, TJ and Bahn, M and Blonder, B and van Bodegom, PM and Bond-Lamberty, B and Campetella, G and Cerabolini, BEL and Chapin, FS and Craine, JM and Dainese, M and Green, WA and Jansen, S and Kleyer, M and Manning, P and Niinemets, Ü and Onoda, Y and Ozinga, WA and Peñuelas, J and Poschlod, P and Reich, PB and Sandel, B and Schamp, BS and Sheremetiev, SN and de Vries, FT}, title = {Global plant trait relationships extend to the climatic extremes of the tundra biome.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1351}, pmid = {32165619}, issn = {2041-1723}, mesh = {Climate ; Ecosystem ; *Plant Development ; Plants/classification/genetics ; *Tundra ; }, abstract = {The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community change in a warming world.}, }
@article {pmid32151872, year = {2020}, author = {Wan, Y and Jiang, B and Wei, D and Ma, Y}, title = {Ecological criteria for zinc in Chinese soil as affected by soil properties.}, journal = {Ecotoxicology and environmental safety}, volume = {194}, number = {}, pages = {110418}, doi = {10.1016/j.ecoenv.2020.110418}, pmid = {32151872}, issn = {1090-2414}, mesh = {Agriculture ; China ; Databases, Factual ; Ecotoxicology ; Environmental Monitoring/*methods ; Models, Theoretical ; Risk Assessment ; *Soil/chemistry/standards ; Soil Pollutants/*analysis ; Zinc/*analysis ; }, abstract = {The increasing accumulation of zinc (Zn) in agricultural soils has led to the need to assess the potential risk of this element for terrestrial organisms. However, the soil ecological criteria in agricultural soil as a function of soil properties have been sparsely reported. In the present study, we derived the ecological criteria (expressed as predicted no effect concentration (PNEC)) for Zn in soils, based on ecotoxicity data for 19 terrestrial species in Chinese soils, the effect of soil properties on Zn ecotoxicity, differences in species sensitivity, and differences between laboratory and realistic field conditions. First, all ecotoxicity data of Zn for terrestrial organisms in Chinese soils were collected and filtered with given criteria to obtain reliable database. Second, the ecotoxicity data were normalized using Zn ecotoxicity predictive models to eliminate the effect of soil properties on Zn ecotoxicity, and corrected with leaching and aging factors to minimize the differences in Zn ecotoxicity under laboratory and field conditions. Then, species sensitivity distribution (SSD) curves were generated with a Burr Ⅲ function based on corrected ecotoxicity data. The concentration of Zn in soil that provides ecological safety for (100 - x)% of species (HCx), was calculated from the SSD curve and HC5 was used for estimation of PNEC. Finally, we developed the predictive models for HCx by quantifying the relationship between the Zn HCx and soil properties. Results showed that soil pH was the most crucial factor affecting Zn HCx values, with HC5 values varying from 38.3 mg/kg in an acidic soil to 263.3 mg/kg in an alkaline calcareous soil. Both the two-factor (soil pH and OC) and the three-factor (soil pH, OC and CEC) models predicted HCx values well, with determination coefficients (R2) of 0.941-0.959 and 0.978-0.982, respectively. This study provides a scientific and reliable basis for the improvement of ecological risk assessment and the establishment of soil environmental quality standards.}, }
@article {pmid32140140, year = {2020}, author = {Cullen, CM and Aneja, KK and Beyhan, S and Cho, CE and Woloszynek, S and Convertino, M and McCoy, SJ and Zhang, Y and Anderson, MZ and Alvarez-Ponce, D and Smirnova, E and Karstens, L and Dorrestein, PC and Li, H and Sen Gupta, A and Cheung, K and Powers, JG and Zhao, Z and Rosen, GL}, title = {Emerging Priorities for Microbiome Research.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {136}, pmid = {32140140}, issn = {1664-302X}, abstract = {Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration.}, }
@article {pmid32066887, year = {2020}, author = {Gallagher, RV and Falster, DS and Maitner, BS and Salguero-Gómez, R and Vandvik, V and Pearse, WD and Schneider, FD and Kattge, J and Poelen, JH and Madin, JS and Ankenbrand, MJ and Penone, C and Feng, X and Adams, VM and Alroy, J and Andrew, SC and Balk, MA and Bland, LM and Boyle, BL and Bravo-Avila, CH and Brennan, I and Carthey, AJR and Catullo, R and Cavazos, BR and Conde, DA and Chown, SL and Fadrique, B and Gibb, H and Halbritter, AH and Hammock, J and Hogan, JA and Holewa, H and Hope, M and Iversen, CM and Jochum, M and Kearney, M and Keller, A and Mabee, P and Manning, P and McCormack, L and Michaletz, ST and Park, DS and Perez, TM and Pineda-Munoz, S and Ray, CA and Rossetto, M and Sauquet, H and Sparrow, B and Spasojevic, MJ and Telford, RJ and Tobias, JA and Violle, C and Walls, R and Weiss, KCB and Westoby, M and Wright, IJ and Enquist, BJ}, title = {Open Science principles for accelerating trait-based science across the Tree of Life.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {3}, pages = {294-303}, doi = {10.1038/s41559-020-1109-6}, pmid = {32066887}, issn = {2397-334X}, mesh = {*Biodiversity ; Biological Evolution ; *Ecology ; Phenotype ; Research ; }, abstract = {Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.}, }
@article {pmid32065938, year = {2020}, author = {Douterelo, I and Dutilh, BE and Arkhipova, K and Calero, C and Husband, S}, title = {Microbial diversity, ecological networks and functional traits associated to materials used in drinking water distribution systems.}, journal = {Water research}, volume = {173}, number = {}, pages = {115586}, doi = {10.1016/j.watres.2020.115586}, pmid = {32065938}, issn = {1879-2448}, mesh = {Bacteria ; Biofilms ; *Drinking Water ; Ecology ; Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Drinking water distribution systems host complex microbial communities as biofilms that interact continuously with delivered water. Understanding the diversity, behavioural and functional characteristics will be a requisite for developing future monitoring strategies and protection against water-borne health risks. To improve understanding, this study investigates mobilisation and accumulation behaviour, microbial community structure and functional variations of biofilms developing on different pipe materials from within an operational network. Samples were collected from four pipes during a repeated flushing operation three months after an initial visit that used hydraulic forces to mobilise regenerating biofilms yet without impacting the upstream network. To minimise confounding factors, test sections were chosen with comparable daily hydraulic regimes, physical dimensions, and all connected straight of a common trunk main and within close proximity, hence similar water chemistry, pressure and age. Taxonomical results showed differences in colonising communities between pipe materials, with several genera, including the bacteria Pseudomonas and the fungi Cladosporium, present in every sample. Diverse bacterial communities dominated compared to more homogeneous fungal, or mycobiome, community distribution. The analysis of bacterial/fungal networks based on relative abundance of operational taxonomic units (OTUs) indicated microbial communities from cast iron pipes were more stable than communities from the non-ferrous pipe materials. Novel analysis of functional traits between all samples were found to be mainly associated to mobile genetic elements that play roles in determining links between cells, including phages, prophages, transposable elements, and plasmids. The use of functional traits can be considered for development in future surveillance methods, capable of delivering network condition information beyond that of limited conventional faecal indicator tests, that will help protect water quality and public health.}, }
@article {pmid32019442, year = {2020}, author = {Liddell, C and Morgan, ER and Bull, K and Ioannou, CC}, title = {Response to resources and parasites depends on health status in extensively grazed sheep.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1920}, pages = {20192905}, pmid = {32019442}, issn = {1471-2954}, support = {BB/S014748/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Ecology ; Ecosystem ; Geographic Information Systems ; Health Status ; *Host-Parasite Interactions ; Parasites/*physiology ; Sheep/*parasitology ; }, abstract = {A fundamental question in animal ecology is how an individual's internal state and the external environment together shape species distributions across habitats. The increasing availability of biologgers is driving a revolution in answering this question in a wide range of species. In this study, the position of sheep (Ovis aries) from Global Positioning System collars was integrated with remote sensing data, field sampling of parasite distributions, and parasite load and health measures for each tagged individual. This allowed inter-individual variation in habitat use to be examined. Once controlling for a positive relationship between vegetation productivity and tick abundance, healthier individuals spent more of their time at sites with higher vegetation productivity, while less healthy individuals showed a stronger (negative) response to tick abundance. These trends are likely to represent a trade-off in foraging decisions that vary between individuals based on their health status. Given the rarity of studies that explore how animal distributions are affected by health and external factors, we demonstrate the value of integrating biologging technology with remote sensing data, traditional ecological sampling and individual measures of animal health. Our study, using extensively grazed sheep as a model system, opens new possibilities to study free-living grazing systems.}, }
@article {pmid32010196, year = {2019}, author = {Mascarenhas, R and Ruziska, FM and Moreira, EF and Campos, AB and Loiola, M and Reis, K and Trindade-Silva, AE and Barbosa, FAS and Salles, L and Menezes, R and Veiga, R and Coutinho, FH and Dutilh, BE and Guimarães, PR and Assis, APA and Ara, A and Miranda, JGV and Andrade, RFS and Vilela, B and Meirelles, PM}, title = {Integrating Computational Methods to Investigate the Macroecology of Microbiomes.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1344}, pmid = {32010196}, issn = {1664-8021}, abstract = {Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as &quot;everything is everywhere, but the environment selects&quot;) as well as applied ecological problems, such as those posed by human induced global environmental changes.}, }
@article {pmid31972020, year = {2020}, author = {Pippel, M and Jebb, D and Patzold, F and Winkler, S and Vogel, H and Myers, G and Hiller, M and Hundsdoerfer, AK}, title = {A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).}, journal = {GigaScience}, volume = {9}, number = {1}, pages = {}, pmid = {31972020}, issn = {2047-217X}, mesh = {Animals ; Chiroptera/parasitology ; Computational Biology/methods ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Moths/*genetics ; }, abstract = {BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation.<br><br>RESULTS: Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations.<br><br>CONCLUSIONS: Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.}, }
@article {pmid31940344, year = {2020}, author = {Bahlai, CA and Zipkin, EF}, title = {The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations.}, journal = {PLoS computational biology}, volume = {16}, number = {1}, pages = {e1007542}, pmid = {31940344}, issn = {1553-7358}, mesh = {*Algorithms ; Animals ; Butterflies/physiology ; Coleoptera/physiology ; Computational Biology/*methods ; Ecosystem ; Information Theory ; *Models, Biological ; Models, Statistical ; *Population Dynamics ; }, abstract = {Environmental factors interact with internal rules of population regulation, sometimes perturbing systems to alternate dynamics though changes in parameter values. Yet, pinpointing when such changes occur in naturally fluctuating populations is difficult. An algorithmic approach that can identify the timing and magnitude of parameter shifts would facilitate understanding of abrupt ecological transitions with potential to inform conservation and management of species. The &quot;Dynamic Shift Detector&quot; is an algorithm to identify changes in parameter values governing temporal fluctuations in populations with nonlinear dynamics. The algorithm examines population time series data for the presence, location, and magnitude of parameter shifts. It uses an iterative approach to fitting subsets of time series data, then ranks the fit of break point combinations using model selection, assigning a relative weight to each break. We examined the performance of the Dynamic Shift Detector with simulations and two case studies. Under low environmental/sampling noise, the break point sets selected by the Dynamic Shift Detector contained the true simulated breaks with 70-100% accuracy. The weighting tool generally assigned breaks intentionally placed in simulated data (i.e., true breaks) with weights averaging >0.8 and those due to sampling error (i.e., erroneous breaks) with weights averaging <0.2. In our case study examining an invasion process, the algorithm identified shifts in population cycling associated with variations in resource availability. The shifts identified for the conservation case study highlight a decline process that generally coincided with changing management practices affecting the availability of hostplant resources. When interpreted in the context of species biology, the Dynamic Shift Detector algorithm can aid management decisions and identify critical time periods related to species' dynamics. In an era of rapid global change, such tools can provide key insights into the conditions under which population parameters, and their corresponding dynamics, can shift.}, }
@article {pmid31938524, year = {2019}, author = {Llanos-Garrido, A and Pérez-Tris, J and Díaz, JA}, title = {The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome-wide dynamics of local adaptation in a lizard.}, journal = {Ecology and evolution}, volume = {9}, number = {24}, pages = {14356-14367}, pmid = {31938524}, issn = {2045-7758}, abstract = {Local adaptation is a dynamic process by which different allele combinations are selected in different populations at different times, and whose genetic signature can be inferred by genome-wide outlier analyses. We combined gene flow estimates with two methods of outlier detection, one of them independent of population coancestry (CIOA) and the other one not (ROA), to identify genetic variants favored when ecology promotes phenotypic convergence. We analyzed genotyping-by-sequencing data from five populations of a lizard distributed over an environmentally heterogeneous range that has been changing since the split of eastern and western lineages ca. 3 mya. Overall, western lizards inhabit forest habitat and are unstriped, whereas eastern ones inhabit shrublands and are striped. However, one population (Lerma) has unstriped phenotype despite its eastern ancestry. The analysis of 73,291 SNPs confirmed the east-west division and identified nonoverlapping sets of outliers (12 identified by ROA and 9 by CIOA). ROA revealed ancestral adaptive variation in the uncovered outliers that were subject to divergent selection and differently fixed for eastern and western populations at the extremes of the environmental gradient. Interestingly, such variation was maintained in Lerma, where we found high levels of heterozygosity for ROA outliers, whereas CIOA uncovered innovative variants that were selected only there. Overall, it seems that both the maintenance of ancestral variation and asymmetric migration have counterbalanced adaptive lineage splitting in our model species. This scenario, which is likely promoted by a changing and heterogeneous environment, could hamper ecological speciation of locally adapted populations despite strong genetic structure between lineages.}, }
@article {pmid31937838, year = {2020}, author = {Li, W and Ma, ZS}, title = {FBA Ecological Guild: Trio of Firmicutes-Bacteroidetes Alliance against Actinobacteria in Human Oral Microbiome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {287}, pmid = {31937838}, issn = {2045-2322}, mesh = {Actinobacteria/genetics/growth &amp; development/*isolation &amp; purification ; Bacteroidetes/genetics/growth &amp; development/*isolation &amp; purification ; Databases, Factual ; Firmicutes/genetics/growth &amp; development/*isolation &amp; purification ; Humans ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In a pioneering study, Zaura et al. (2009) found that majority of oral microbes fall within the five phyla including, Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Subsequent studies further identified a set of microbes that were commonly shared among unrelated individuals (i.e., core). However, these existing studies may have not been designed to investigate the interactions among various core species. Here by harnessing the power of ecological network analysis, we identified some important ecological guilds in the form of network clusters. In particular, we found that the strongest cluster is an alliance between Firmicutes and Bacteroidetes against Actinobacteria (FBA-guild). Within the guild, we further identified two sub-guilds, the Actinobacteria-dominant sub-guild (ASG) and Firmicutes-dominant allied with Bacteroidetes sub-guild (FBSG). Furthermore, we identified so-termed guard nodes in both sub-guilds, and their role may be to inhibit the peer sub-guild given they held competitive interactions only with the outside nodes only but held cooperative interactions only with the internal nodes, which we termed civilian nodes given that they only held cooperative interactions. We postulated that FBA-guild might be to do with protection of oral health against some opportunistic pathogens from Corynebacterium and Actinomyces, the two major genera of Actinobacteria (target of FB alliance).}, }
@article {pmid31937263, year = {2020}, author = {Herndon, N and Shelton, J and Gerischer, L and Ioannidis, P and Ninova, M and Dönitz, J and Waterhouse, RM and Liang, C and Damm, C and Siemanowski, J and Kitzmann, P and Ulrich, J and Dippel, S and Oberhofer, G and Hu, Y and Schwirz, J and Schacht, M and Lehmann, S and Montino, A and Posnien, N and Gurska, D and Horn, T and Seibert, J and Vargas Jentzsch, IM and Panfilio, KA and Li, J and Wimmer, EA and Stappert, D and Roth, S and Schröder, R and Park, Y and Schoppmeier, M and Chung, HR and Klingler, M and Kittelmann, S and Friedrich, M and Chen, R and Altincicek, B and Vilcinskas, A and Zdobnov, E and Griffiths-Jones, S and Ronshaugen, M and Stanke, M and Brown, SJ and Bucher, G}, title = {Enhanced genome assembly and a new official gene set for Tribolium castaneum.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {47}, pmid = {31937263}, issn = {1471-2164}, support = {SFB680//Deutsche Forschungsgemeinschaft/ ; P20 GM103418/GM/NIGMS NIH HHS/United States ; PA2044/1//Deutsche Forschungsgemeinschaft/ ; KL656/7//Deutsche Forschungsgemeinschaft/ ; BU1443/6//Deutsche Forschungsgemeinschaft/ ; WI1797/5//Deutsche Forschungsgemeinschaft/ ; FOR1234//Deutsche Forschungsgemeinschaft/ ; STA1009/10//Deutsche Forschungsgemeinschaft/ ; BU1443/7//Deutsche Forschungsgemeinschaft/ ; PP00P3_170664//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)/ ; Department Herbert Jäckle//Max-Planck-Gesellschaft/ ; SFB 680 / A12//Deutsche Forschungsgemeinschaft/ ; Scho1058/4//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Binding Sites ; Computational Biology/methods ; *Genes, Insect ; *Genome, Insect ; *Genomics/methods ; MicroRNAs/genetics ; Molecular Sequence Annotation ; Phylogeny ; RNA Interference ; Reproducibility of Results ; Tribolium/*genetics ; }, abstract = {BACKGROUND: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality.<br><br>RESULTS: Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI.<br><br>CONCLUSIONS: The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.}, }
@article {pmid31914166, year = {2020}, author = {Joshi, J and Brännström, Å and Dieckmann, U}, title = {Emergence of social inequality in the spatial harvesting of renewable public goods.}, journal = {PLoS computational biology}, volume = {16}, number = {1}, pages = {e1007483}, pmid = {31914166}, issn = {1553-7358}, mesh = {*Biobehavioral Sciences ; Computational Biology ; *Consumer Behavior ; *Ecology ; Humans ; *Socioeconomic Factors ; }, abstract = {Spatially extended ecological public goods, such as forests, grasslands, and fish stocks, are at risk of being overexploited by selfish consumers-a phenomenon widely recognized as the 'tragedy of the commons.' The interplay of spatial and ecological dimensions introduces new features absent in non-spatial ecological contexts, such as consumer mobility, local information availability, and strategy evolution through social learning in neighborhoods. It is unclear how these features interact to influence the harvesting and dispersal strategies of consumers. To answer these questions, we develop and analyze an individual-based, spatially structured, eco-evolutionary model with explicit resource dynamics. We report the following findings. (1) When harvesting efficiency is low, consumers evolve a sedentary consumption strategy, through which the resource is harvested sustainably, but with harvesting rates far below their maximum sustainable value. (2) As harvesting efficiency increases, consumers adopt a mobile 'consume-and-disperse' strategy, which is sustainable, equitable, and gives maximum sustainable yield. (3) A further increase in harvesting efficiency leads to large-scale overexploitation. (4) If costs of dispersal are significant, increased harvesting efficiency also leads to social inequality between frugal sedentary consumers and overexploitative mobile consumers. Whereas overexploitation can occur without social inequality, social inequality always leads to overexploitation. Thus, we identify four conditions that-while being characteristic of technological progress in modern societies-risk social inequality and overexploitation: high harvesting efficiency, moderately low costs of dispersal, high consumer density, and the tendency of consumers to adopt new strategies rapidly. We also show how access to global information-another feature widespread in modern societies-helps mitigate these risks.}, }
@article {pmid31911493, year = {2020}, author = {Saw, JHW and Nunoura, T and Hirai, M and Takaki, Y and Parsons, R and Michelsen, M and Longnecker, K and Kujawinski, EB and Stepanauskas, R and Landry, Z and Carlson, CA and Giovannoni, SJ}, title = {Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31911493}, issn = {2150-7511}, mesh = {Biodiversity ; Chloroflexi/*enzymology/*genetics ; Computational Biology/methods ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Metabolomics/methods ; *Metagenome ; *Metagenomics ; *Multigene Family ; Phylogeny ; Phylogeography ; }, abstract = {It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns.IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.}, }
@article {pmid31907310, year = {2020}, author = {Le Provost, G and Badenhausser, I and Le Bagousse-Pinguet, Y and Clough, Y and Henckel, L and Violle, C and Bretagnolle, V and Roncoroni, M and Manning, P and Gross, N}, title = {Land-use history impacts functional diversity across multiple trophic groups.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {3}, pages = {1573-1579}, pmid = {31907310}, issn = {1091-6490}, mesh = {Agriculture ; Animals ; *Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecology ; *Ecosystem ; *Grassland ; Herbivory/classification ; Invertebrates/classification ; Plants/classification ; Population Density ; }, abstract = {Land-use change is a major driver of biodiversity loss worldwide. Although biodiversity often shows a delayed response to land-use change, previous studies have typically focused on a narrow range of current landscape factors and have largely ignored the role of land-use history in shaping plant and animal communities and their functional characteristics. Here, we used a unique database of 220,000 land-use records to investigate how 20-y of land-use changes have affected functional diversity across multiple trophic groups (primary producers, mutualists, herbivores, invertebrate predators, and vertebrate predators) in 75 grassland fields with a broad range of land-use histories. The effects of land-use history on multitrophic trait diversity were as strong as other drivers known to impact biodiversity, e.g., grassland management and current landscape composition. The diversity of animal mobility and resource-acquisition traits was lower in landscapes where much of the land had been historically converted from grassland to crop. In contrast, functional biodiversity was higher in landscapes containing old permanent grasslands, most likely because they offer a stable and high-quality habitat refuge for species with low mobility and specialized feeding niches. Our study shows that grassland-to-crop conversion has long-lasting impacts on the functional biodiversity of agricultural ecosystems. Accordingly, land-use legacy effects must be considered in conservation programs aiming to protect agricultural biodiversity. In particular, the retention of permanent grassland sanctuaries within intensive landscapes may offset ecological debts.}, }
@article {pmid31905256, year = {2020}, author = {vonHoldt, BM and DeCandia, AL and Heppenheimer, E and Janowitz-Koch, I and Shi, R and Zhou, H and German, CA and Brzeski, KE and Cassidy, KA and Stahler, DR and Sinsheimer, JS}, title = {Heritability of interpack aggression in a wild pedigreed population of North American grey wolves.}, journal = {Molecular ecology}, volume = {29}, number = {10}, pages = {1764-1775}, pmid = {31905256}, issn = {1365-294X}, support = {R01 HG009120/HG/NHGRI NIH HHS/United States ; R01 GM053275/GM/NIGMS NIH HHS/United States ; }, abstract = {Aggression is a quantitative trait deeply entwined with individual fitness. Mapping the genomic architecture underlying such traits is complicated by complex inheritance patterns, social structure, pedigree information and gene pleiotropy. Here, we leveraged the pedigree of a reintroduced population of grey wolves (Canis lupus) in Yellowstone National Park, Wyoming, USA, to examine the heritability of and the genetic variation associated with aggression. Since their reintroduction, many ecological and behavioural aspects have been documented, providing unmatched records of aggressive behaviour across multiple generations of a wild population of wolves. Using a linear mixed model, a robust genetic relationship matrix, 12,288 single nucleotide polymorphisms (SNPs) and 111 wolves, we estimated the SNP-based heritability of aggression to be 37% and an additional 14% of the phenotypic variation explained by shared environmental exposures. We identified 598 SNP genotypes from 425 grey wolves to resolve a consensus pedigree that was included in a heritability analysis of 141 individuals with SNP genotype, metadata and aggression data. The pedigree-based heritability estimate for aggression is 14%, and an additional 16% of the phenotypic variation was explained by shared environmental exposures. We find strong effects of breeding status and relative pack size on aggression. Through an integrative approach, these results provide a framework for understanding the genetic architecture of a complex trait that influences individual fitness, with linkages to reproduction, in a social carnivore. Along with a few other studies, we show here the incredible utility of a pedigreed natural population for dissecting a complex, fitness-related behavioural trait.}, }
@article {pmid31904811, year = {2020}, author = {Tang, B and Zhang, D and Li, H and Jiang, S and Zhang, H and Xuan, F and Ge, B and Wang, Z and Liu, Y and Sha, Z and Cheng, Y and Jiang, W and Jiang, H and Wang, Z and Wang, K and Li, C and Sun, Y and She, S and Qiu, Q and Wang, W and Li, X and Li, Y and Liu, Q and Ren, Y}, title = {Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus).}, journal = {GigaScience}, volume = {9}, number = {1}, pages = {}, pmid = {31904811}, issn = {2047-217X}, mesh = {Animals ; Brachyura/genetics ; *Chromosomes ; Computational Biology/methods ; *Evolution, Molecular ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Transcriptome ; }, abstract = {BACKGROUND: The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking.<br><br>FINDINGS: Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology.<br><br>CONCLUSIONS: We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.}, }
@article {pmid31891233, year = {2020}, author = {Kattge, J and Bönisch, G and Díaz, S and Lavorel, S and Prentice, IC and Leadley, P and Tautenhahn, S and Werner, GDA and Aakala, T and Abedi, M and Acosta, ATR and Adamidis, GC and Adamson, K and Aiba, M and Albert, CH and Alcántara, JM and Alcázar C, C and Aleixo, I and Ali, H and Amiaud, B and Ammer, C and Amoroso, MM and Anand, M and Anderson, C and Anten, N and Antos, J and Apgaua, DMG and Ashman, TL and Asmara, DH and Asner, GP and Aspinwall, M and Atkin, O and Aubin, I and Baastrup-Spohr, L and Bahalkeh, K and Bahn, M and Baker, T and Baker, WJ and Bakker, JP and Baldocchi, D and Baltzer, J and Banerjee, A and Baranger, A and Barlow, J and Barneche, DR and Baruch, Z and Bastianelli, D and Battles, J and Bauerle, W and Bauters, M and Bazzato, E and Beckmann, M and Beeckman, H and Beierkuhnlein, C and Bekker, R and Belfry, G and Belluau, M and Beloiu, M and Benavides, R and Benomar, L and Berdugo-Lattke, ML and Berenguer, E and Bergamin, R and Bergmann, J and Bergmann Carlucci, M and Berner, L and Bernhardt-Römermann, M and Bigler, C and Bjorkman, AD and Blackman, C and Blanco, C and Blonder, B and Blumenthal, D and Bocanegra-González, KT and Boeckx, P and Bohlman, S and Böhning-Gaese, K and Boisvert-Marsh, L and Bond, W and Bond-Lamberty, B and Boom, A and Boonman, CCF and Bordin, K and Boughton, EH and Boukili, V and Bowman, DMJS and Bravo, S and Brendel, MR and Broadley, MR and Brown, KA and Bruelheide, H and Brumnich, F and Bruun, HH and Bruy, D and Buchanan, SW and Bucher, SF and Buchmann, N and Buitenwerf, R and Bunker, DE and Bürger, J and Burrascano, S and Burslem, DFRP and Butterfield, BJ and Byun, C and Marques, M and Scalon, MC and Caccianiga, M and Cadotte, M and Cailleret, M and Camac, J and Camarero, JJ and Campany, C and Campetella, G and Campos, JA and Cano-Arboleda, L and Canullo, R and Carbognani, M and Carvalho, F and Casanoves, F and Castagneyrol, B and Catford, JA and Cavender-Bares, J and Cerabolini, BEL and Cervellini, M and Chacón-Madrigal, E and Chapin, K and Chapin, FS and Chelli, S and Chen, SC and Chen, A and Cherubini, P and Chianucci, F and Choat, B and Chung, KS and Chytrý, M and Ciccarelli, D and Coll, L and Collins, CG and Conti, L and Coomes, D and Cornelissen, JHC and Cornwell, WK and Corona, P and Coyea, M and Craine, J and Craven, D and Cromsigt, JPGM and Csecserits, A and Cufar, K and Cuntz, M and da Silva, AC and Dahlin, KM and Dainese, M and Dalke, I and Dalle Fratte, M and Dang-Le, AT and Danihelka, J and Dannoura, M and Dawson, S and de Beer, AJ and De Frutos, A and De Long, JR and Dechant, B and Delagrange, S and Delpierre, N and Derroire, G and Dias, AS and Diaz-Toribio, MH and Dimitrakopoulos, PG and Dobrowolski, M and Doktor, D and Dřevojan, P and Dong, N and Dransfield, J and Dressler, S and Duarte, L and Ducouret, E and Dullinger, S and Durka, W and Duursma, R and Dymova, O and E-Vojtkó, A and Eckstein, RL and Ejtehadi, H and Elser, J and Emilio, T and Engemann, K and Erfanian, MB and Erfmeier, A and Esquivel-Muelbert, A and Esser, G and Estiarte, M and Domingues, TF and Fagan, WF and Fagúndez, J and Falster, DS and Fan, Y and Fang, J and Farris, E and Fazlioglu, F and Feng, Y and Fernandez-Mendez, F and Ferrara, C and Ferreira, J and Fidelis, A and Finegan, B and Firn, J and Flowers, TJ and Flynn, DFB and Fontana, V and Forey, E and Forgiarini, C and François, L and Frangipani, M and Frank, D and Frenette-Dussault, C and Freschet, GT and Fry, EL and Fyllas, NM and Mazzochini, GG and Gachet, S and Gallagher, R and Ganade, G and Ganga, F and García-Palacios, P and Gargaglione, V and Garnier, E and Garrido, JL and de Gasper, AL and Gea-Izquierdo, G and Gibson, D and Gillison, AN and Giroldo, A and Glasenhardt, MC and Gleason, S and Gliesch, M and Goldberg, E and Göldel, B and Gonzalez-Akre, E and Gonzalez-Andujar, JL and González-Melo, A and González-Robles, A and Graae, BJ and Granda, E and Graves, S and Green, WA and Gregor, T and Gross, N and Guerin, GR and Günther, A and Gutiérrez, AG and Haddock, L and Haines, A and Hall, J and Hambuckers, A and Han, W and Harrison, SP and Hattingh, W and Hawes, JE and He, T and He, P and Heberling, JM and Helm, A and Hempel, S and Hentschel, J and Hérault, B and Hereş, AM and Herz, K and Heuertz, M and Hickler, T and Hietz, P and Higuchi, P and Hipp, AL and Hirons, A and Hock, M and Hogan, JA and Holl, K and Honnay, O and Hornstein, D and Hou, E and Hough-Snee, N and Hovstad, KA and Ichie, T and Igić, B and Illa, E and Isaac, M and Ishihara, M and Ivanov, L and Ivanova, L and Iversen, CM and Izquierdo, J and Jackson, RB and Jackson, B and Jactel, H and Jagodzinski, AM and Jandt, U and Jansen, S and Jenkins, T and Jentsch, A and Jespersen, JRP and Jiang, GF and Johansen, JL and Johnson, D and Jokela, EJ and Joly, CA and Jordan, GJ and Joseph, GS and Junaedi, D and Junker, RR and Justes, E and Kabzems, R and Kane, J and Kaplan, Z and Kattenborn, T and Kavelenova, L and Kearsley, E and Kempel, A and Kenzo, T and Kerkhoff, A and Khalil, MI and Kinlock, NL and Kissling, WD and Kitajima, K and Kitzberger, T and Kjøller, R and Klein, T and Kleyer, M and Klimešová, J and Klipel, J and Kloeppel, B and Klotz, S and Knops, JMH and Kohyama, T and Koike, F and Kollmann, J and Komac, B and Komatsu, K and König, C and Kraft, NJB and Kramer, K and Kreft, H and Kühn, I and Kumarathunge, D and Kuppler, J and Kurokawa, H and Kurosawa, Y and Kuyah, S and Laclau, JP and Lafleur, B and Lallai, E and Lamb, E and Lamprecht, A and Larkin, DJ and Laughlin, D and Le Bagousse-Pinguet, Y and le Maire, G and le Roux, PC and le Roux, E and Lee, T and Lens, F and Lewis, SL and Lhotsky, B and Li, Y and Li, X and Lichstein, JW and Liebergesell, M and Lim, JY and Lin, YS and Linares, JC and Liu, C and Liu, D and Liu, U and Livingstone, S and Llusià, J and Lohbeck, M and López-García, Á and Lopez-Gonzalez, G and Lososová, Z and Louault, F and Lukács, BA and Lukeš, P and Luo, Y and Lussu, M and Ma, S and Maciel Rabelo Pereira, C and Mack, M and Maire, V and Mäkelä, A and Mäkinen, H and Malhado, ACM and Mallik, A and Manning, P and Manzoni, S and Marchetti, Z and Marchino, L and Marcilio-Silva, V and Marcon, E and Marignani, M and Markesteijn, L and Martin, A and Martínez-Garza, C and Martínez-Vilalta, J and Mašková, T and Mason, K and Mason, N and Massad, TJ and Masse, J and Mayrose, I and McCarthy, J and McCormack, ML and McCulloh, K and McFadden, IR and McGill, BJ and McPartland, MY and Medeiros, JS and Medlyn, B and Meerts, P and Mehrabi, Z and Meir, P and Melo, FPL and Mencuccini, M and Meredieu, C and Messier, J and Mészáros, I and Metsaranta, J and Michaletz, ST and Michelaki, C and Migalina, S and Milla, R and Miller, JED and Minden, V and Ming, R and Mokany, K and Moles, AT and Molnár, A and Molofsky, J and Molz, M and Montgomery, RA and Monty, A and Moravcová, L and Moreno-Martínez, A and Moretti, M and Mori, AS and Mori, S and Morris, D and Morrison, J and Mucina, L and Mueller, S and Muir, CD and Müller, SC and Munoz, F and Myers-Smith, IH and Myster, RW and Nagano, M and Naidu, S and Narayanan, A and Natesan, B and Negoita, L and Nelson, AS and Neuschulz, EL and Ni, J and Niedrist, G and Nieto, J and Niinemets, Ü and Nolan, R and Nottebrock, H and Nouvellon, Y and Novakovskiy, A and ,  and Nystuen, KO and O'Grady, A and O'Hara, K and O'Reilly-Nugent, A and Oakley, S and Oberhuber, W and Ohtsuka, T and Oliveira, R and Öllerer, K and Olson, ME and Onipchenko, V and Onoda, Y and Onstein, RE and Ordonez, JC and Osada, N and Ostonen, I and Ottaviani, G and Otto, S and Overbeck, GE and Ozinga, WA and Pahl, AT and Paine, CET and Pakeman, RJ and Papageorgiou, AC and Parfionova, E and Pärtel, M and Patacca, M and Paula, S and Paule, J and Pauli, H and Pausas, JG and Peco, B and Penuelas, J and Perea, A and Peri, PL and Petisco-Souza, AC and Petraglia, A and Petritan, AM and Phillips, OL and Pierce, S and Pillar, VD and Pisek, J and Pomogaybin, A and Poorter, H and Portsmuth, A and Poschlod, P and Potvin, C and Pounds, D and Powell, AS and Power, SA and Prinzing, A and Puglielli, G and Pyšek, P and Raevel, V and Rammig, A and Ransijn, J and Ray, CA and Reich, PB and Reichstein, M and Reid, DEB and Réjou-Méchain, M and de Dios, VR and Ribeiro, S and Richardson, S and Riibak, K and Rillig, MC and Riviera, F and Robert, EMR and Roberts, S and Robroek, B and Roddy, A and Rodrigues, AV and Rogers, A and Rollinson, E and Rolo, V and Römermann, C and Ronzhina, D and Roscher, C and Rosell, JA and Rosenfield, MF and Rossi, C and Roy, DB and Royer-Tardif, S and Rüger, N and Ruiz-Peinado, R and Rumpf, SB and Rusch, GM and Ryo, M and Sack, L and Saldaña, A and Salgado-Negret, B and Salguero-Gomez, R and Santa-Regina, I and Santacruz-García, AC and Santos, J and Sardans, J and Schamp, B and Scherer-Lorenzen, M and Schleuning, M and Schmid, B and Schmidt, M and Schmitt, S and Schneider, JV and Schowanek, SD and Schrader, J and Schrodt, F and Schuldt, B and Schurr, F and Selaya Garvizu, G and Semchenko, M and Seymour, C and Sfair, JC and Sharpe, JM and Sheppard, CS and Sheremetiev, S and Shiodera, S and Shipley, B and Shovon, TA and Siebenkäs, A and Sierra, C and Silva, V and Silva, M and Sitzia, T and Sjöman, H and Slot, M and Smith, NG and Sodhi, D and Soltis, P and Soltis, D and Somers, B and Sonnier, G and Sørensen, MV and Sosinski, EE and Soudzilovskaia, NA and Souza, AF and Spasojevic, M and Sperandii, MG and Stan, AB and Stegen, J and Steinbauer, K and Stephan, JG and Sterck, F and Stojanovic, DB and Strydom, T and Suarez, ML and Svenning, JC and Svitková, I and Svitok, M and Svoboda, M and Swaine, E and Swenson, N and Tabarelli, M and Takagi, K and Tappeiner, U and Tarifa, R and Tauugourdeau, S and Tavsanoglu, C and Te Beest, M and Tedersoo, L and Thiffault, N and Thom, D and Thomas, E and Thompson, K and Thornton, PE and Thuiller, W and Tichý, L and Tissue, D and Tjoelker, MG and Tng, DYP and Tobias, J and Török, P and Tarin, T and Torres-Ruiz, JM and Tóthmérész, B and Treurnicht, M and Trivellone, V and Trolliet, F and Trotsiuk, V and Tsakalos, JL and Tsiripidis, I and Tysklind, N and Umehara, T and Usoltsev, V and Vadeboncoeur, M and Vaezi, J and Valladares, F and Vamosi, J and van Bodegom, PM and van Breugel, M and Van Cleemput, E and van de Weg, M and van der Merwe, S and van der Plas, F and van der Sande, MT and van Kleunen, M and Van Meerbeek, K and Vanderwel, M and Vanselow, KA and Vårhammar, A and Varone, L and Vasquez Valderrama, MY and Vassilev, K and Vellend, M and Veneklaas, EJ and Verbeeck, H and Verheyen, K and Vibrans, A and Vieira, I and Villacís, J and Violle, C and Vivek, P and Wagner, K and Waldram, M and Waldron, A and Walker, AP and Waller, M and Walther, G and Wang, H and Wang, F and Wang, W and Watkins, H and Watkins, J and Weber, U and Weedon, JT and Wei, L and Weigelt, P and Weiher, E and Wells, AW and Wellstein, C and Wenk, E and Westoby, M and Westwood, A and White, PJ and Whitten, M and Williams, M and Winkler, DE and Winter, K and Womack, C and Wright, IJ and Wright, SJ and Wright, J and Pinho, BX and Ximenes, F and Yamada, T and Yamaji, K and Yanai, R and Yankov, N and Yguel, B and Zanini, KJ and Zanne, AE and Zelený, D and Zhao, YP and Zheng, J and Zheng, J and Ziemińska, K and Zirbel, CR and Zizka, G and Zo-Bi, IC and Zotz, G and Wirth, C}, title = {TRY plant trait database - enhanced coverage and open access.}, journal = {Global change biology}, volume = {26}, number = {1}, pages = {119-188}, doi = {10.1111/gcb.14904}, pmid = {31891233}, issn = {1365-2486}, support = {//International Geosphere-Biosphere Programme (IGBP)/International ; //GIS 'Climat, Environnement et Société' France/International ; //German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig/International ; //AXA Research Fund/International ; //Max Planck Society/International ; //UK Natural Environment Research Council (NERC)/International ; //French Foundation for Biodiversity Research (FRB)/International ; //Max Planck Institute for Biogeochemistry/International ; //International Programme of Biodiversity Science (DIVERSITAS)/International ; P 29142/FWF_/Austrian Science Fund FWF/Austria ; //Future Earth/International ; }, mesh = {*Access to Information ; Biodiversity ; Ecology ; *Ecosystem ; Plants ; }, abstract = {Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.}, }
@article {pmid31887177, year = {2019}, author = {Franckowiak, GA and Perdicas, M and Smith, GA}, title = {Spatial ecology of coyotes in the urbanizing landscape of the Cuyahoga Valley, Ohio.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0227028}, pmid = {31887177}, issn = {1932-6203}, mesh = {Age Factors ; Animal Migration/*physiology ; Animals ; Coyotes/*physiology ; Female ; Geographic Information Systems ; Homing Behavior/*physiology ; Male ; Ohio ; Photoperiod ; Remote Sensing Technology ; Seasons ; Sex Factors ; *Spatio-Temporal Analysis ; *Urbanization ; }, abstract = {Urban landscapes can present ecological challenges for wildlife species, yet many species survive, and even thrive, near dense human populations. Coyotes (Canis latrans), for example, have expanded their geographic range across North America and, as a result of their adaptability and behavioral flexibility, are now a common occupant of many urban areas in the United States. We investigated the spatial ecology of 27 coyotes fitted with Global Positioning System (GPS) telemetry collars radio-collared in the Cuyahoga Valley, Ohio. Our objectives were to quantify coyote space use, evaluate resource selection, and investigate coyote movement and activity patterns. To measure space use, we estimated home range (95%) and core area (50%) size of coyotes using the adaptive local convex hull (a-LoCoH) method. We found the mean (± SE) home range size of resident coyotes (4.7 ± 1.8 km2) was significantly smaller than ranges of transient coyotes (67.7 ± 89.6 km2). Similarly, mean (± SE) core area size of resident coyotes (0.9 ± 0.6 km2) was significantly smaller than core areas of transient coyotes (11.9 ± 16.7 km2). Home range and core area size of both resident and transient coyotes did not vary by sex, age, or season. For all coyotes, use of natural land cover was significantly greater than use of altered and developed land. When coyotes were using altered and developed land, GPS fixes were most common at night. Coyote movement patterns differed with respect to status, time period, and season; peaking during nighttime hours. A better understanding of coyote space use and movement within anthropogenic landscapes aids management of people, parks, and wildlife by providing the data necessary for research-based management decisions.}, }
@article {pmid31882957, year = {2019}, author = {Jiguet, F and Burgess, M and Thorup, K and Conway, G and Arroyo Matos, JL and Barber, L and Black, J and Burton, N and Castelló, J and Clewley, G and Copete, JL and Czajkowski, MA and Dale, S and Davis, T and Dombrovski, V and Drew, M and Elts, J and Gilson, V and Grzegorczyk, E and Henderson, I and Holdsworth, M and Husbands, R and Lorrilliere, R and Marja, R and Minkevicius, S and Moussy, C and Olsson, P and Onrubia, A and Pérez, M and Piacentini, J and Piha, M and Pons, JM and Procházka, P and Raković, M and Robins, H and Seimola, T and Selstam, G and Skierczyński, M and Sondell, J and Thibault, JC and Tøttrup, AP and Walker, J and Hewson, C}, title = {Desert crossing strategies of migrant songbirds vary between and within species.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {20248}, pmid = {31882957}, issn = {2045-2322}, mesh = {Altitude ; Animal Migration/*physiology ; Animals ; Circadian Rhythm/physiology ; *Desert Climate ; *Environment ; Flight, Animal/*physiology ; Geographic Information Systems ; Light ; Seasons ; Songbirds/classification/*physiology ; Species Specificity ; Temperature ; Time Factors ; }, abstract = {Each year, billions of songbirds cross large ecological barriers during their migration. Understanding how they perform this incredible task is crucial to predict how global change may threaten the safety of such journeys. Earlier studies based on radar suggested that most songbirds cross deserts in intermittent flights at high altitude, stopping in the desert during the day, while recent tracking with light loggers suggested diurnal prolongation of nocturnal flights and common non-stop flights for some species. We analyzed light intensity and temperature data obtained from geolocation loggers deployed on 130 individuals of ten migratory songbird species, and show that a large variety of strategies for crossing deserts exists between, but also sometimes within species. Diurnal stopover in the desert is a common strategy in autumn, while most species prolonged some nocturnal flights into the day. Non-stop flights over the desert occurred more frequently in spring than in autumn, and more frequently in foliage gleaners. Temperature recordings suggest that songbirds crossed deserts with flight bouts performed at various altitudes according to species and season, along a gradient ranging from low above ground in autumn to probably >2000 m above ground level, and possibly at higher altitude in spring. High-altitude flights are therefore not the general rule for crossing deserts in migrant songbirds. We conclude that a diversity of migration strategies exists for desert crossing among songbirds, with variations between but also within species.}, }
@article {pmid31869356, year = {2019}, author = {Buchner, D and Beermann, AJ and Laini, A and Rolauffs, P and Vitecek, S and Hering, D and Leese, F}, title = {Analysis of 13,312 benthic invertebrate samples from German streams reveals minor deviations in ecological status class between abundance and presence/absence data.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0226547}, pmid = {31869356}, issn = {1932-6203}, mesh = {Animals ; Aquatic Organisms/*classification/cytology/genetics/growth &amp; development ; *Biodiversity ; *Biological Evolution ; Databases, Factual/trends ; Ecosystem ; Environmental Monitoring ; Extinction, Biological ; Germany ; Invertebrates/*classification/cytology/genetics/growth &amp; development ; Population Dynamics/trends ; *Rivers ; }, abstract = {Benthic invertebrates are the most commonly used organisms used to assess ecological status as required by the EU Water Framework Directive (WFD). For WFD-compliant assessments, benthic invertebrate communities are sampled, identified and counted. Taxa × abundance matrices are used to calculate indices and the resulting scores are compared to reference values to determine the ecological status class. DNA-based tools, such as DNA metabarcoding, provide a new and precise method for species identification but cannot deliver robust abundance data. To evaluate the applicability of DNA-based tools to ecological status assessment, we evaluated whether the results derived from presence/absence data are comparable to those derived from abundance data. We analysed benthic invertebrate community data obtained from 13,312 WFD assessments of German streams. Broken down to 30 official stream types, we compared assessment results based on abundance and presence/absence data for the assessment modules &quot;organic pollution&quot; (i.e., the saprobic index) and &quot;general degradation&quot; (a multimetric index) as well as their underlying metrics. In 76.6% of cases, the ecological status class did not change after transforming abundance data to presence/absence data. In 12% of cases, the status class was reduced by one (e.g., from good to moderate), and in 11.2% of cases, the class increased by one. In only 0.2% of cases, the status shifted by two classes. Systematic stream type-specific deviations were found and differences between abundance and presence/absence data were most prominent for stream types where abundance information contributed directly to one or several metrics of the general degradation module. For a single stream type, these deviations led to a systematic shift in status from 'good' to 'moderate' (n = 201; with only n = 3 increasing). The systematic decrease in scores was observed, even when considering simulated confidence intervals for abundance data. Our analysis suggests that presence/absence data can yield similar assessment results to those for abundance-based data, despite type-specific deviations. For most metrics, it should be possible to intercalibrate the two data types without substantial efforts. Thus, benthic invertebrate taxon lists generated by standardised DNA-based methods should be further considered as a complementary approach.}, }
@article {pmid31847345, year = {2019}, author = {Tomazatos, A and Jansen, S and Pfister, S and Török, E and Maranda, I and Horváth, C and Keresztes, L and Spînu, M and Tannich, E and Jöst, H and Schmidt-Chanasit, J and Cadar, D and Lühken, R}, title = {Ecology of West Nile Virus in the Danube Delta, Romania: Phylogeography, Xenosurveillance and Mosquito Host-Feeding Patterns.}, journal = {Viruses}, volume = {11}, number = {12}, pages = {}, pmid = {31847345}, issn = {1999-4915}, mesh = {Animals ; Antibodies, Viral/immunology ; *Ecology ; Feeding Behavior ; Genome, Viral ; Humans ; Immunoglobulin G/immunology ; Mosquito Vectors/virology ; Phylogeny ; Phylogeography ; Public Health Surveillance ; RNA, Viral ; Romania/epidemiology ; West Nile Fever/*epidemiology/transmission/*virology ; West Nile virus/*classification/*genetics ; }, abstract = {The ecology of West Nile virus (WNV) in the Danube Delta Biosphere Reserve (Romania) was investigated by combining studies on the virus genetics, phylogeography, xenosurveillance and host-feeding patterns of mosquitoes. Between 2014 and 2016, 655,667 unfed and 3842 engorged mosquito females were collected from four sampling sites. Blood-fed mosquitoes were negative for WNV-RNA, but two pools of unfed Culex pipiens s.l./torrentium collected in 2014 were tested positive. Our results suggest that Romania experienced at least two separate WNV lineage 2 introductions: from Africa into Danube Delta and from Greece into south-eastern Romania in the 1990s and early 2000s, respectively. The genetic diversity of WNV in Romania is primarily shaped by in situ evolution. WNV-specific antibodies were detected for 19 blood-meals from dogs and horses, but not from birds or humans. The hosts of mosquitoes were dominated by non-human mammals (19 species), followed by human and birds (23 species). Thereby, the catholic host-feeding pattern of Culex pipiens s.l./torrentium with a relatively high proportion of birds indicates the species' importance as a potential bridge vector. The low virus prevalence in combination with WNV-specific antibodies indicate continuous, but low activity of WNV in the Danube Delta during the study period.}, }
@article {pmid31840098, year = {2019}, author = {Montesinos-Navarro, A and Díaz, G and Torres, P and Caravaca, F and Roldán, A}, title = {Phylogenetic rewiring in mycorrhizal-plant interaction networks increases community stability in naturally fragmented landscapes.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {452}, pmid = {31840098}, issn = {2399-3642}, mesh = {Computational Biology/methods ; Ecosystem ; Microbiota ; Mycorrhizae/*classification/*genetics ; *Phylogeny ; Plants/*classification/*genetics ; Reproducibility of Results ; *Symbiosis ; }, abstract = {Although ecological networks are usually considered a static representation of species' interactions, the interactions can change when the preferred partners are absent (rewiring). In mutualistic networks, rewiring with non-preferred partners can palliate extinction cascades, contributing to communities' stability. In spite of its significance, whether general patterns can shape the rewiring of ecological interactions remains poorly understood. Here, we show a phylogenetic constraint in the rewiring of mycorrhizal networks, so that rewired interactions (i.e., with non-preferred hosts) tend to involve close relatives of preferred hosts. Despite this constraint, rewiring increases the robustness of the fungal community to the simulated loss of their host species. We identify preferred and non-preferred hosts based on the probability that, when the two partners co-occur, they actually interact. Understanding general patterns in the rewiring of interactions can improve our predictions of community responses to interactions' loss, which influences how global changes will affect ecosystem stability.}, }
@article {pmid31834896, year = {2019}, author = {Mair, C and Nickbakhsh, S and Reeve, R and McMenamin, J and Reynolds, A and Gunson, RN and Murcia, PR and Matthews, L}, title = {Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models.}, journal = {PLoS computational biology}, volume = {15}, number = {12}, pages = {e1007492}, pmid = {31834896}, issn = {1553-7358}, support = {MR/S004815/1/MRC_/Medical Research Council/United Kingdom ; BB/L018926/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M003949/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L004070/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012679/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/R00241X/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; Computational Biology ; Computer Simulation ; Host Microbial Interactions ; *Host-Pathogen Interactions ; Humans ; *Models, Biological ; Multivariate Analysis ; Public Health Informatics ; Respiratory Tract Infections/epidemiology ; Spatio-Temporal Analysis ; Time Factors ; Virus Diseases/epidemiology ; }, abstract = {It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts, and there is growing interest in the health implications of such pathogen interactions. Although community ecology approaches have been used to identify pathogen interactions at the within-host scale, methodologies enabling robust identification of interactions from population-scale data such as that available from health authorities are lacking. To address this gap, we developed a statistical framework that jointly identifies interactions between multiple viruses from contemporaneous non-stationary infection time series. Our conceptual approach is derived from a Bayesian multivariate disease mapping framework. Importantly, our approach captures within- and between-year dependencies in infection risk while controlling for confounding factors such as seasonality, demographics and infection frequencies, allowing genuine pathogen interactions to be distinguished from simple correlations. We validated our framework using a broad range of synthetic data. We then applied it to diagnostic data available for five respiratory viruses co-circulating in a major urban population between 2005 and 2013: adenovirus, human coronavirus, human metapneumovirus, influenza B virus and respiratory syncytial virus. We found positive and negative covariances indicative of epidemiological interactions among specific virus pairs. This statistical framework enables a community ecology perspective to be applied to infectious disease epidemiology with important utility for public health planning and preparedness.}, }
@article {pmid31796765, year = {2019}, author = {Romanuk, TN and Binzer, A and Loeuille, N and Carscallen, WMA and Martinez, ND}, title = {Simulated evolution assembles more realistic food webs with more functionally similar species than invasion.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18242}, doi = {10.1038/s41598-019-54443-0}, pmid = {31796765}, issn = {2045-2322}, abstract = {While natural communities are assembled by both ecological and evolutionary processes, ecological assembly processes have been studied much more and are rarely compared with evolutionary assembly processes. We address these disparities here by comparing community food webs assembled by simulating introductions of species from regional pools of species and from speciation events. Compared to introductions of trophically dissimilar species assumed to be more typical of invasions, introducing species trophically similar to native species assumed to be more typical of sympatric or parapatric speciation events caused fewer extinctions and assembled more empirically realistic networks by introducing more persistent species with higher trophic generality, vulnerability, and enduring similarity to native species. Such events also increased niche overlap and the persistence of both native and introduced species. Contrary to much competition theory, these findings suggest that evolutionary and other processes that more tightly pack ecological niches contribute more to ecosystem structure and function than previously thought.}, }
@article {pmid31791702, year = {2020}, author = {Grebogi, C}, title = {Sudden regime shifts after apparent stasis: Comment on &quot;Long transients in ecology: Theory and applications&quot; by Andrew Morozov et al.}, journal = {Physics of life reviews}, volume = {32}, number = {}, pages = {41-43}, doi = {10.1016/j.plrev.2019.11.009}, pmid = {31791702}, issn = {1873-1457}, mesh = {Databases, Genetic ; *Ecology ; *Ecosystem ; Humans ; }, }
@article {pmid31758057, year = {2019}, author = {Sergio, F and Tavecchia, G and Tanferna, A and Blas, J and Blanco, G and Hiraldo, F}, title = {When and where mortality occurs throughout the annual cycle changes with age in a migratory bird: individual vs population implications.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17352}, doi = {10.1038/s41598-019-54026-z}, pmid = {31758057}, issn = {2045-2322}, mesh = {Africa, Western ; Age Factors ; Animal Migration/*physiology ; Animals ; Birds/*physiology ; Geographic Information Systems ; Geography ; Longevity/physiology ; Mauritania ; Morocco ; *Mortality ; Population Dynamics ; Raptors/physiology ; Reproduction/physiology ; *Seasons ; Spain ; Time Factors ; }, abstract = {The annual cycle of most animals is structured into discrete stages, such as breeding, migration and dispersal. While there is growing appreciation of the importance of different stages of an organism's annual cycle for its fitness and population dynamics, almost nothing is known about if and how such seasonal effects can change through a species lifespan. Here, we take advantage of the opportunity offered by a long-term satellite/GPS-tracking study and a reliable method of remote death-detection to show that certain stages of both the annual and life cycle of a migratory long-lived raptor, the Black kite Milvus migrans, may represent sensitive bottlenecks for survival. In particular, migratory journeys caused bursts of concentrated-mortality throughout life, but the relative importance of stage-specific survival changed with age. On the other hand, the balance between short-stages of high mortality and long-stages of low mortality made population-growth similarly dependent on all portions of the annual cycle. Our results illustrate how the population dynamics of migratory organisms can be inextricably linked to ecological pressures balanced over multiple stages of the annual cycle and thus multiple areas of the globe, suggesting the frequent need for challenging conservation strategies targeting all portions of a species year-round range.}, }
@article {pmid31736538, year = {2019}, author = {Podar, D and Macalik, K and Réti, KO and Martonos, I and Török, E and Carpa, R and Weindorf, DC and Csiszár, J and Székely, G}, title = {Morphological, physiological and biochemical aspects of salt tolerance of halophyte Petrosimonia triandra grown in natural habitat.}, journal = {Physiology and molecular biology of plants : an international journal of functional plant biology}, volume = {25}, number = {6}, pages = {1335-1347}, pmid = {31736538}, issn = {0971-5894}, abstract = {Salt tolerance mechanisms of halophyte Petrosimonia triandra, growing in its natural habitat in Cluj County, Romania, were investigated via biomass, growth parameters, water status, ion content, photosynthetic and antioxidative system efficiency, proline accumulation and lipid degradation. Two sampling sites with different soil electrical conductivities were selected: site 1: 3.14 dS m-1 and site 2: 4.45 dS m-1. Higher salinity proved to have a positive effect on growth. The relative water content did not decline severely, Na+ and K+ content of the roots, stem and leaves was more, and the functions of the photosynthetic apparatus and photosynthetic pigment contents were not altered. The efficiency of the antioxidative defence system was found to be assured by coordination of several reactive oxygen species scavengers. The presence of higher salinity led to accumulation of the osmolyte proline, while degradation of membrane lipids was reduced. As a whole, P. triandra evolved different adaptational strategies to counteract soil salinity, including morphological and physiological adaptations, preservation of photosynthetic activity, development of an efficient antioxidative system and accumulation of the osmotic compound, proline.}, }
@article {pmid31732338, year = {2020}, author = {Wang, Y and Qiao, M and Baikeli, Y and Mamat, X and Li, L and Hu, X and Dong, Y and Chang, F and Zhang, H and Hu, G}, title = {Soft-templated mesoporous carbon-modified glassy carbon electrode for sensitive and selective detection of aristolochic acids.}, journal = {Journal of hazardous materials}, volume = {385}, number = {}, pages = {121550}, doi = {10.1016/j.jhazmat.2019.121550}, pmid = {31732338}, issn = {1873-3336}, abstract = {In this study, ordered mesoporous carbon (OMC) was synthesized by applying a soft template method, and its mesoporous structure was characterized by scanning electron microscopy, transmission electron microscopy, and nitrogen adsorption-desorption techniques. X-ray diffraction and Raman spectroscopic analyses were conducted to demonstrate the high graphitization and topological defects at the sample surface. An electrochemical sensor based on an OMC-modified glassy carbon electrode (OMC/GCE) was constructed to detect aristolochic acids (AAs) using cyclic voltammetry and linear sweep voltammetry. The dependence of the experimental parameters including solution pH, scan rate, and accumulation time were examined and optimized. Under the optimal conditions, the response of OMC/GCE was linear over wide concentration ranges of AAs (0.6-10 μM and 10-50 μM), with sensitivities of -1.77 and -0.31 μA/μM, respectively. The limit of detection was calculated to be 0.186 μM (at S/N = 3). Furthermore, the proposed OMC/GCE was applied to detect AAs in Asarum sieboldini and the content of AAs was calculated to be 8.9 μg/g with high accuracy and precision. In addition, the modified electrode also exhibited good selectivity, reproducibility, and stability. Therefore, the OMC/GCE can be used as a platform for the determination of AAs.}, }
@article {pmid31729401, year = {2019}, author = {Mittermayer, FH and Stiasny, MH and Clemmesen, C and Bayer, T and Puvanendran, V and Chierici, M and Jentoft, S and Reusch, TBH}, title = {Transcriptome profiling reveals exposure to predicted end-of-century ocean acidification as a stealth stressor for Atlantic cod larvae.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16908}, doi = {10.1038/s41598-019-52628-1}, pmid = {31729401}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/methods ; Gadus morhua/*genetics ; *Gene Expression Profiling ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; *Hydrogen-Ion Concentration ; Larva ; Osmoregulation ; Seawater/*analysis/*chemistry ; *Stress, Physiological ; *Transcriptome ; }, abstract = {Ocean acidification (OA), a direct consequence of increasing atmospheric CO2 concentration dissolving in ocean waters, is impacting many fish species. Little is known about the molecular mechanisms underlying the observed physiological impacts in fish. We used RNAseq to characterize the transcriptome of 3 different larval stages of Atlantic cod (Gadus morhua) exposed to simulated OA at levels (1179 µatm CO2) representing end-of-century predictions compared to controls (503 µatm CO2), which were shown to induce tissue damage and elevated mortality in G. morhua. Only few genes were differentially expressed in 6 and 13 days-post-hatching (dph) (3 and 16 genes, respectively), during a period when maximal mortality as a response to elevated pCO2 occurred. At 36 dph, 1413 genes were differentially expressed, most likely caused by developmental asynchrony between the treatment groups, with individuals under OA growing faster. A target gene analysis revealed only few genes of the universal and well-defined cellular stress response to be differentially expressed. We thus suggest that predicted ocean acidification levels constitute a &quot;stealth stress&quot; for early Atlantic cod larvae, with a rapid breakdown of cellular homeostasis leading to organismal death that was missed even with an 8-fold replication implemented in this study.}, }
@article {pmid31724378, year = {2019}, author = {Sarkar, S and Singh, P and Lingala, MAL and Verma, P and Dhiman, RC}, title = {Malaria risk map for India based on climate, ecology and geographical modelling.}, journal = {Geospatial health}, volume = {14}, number = {2}, pages = {}, doi = {10.4081/gh.2019.767}, pmid = {31724378}, issn = {1970-7096}, mesh = {Animals ; Anopheles/growth &amp; development ; Climate ; Geographic Information Systems ; *Geographic Mapping ; India/epidemiology ; Malaria/*epidemiology ; Malaria, Falciparum/*epidemiology ; Malaria, Vivax/*epidemiology ; Mosquito Vectors/growth &amp; development ; Plants ; Risk Assessment ; Risk Factors ; Seasons ; Soil/chemistry ; }, abstract = {Mapping the malaria risk at various geographical levels is often undertaken considering climate suitability, infection rate and/or malaria vector distribution, while the ecological factors related to topography and vegetation cover are generally neglected. The present study abides a holistic approach to risk mapping by including topographic, climatic and vegetation components into the framework of malaria risk modelling. This work attempts to delineate the areas of Plasmodium falciparum and Plasmodium vivax malaria transmission risk in India using seven geo-ecological indicators: temperature, relative humidity, rainfall, forest cover, soil, slope, altitude and the normalized difference vegetation index using multi-criteria decision analysis based on geographical information system (GIS). The weight of the risk indicators was assigned by an analytical hierarchical process with the climate suitability (temperature and humidity) data generated using fuzzy logic. Model validation was done through both primary and secondary datasets. The spatio-ecological model was based on GIS to classify the country into five zones characterized by various levels of malaria transmission risk (very high; high; moderate; low; and very low. The study found that about 13% of the country is under very high malaria risk, which includes the malaria- endemic districts of the states of Chhattisgarh, Odisha, Jharkhand, Tripura, Assam, Meghalaya and Manipur. The study also showed that the transmission risk suitability for P. vivax is higher than that for P. falciparum in the Himalayan region. The field study corroborates the identified malaria risk zones and highlights that the low to moderate risk zones are outbreak-prone. It is expected that this information will help the National Vector Borne Disease Control Programme in India to undertake improved surveillance and conduct target based interventions.}, }
@article {pmid31720122, year = {2019}, author = {Näpflin, K and O'Connor, EA and Becks, L and Bensch, S and Ellis, VA and Hafer-Hahmann, N and Harding, KC and Lindén, SK and Olsen, MT and Roved, J and Sackton, TB and Shultz, AJ and Venkatakrishnan, V and Videvall, E and Westerdahl, H and Winternitz, JC and Edwards, SV}, title = {Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e8013}, pmid = {31720122}, issn = {2167-8359}, abstract = {Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.}, }
@article {pmid31694865, year = {2019}, author = {Greenbaum, G and Rubin, A and Templeton, AR and Rosenberg, NA}, title = {Network-based hierarchical population structure analysis for large genomic data sets.}, journal = {Genome research}, volume = {29}, number = {12}, pages = {2020-2033}, pmid = {31694865}, issn = {1549-5469}, support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; *Databases, Nucleic Acid ; *Genome, Human ; *Genomics ; Humans ; *Sequence Analysis, DNA ; }, abstract = {Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is becoming increasingly possible to reveal many hierarchical levels of structure, including fine-scale genetic clusters. To analyze these data sets, methods need to be appropriately suited to the challenges of extracting multilevel structure from whole-genome data. Here, we present a network-based approach for constructing population structure representations from genetic data. The use of community-detection algorithms from network theory generates a natural hierarchical perspective on the representation that the method produces. The method is computationally efficient, and it requires relatively few assumptions regarding the biological processes that underlie the data. We show the approach by analyzing population structure in the model plant species Arabidopsis thaliana and in human populations. These examples illustrate how network-based approaches for population structure analysis are well-suited to extracting valuable ecological and evolutionary information in the era of large genomic data sets.}, }
@article {pmid31685936, year = {2020}, author = {Bjorbækmo, MFM and Evenstad, A and Røsæg, LL and Krabberød, AK and Logares, R}, title = {The planktonic protist interactome: where do we stand after a century of research?.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {544-559}, doi = {10.1038/s41396-019-0542-5}, pmid = {31685936}, issn = {1751-7370}, mesh = {Alveolata ; Animals ; Aquatic Organisms ; Bacteria/*classification ; Biological Evolution ; Databases, Factual ; Ecology ; Ecosystem ; Eukaryota/*classification ; Metagenomics ; Microalgae ; *Microbial Interactions ; *Oceans and Seas ; Parasites ; Phylogeny ; Plankton/classification/microbiology/parasitology ; Rhizaria ; Stramenopiles ; Symbiosis ; }, abstract = {Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and 'unresolved interactions' (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Using bipartite networks, we found that protist predators seem to be 'multivorous' while parasite-host and symbiont-host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. Despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.}, }
@article {pmid31677344, year = {2020}, author = {Dumack, K and Fiore-Donno, AM and Bass, D and Bonkowski, M}, title = {Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria).}, journal = {Molecular ecology resources}, volume = {20}, number = {2}, pages = {398-403}, doi = {10.1111/1755-0998.13112}, pmid = {31677344}, issn = {1755-0998}, support = {BO 1907/13-2//Deutsche Forschungsgemeinschaft/ ; BO 1907/18-1//Deutsche Forschungsgemeinschaft/ ; Priority Program 1374//Deutsche Forschungsgemeinschaft/ ; NE/H000887/1//NERC Science of the Environment/ ; NE/H009426/1//NERC Science of the Environment/ ; }, mesh = {Cercozoa/classification/genetics ; Databases, Genetic ; Ecosystem ; Environmental DNA/genetics ; Phenotype ; Phylogeny ; Rhizaria/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {We have compiled a database of functional traits for two widespread and ecologically important groups of protists, Cercozoa and Endomyxa (Rhizaria). The functional traits of microorganisms are crucially important for interpreting results from environmental sequencing surveys. Linking morphological and ecological traits to environmental factors is common practice in studies involving micro- and macroorganisms, but is rarely applied to protists. Our database provides functional and ecologically significant traits linked to morphology, nutrition, locomotion and habitats. We discuss how the use of functional traits may help to unveil underlying ecosystem processes. This database is intended as a common reference for the molecular ecology community and will boost the understanding of ecosystem functions, especially those driven by biological interactions.}, }
@article {pmid31652294, year = {2019}, author = {Tamburello, L and Papa, L and Guarnieri, G and Basconi, L and Zampardi, S and Scipione, MB and Terlizzi, A and Zupo, V and Fraschetti, S}, title = {Are we ready for scaling up restoration actions? An insight from Mediterranean macroalgal canopies.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0224477}, pmid = {31652294}, issn = {1932-6203}, mesh = {Conservation of Natural Resources/economics/*methods ; Costs and Cost Analysis ; Herbivory ; *Mediterranean Region ; *Phaeophyta ; }, abstract = {Extensive loss of macroalgal forests advocates for large-scale restoration interventions, to compensate habitat degradation and recover the associated ecological functions and services. Yet, restoration attempts have generally been limited to small spatial extensions, with the principal aim of developing efficient restoration techniques. Here, the success of outplanting Cystoseira amentacea v. stricta germlings cultured in aquaria was experimentally explored at a scale of tens of kms, by means of a multifactorial experimental design. In the intertidal rocky shores of SE Italy, locations with a continuous distribution for hundreds of meters or with few thalli forming patches of few centimeters of C. amentacea canopy were selected. In each location, the effects of adult conspecifics and the exclusion of macrograzers (salema fish and sea urchins) on the survival of germlings were tested. We evaluated the most critical determinants of mortality for germlings, including the overlooked pressure of mesograzers (e.g. amphipods, small mollusks, polychaetes). Despite the high mortality observed during outplanting and early settlement stages, survival of C. amentacea germlings was consistently favored by the exclusion of macrograzers, while the presence of adult conspecifics had no effects. In addition, the cost analysis of the interventions showed the feasibility of the ex-situ method, representing an essential tool for preserving Cystoseira forests. Large scale restoration is possible but requires baseline information with an in-depth knowledge of the species ecology and of the areas to be restored, together with the development of specific cultivation protocols to make consistently efficient restoration interventions.}, }
@article {pmid31636201, year = {2019}, author = {Palomo, I and Dujardin, Y and Midler, E and Robin, M and Sanz, MJ and Pascual, U}, title = {Modeling trade-offs across carbon sequestration, biodiversity conservation, and equity in the distribution of global REDD+ funds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {45}, pages = {22645-22650}, pmid = {31636201}, issn = {1091-6490}, mesh = {Biodiversity ; *Carbon Sequestration ; Climate Change ; Conservation of Natural Resources/*economics ; Financial Management/economics ; Forests ; Models, Econometric ; Trees/growth &amp; development ; }, abstract = {The program on Reducing Emissions from Deforestation and Forest Degradation (REDD+) is one of the major attempts to tackle climate change mitigation in developing countries. REDD+ seeks to provide result-based incentives to promote emission reductions and increase carbon sinks in forest land while promoting other cobenefits, such as the conservation of biodiversity. We model different scenarios of international REDD+ funds distribution toward potential recipient countries using 2 carbon emission reduction targets (20% and 50% compared to the baseline scenario, i.e., deforestation and forest degradation without REDD+) by 2030. The model combines the prioritization of environmental outcomes in terms of carbon sequestration and biodiversity conservation and social equity, accounting for the equitable distribution of international REDD+ funds. Results highlight the synergy between carbon sequestration and biodiversity conservation under alternative fund allocation criteria, especially for scenarios of low carbon emission reduction. Trade-offs increase when distributional equity is considered as an additional criterion, especially under higher equity requirements. The analysis helps to better understand the inherent trade-offs between enhancing distributional equity and meeting environmental targets under alternative REDD+ fund allocation options.}, }
@article {pmid31631517, year = {2020}, author = {Li, X and Wang, X and Fang, L and Batbayar, N and Natsagdorj, T and Davaasuren, B and Damba, I and Xu, Z and Cao, L and Fox, AD}, title = {Annual migratory patterns of Far East Greylag Geese (Anser anser rubrirostris) revealed by GPS tracking.}, journal = {Integrative zoology}, volume = {15}, number = {3}, pages = {213-223}, doi = {10.1111/1749-4877.12414}, pmid = {31631517}, issn = {1749-4877}, mesh = {*Animal Migration ; Animals ; China ; Geese/*physiology ; Geographic Information Systems ; Mongolia ; Seasons ; Telemetry/*veterinary ; }, abstract = {Twenty Far East Greylag Geese, Anser anser rubrirostris, were captured and fitted with Global Positioning System/Global System for Mobile Communications (GPS/GSM) loggers to identify breeding and wintering areas, migration routes and stopover sites. Telemetry data for the first time showed linkages between their Yangtze River wintering areas, stopover sites in northeastern China, and breeding/molting grounds in eastern Mongolia and northeast China. 10 of the 20 tagged individuals provided sufficient data. They stopped on migration at the Yellow River Estuary, Beidagang Reservoir and Xar Moron River, confirming these areas as being important stopover sites for this population. The median spring migration duration was 33.7 days (individuals started migrating between 25 February and 16 March and completed migrating from 1 to 9 April) compared to 52.7 days in autumn (26 September-13 October until 4 November-11 December). The median stopover duration was 31.1 and 51.3 days and the median speed of travel was 62.6 and 47.9 km/day for spring and autumn migration, respectively. The significant differences between spring and autumn migration on the migration duration, the stopover duration and the migration speed confirmed that tagged adult Greylag Geese traveled faster in spring than autumn, supporting the hypothesis that they should be more time-limited during spring migration.}, }
@article {pmid31624369, year = {2019}, author = {Habel, JC and Trusch, R and Schmitt, T and Ochse, M and Ulrich, W}, title = {Long-term large-scale decline in relative abundances of butterfly and burnet moth species across south-western Germany.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14921}, doi = {10.1038/s41598-019-51424-1}, pmid = {31624369}, issn = {2045-2322}, mesh = {Agriculture ; *Animal Distribution ; Animals ; Biodiversity ; Butterflies/*physiology ; *Conservation of Natural Resources ; Datasets as Topic ; Ecological Parameter Monitoring/statistics &amp; numerical data ; Germany ; Grassland ; Moths/*physiology ; Population Dynamics/statistics &amp; numerical data/trends ; }, abstract = {Current studies have shown a severe general decline in insect species diversity, their abundance, and a biomass reduction of flying insects. Most of previous studies have been performed at single sites, or were spatially restricted at the landscape level. In this study, we analyse trends of species richness and shifts in species composition of butterflies and burnet moth species across the federal state of Baden-Württemberg in south-western Germany, covering an area of 35,750 km2. The data set consists of 233,474 records and covers a period from 1750 until today. We grouped species according to their species´ specific functional traits and analyse how species with different habitat requirements and behaviour respond to land-use changes over time. Our data document a significant loss of relative abundance for most species, especially since the 1950s until today. Species demanding specific habitat requirements are more seriously suffering under this trend than generalists. This in particular affects taxa adapted to extensively used xerothermic grasslands, bogs or other habitats maintained by traditional low-productivity agricultural practices of the past. Our data indicate large-scale decline in relative abundance of many butterfly and burnet moth species, which happened in particular during the past few decades.}, }
@article {pmid31596250, year = {2020}, author = {Kaufman, JH and Elkins, CA and Davis, M and Weis, AM and Huang, BC and Mammel, MK and Patel, IR and Beck, KL and Edlund, S and Chambliss, D and Douglas, J and Bianco, S and Kunitomi, M and Weimer, BC}, title = {Insular Microbiogeography: Three Pathogens as Exemplars.}, journal = {Current issues in molecular biology}, volume = {36}, number = {}, pages = {89-108}, doi = {10.21775/cimb.036.089}, pmid = {31596250}, issn = {1467-3045}, mesh = {Bacteria/classification/*genetics/pathogenicity ; Databases, Genetic ; Ecology ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Metagenome ; Microbiota/*genetics ; *Phylogeny ; Phylogeography/methods ; Whole Genome Sequencing ; }, abstract = {Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.}, }
@article {pmid31594929, year = {2019}, author = {Hua, ZS and Wang, YL and Evans, PN and Qu, YN and Goh, KM and Rao, YZ and Qi, YL and Li, YX and Huang, MJ and Jiao, JY and Chen, YT and Mao, YP and Shu, WS and Hozzein, W and Hedlund, BP and Tyson, GW and Zhang, T and Li, WJ}, title = {Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4574}, doi = {10.1038/s41467-019-12574-y}, pmid = {31594929}, issn = {2041-1723}, mesh = {Alkanes/metabolism ; Archaea/enzymology/*genetics/isolation &amp; purification ; *Biological Evolution ; China ; Computational Biology ; Genome, Archaeal ; Hot Springs/*microbiology ; Hot Temperature ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Methane/metabolism ; Multigene Family/genetics ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; }, abstract = {Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.}, }
@article {pmid31553801, year = {2019}, author = {Hoondert, RPJ and Oldenkamp, R and de Zwart, D and van de Meent, D and Posthuma, L}, title = {QSAR-Based Estimation of Species Sensitivity Distribution Parameters: An Exploratory Investigation.}, journal = {Environmental toxicology and chemistry}, volume = {38}, number = {12}, pages = {2764-2770}, pmid = {31553801}, issn = {1552-8618}, support = {603437//FP7 Environment/International ; }, mesh = {Databases, Chemical ; Ecotoxicology ; Models, Theoretical ; *Quantitative Structure-Activity Relationship ; Risk Assessment ; }, abstract = {Ecological risk assessments are hampered by limited availability of ecotoxicity data. The present study aimed to explore the possibility of deriving species sensitivity distribution (SSD) parameters for nontested compounds, based on simple physicochemical characteristics, known SSDs for data-rich compounds, and a quantitative structure-activity relationship (QSAR)-type approach. The median toxicity of a data-poor chemical for species assemblages significantly varies with values of the physicochemical descriptors, especially when based on high-quality SSD data (from either acute median effect concentrations or chronic no-observed-effect concentrations). Beyond exploratory uses, we discuss how the precision of QSAR-based SSDs can be improved to construct models that accurately predict the SSD parameters of data-poor chemicals. The current models show that the concept of QSAR-based SSDs supports screening-level evaluations of the potential ecotoxicity of compounds for which data are lacking. Environ Toxicol Chem 2019;38:2764-2770. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.}, }
@article {pmid31535335, year = {2020}, author = {Contador, CA and Veas-Castillo, L and Tapia, E and Antipán, M and Miranda, N and Ruiz-Tagle, B and García-Araya, J and Andrews, BA and Marin, M and Dorador, C and Asenjo, JA}, title = {Atacama Database: a platform of the microbiome of the Atacama Desert.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {2}, pages = {185-195}, doi = {10.1007/s10482-019-01328-x}, pmid = {31535335}, issn = {1572-9699}, support = {FB0001//Comisión Nacional de Investigación Científica y Tecnológica/ ; }, mesh = {Archaea/genetics/physiology ; Bacteria/genetics ; Biotechnology ; *Databases, Factual ; Desert Climate ; Microbiota/physiology ; Soil Microbiology ; }, abstract = {The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.}, }
@article {pmid31514979, year = {2019}, author = {Shen, L and Li, XW and Meng, XX and Wu, J and Tang, H and Huang, LF and Xiao, SM and Xu, J and Chen, SL}, title = {Prediction of the globally ecological suitability of Panax quinquefolius by the geographic information system for global medicinal plants (GMPGIS).}, journal = {Chinese journal of natural medicines}, volume = {17}, number = {7}, pages = {481-489}, doi = {10.1016/S1875-5364(19)30069-X}, pmid = {31514979}, issn = {1875-5364}, mesh = {Climate ; Climate Change ; Ecology ; *Geographic Information Systems ; Geography ; Panax/*growth &amp; development ; Plants, Medicinal/*growth &amp; development ; }, abstract = {American ginseng (Panax quinquefolius L.) is a well-known Asian traditional herbal medicine with a large market demand. The plant is native to eastern North America, and its main producing areas worldwide are decreasing due to continuous cropping obstacles and environmental changes. Therefore, the identification of maximum similarities of new ecological distribution of P. quinquefolius, and prediction of its response to climate change in the future are necessary for plant introduction and cultivation. In this study, the areas with potential ecological suitability for P. quinquefolius were predicted using the geographic information system for global medicinal plants (GMPGIS) based on 476 occurrence points and 19 bioclimatic variables. The results indicate that the new ecologically suitable areas for P. quinquefolius are East Asia and the mid-eastern Europe, which are mainly distributed in China, Russia, Japan, Ukraine, Belarus, North Korean, South Korea, andRomania. Under global climate change scenarios, the suitable planting areas for P. quinquefolius would be increased by 9.16%-30.97%, and expandingnorth and west over the current ecologically suitable areas by 2070. The potential increased areas that are ecologically suitable include northern Canada, Eastern Europe, and the Lesser Khingan Mountains of China, and reduced regions are mainly in central China, the southern U.S., and southern Europe. Jackknife tests indicate that the precipitation of the warmest quarter was the important climatic factor controlling the distribution of P. quinquefolius. Our findings can be used as auseful guide for P. quinquefolius introduction and cultivation in ecologically suitable areas.}, }
@article {pmid31513578, year = {2019}, author = {Becker, AD and Wesolowski, A and Bjørnstad, ON and Grenfell, BT}, title = {Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination.}, journal = {PLoS computational biology}, volume = {15}, number = {9}, pages = {e1007305}, pmid = {31513578}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; DP2 LM013102/LM/NLM NIH HHS/United States ; P2C HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Computational Biology ; History, 20th Century ; Humans ; Incidence ; Influenza, Human/epidemiology/history ; London/epidemiology ; *Measles/epidemiology/history/prevention &amp; control/transmission ; Pandemics/history/*statistics &amp; numerical data ; Vaccination/history/*statistics &amp; numerical data ; World War I ; World War II ; }, abstract = {A key question in ecology is the relative impact of internal nonlinear dynamics and external perturbations on the long-term trajectories of natural systems. Measles has been analyzed extensively as a paradigm for consumer-resource dynamics due to the oscillatory nature of the host-pathogen life cycle, the abundance of rich data to test theory, and public health relevance. The dynamics of measles in London, in particular, has acted as a prototypical test bed for such analysis using incidence data from the pre-vaccination era (1944-1967). However, during this timeframe there were few external large-scale perturbations, limiting an assessment of the relative impact of internal and extra demographic perturbations to the host population. Here, we extended the previous London analyses to include nearly a century of data that also contains four major demographic changes: the First and Second World Wars, the 1918 influenza pandemic, and the start of a measles mass vaccination program. By combining mortality and incidence data using particle filtering methods, we show that a simple stochastic epidemic model, with minimal historical specifications, can capture the nearly 100 years of dynamics including changes caused by each of the major perturbations. We show that the majority of dynamic changes are explainable by the internal nonlinear dynamics of the system, tuned by demographic changes. In addition, the 1918 influenza pandemic and World War II acted as extra perturbations to this basic epidemic oscillator. Our analysis underlines that long-term ecological and epidemiological dynamics can follow very simple rules, even in a non-stationary population subject to significant perturbations and major secular changes.}, }
@article {pmid31495042, year = {2020}, author = {Pranovi, F and Libralato, S and Zucchetta, M and Anelli Monti, M and Link, JS}, title = {Cumulative biomass curves describe past and present conditions of Large Marine Ecosystems.}, journal = {Global change biology}, volume = {26}, number = {2}, pages = {786-797}, doi = {10.1111/gcb.14827}, pmid = {31495042}, issn = {1365-2486}, mesh = {Biomass ; *Ecosystem ; }, abstract = {Implementing the Ecosystem Approach in marine ecosystems is moving from preliminary steps-dedicated to defining the optimal features for indicators and developing efficient indicator frameworks-towards an operational phase where multisector marine management decisions are executed using this information. Within this operational context, emergent ecosystem properties are becoming quite promising as they have been demonstrated to be globally widespread and repeatable, and to be quite effective in detecting significant state variations of complex systems. Biomass accumulation across TLs (CumB-TL) combines two important emergent properties of an ecosystem (energy flow, in terms of transfer efficiency, and storage, expressed as biomass), both amenable to detecting rapid ecosystem change. However, for further application, it is crucial to understand which types of drivers an indicator is sensitive to and how robust it is in relation to modifications of the external conditions and/or the system state. Here we address some outstanding questions of these CumB-TL curves related to their sensitivity to various drivers by carrying out a global scale assessment (using data from 62 LMEs) over six decades (1950-2010). We confirm the consistency of the S-pattern across all the LMEs, independent from latitude, ecosystem, environmental conditions, and stress level. The dynamics of the curve shape showed a tendency to stretch (i.e. decrease of steepness), in the presence of external disturbance and conversely to increase in steepness and shift towards higher TL in the case of recovery from stressed conditions. Our results suggest the presence of three main types of ecosystem dynamics, those showing an almost continuous increase in ecological state over time, those showing a continuous decrease in ecological state over time, and finally those showing a mixed behaviour flipping between recovering and degrading phases. These robust patterns suggest that the CumB-TL curve approach has some useful properties for use in further advancing the implementation of the Ecosystem Approach, allowing us to detect the state of a given marine ecosystem based on the dynamics of its curve shape, by using readily available time series data. The value of being able to identify conditions that might require management actions is quite high and, in many respects, represents the main objective in the context of an Ecosystem Approach, with large applications for detecting and responding to global changes in marine ecosystems.}, }
@article {pmid31494409, year = {2019}, author = {Reaney, SM and Mackay, EB and Haygarth, PM and Fisher, M and Molineux, A and Potts, M and Benskin, CMH}, title = {Identifying critical source areas using multiple methods for effective diffuse pollution mitigation.}, journal = {Journal of environmental management}, volume = {250}, number = {}, pages = {109366}, doi = {10.1016/j.jenvman.2019.109366}, pmid = {31494409}, issn = {1095-8630}, mesh = {*Agriculture ; Environmental Monitoring ; Fresh Water ; Geographic Information Systems ; Water Pollution ; *Water Quality ; }, abstract = {Diffuse pollution from agriculture constitutes a key pressure on the water quality of freshwaters and is frequently the cause of ecological degradation. The problem of diffuse pollution can be conceptualised with a source-mobilisation-pathway (or delivery)-impact model, whereby the combination of high source risk and strong connected pathways leads to 'critical source areas' (CSAs). These areas are where most diffuse pollution will originate, and hence are the optimal places to implement mitigation measures. However, identifying the locations of these areas is a key problem across different spatial scales within catchments. A number of approaches are frequently used for this assessment, although comparisons of these assessments are rarely carried out. We evaluate the CSAs identified via traditional walkover surveys supported by three different approaches, highlighting their benefits and disadvantages. These include a custom designed smartphone app; a desktop geographic information system (GIS) and terrain analysis-based SCIMAP (Sensitive Catchment Integrated Modelling and Analysis Platform) approach; and the use of a high spatial resolution drone dataset as an improved input data for SCIMAP modelling. Each of these methods captures the locations of the CSAs, revealing similarities and differences in the prioritisation of CSA features. The differences are due to the temporal and spatial resolution of the three methods such as the use of static land cover information, the ability to capture small scale features, such as gateways and the incomplete catchment coverage of the walkover survey. The relative costs and output resolutions of the three methods indicate that they are suitable for application at different catchment scales in conjunction with other methods. Based on the results in this paper, it is recommended that a multi-evidence-based approach to diffuse pollution management is taken across catchment spatial scales, incorporating local knowledge from the walkover with the different data resolutions of the SCIMAP approach.}, }
@article {pmid31488068, year = {2019}, author = {Pereira-Flores, E and Glöckner, FO and Fernandez-Guerra, A}, title = {Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {453}, pmid = {31488068}, issn = {1471-2105}, support = {57129354//Deutscher Akademischer Austauschdienst/ ; POS_EXT_2012_1_10105//Agencia Nacional de Investigación e Innovación/ ; 634486//Horizon 2020 Framework Programme/ ; }, mesh = {Benchmarking ; DNA Copy Number Variations ; Databases, Genetic ; *Gene Dosage ; *Genome Size ; Metagenome/*genetics ; Metagenomics/*methods ; Oceans and Seas ; RNA, Ribosomal, 16S/*genetics ; Time Factors ; }, abstract = {BACKGROUND: Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis workflows has the potential to improve the exploitation of metagenomic data. Metagenomic traits are organisms' characteristics linked to their performance. They are measured at the genomic level taking a random sample of individuals in a community. As such, these traits provide valuable information to uncover microorganisms' ecological patterns. The Average Genome Size (AGS) and the 16S rRNA gene Average Copy Number (ACN) are two highly informative metagenomic traits that reflect microorganisms' ecological strategies as well as the environmental conditions they inhabit.<br><br>RESULTS: Here, we present the ags.sh and acn.sh tools, which analytically derive the AGS and ACN metagenomic traits. These tools represent an advance on previous approaches to compute the AGS and ACN traits. Benchmarking shows that ags.sh is up to 11 times faster than state-of-the-art tools dedicated to the estimation AGS. Both ags.sh and acn.sh show comparable or higher accuracy than existing tools used to estimate these traits. To exemplify the applicability of both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological strategies associated with different water layers.<br><br>CONCLUSION: We took advantage of recent advances in gene annotation to develop the ags.sh and acn.sh tools to combine easy tool usage with fast and accurate performance. Our tools compute the AGS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metagenomic data analysis to gain deeper insights into microorganisms' ecology. The ags.sh and acn.sh tools are publicly available using Docker container technology at https://github.com/pereiramemo/AGS-and-ACN-tools .}, }
@article {pmid31484218, year = {2019}, author = {Goodman, KR and Prost, S and Bi, K and Brewer, MS and Gillespie, RG}, title = {Host and geography together drive early adaptive radiation of Hawaiian planthoppers.}, journal = {Molecular ecology}, volume = {28}, number = {19}, pages = {4513-4528}, pmid = {31484218}, issn = {1365-294X}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; *Computational Biology ; Ecology ; Exons/genetics ; Genetics, Population ; Geography ; Hawaii ; Hemiptera/genetics/*physiology ; Host Specificity ; Islands ; Male ; *Metagenomics ; Phylogeny ; Plants/*parasitology ; Species Specificity ; *Transcriptome ; }, abstract = {The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects &quot;escape and radiate&quot; on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co-occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.}, }
@article {pmid31465920, year = {2019}, author = {Giri, S and Zhang, Z and Krasnuk, D and Lathrop, RG}, title = {Evaluating the impact of land uses on stream integrity using machine learning algorithms.}, journal = {The Science of the total environment}, volume = {696}, number = {}, pages = {133858}, doi = {10.1016/j.scitotenv.2019.133858}, pmid = {31465920}, issn = {1879-1026}, abstract = {A general pattern of declining aquatic ecological integrity with increasing urban land use has been well established for a number of watersheds worldwide. A more nuanced characterization of the influence of different urban land uses and the determination of cumulative thresholds will further inform watershed planning and management. To this end, we investigated the utility of two machine learning algorithms (Random Forests (RF) and Boosted Regression Trees (BRT)) to model stream impairment through multimetric macroinvertebrate index known as High Gradient Macroinvertebrate Index (HGMI) in an urbanizing watershed located in north-central New Jersey, United States. These machine learning algorithms were able to explain at least 50% of the variability of stream integrity based on watershed land use/land cover. While comparable in results, RF was found to be easier to train and was somewhat more robust to model overfitting compared to BRT. Our results document the influence of increasing high-medium density (> 30% Impervious Surface cover (ISC)), low density (15-30% ISC) urban and transitional/barren land had in negatively affecting stream biological integrity. The thresholds generated by partial plots suggest that the stream integrity decreased abruptly when the percentage of high-medium and low density urban, and transitional/barren land went above 10%, 8%, and 2% of the watershed, respectively. Additionally, when rural residential surpassed 30% threshold, it behaved similar to low density urban towards stream integrity. Identification of such cumulative thresholds can help watershed managers and policymakers to craft land use zoning regulations and design restoration programs that are grounded by objective scientific criteria.}, }
@article {pmid31465440, year = {2019}, author = {Miele, V and Guill, C and Ramos-Jiliberto, R and Kéfi, S}, title = {Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model.}, journal = {PLoS computational biology}, volume = {15}, number = {8}, pages = {e1007269}, pmid = {31465440}, issn = {1553-7358}, mesh = {Animals ; *Biodiversity ; Biomass ; Biota ; Computational Biology ; Computer Simulation ; *Ecosystem ; Energy Metabolism ; Food Chain ; *Models, Biological ; Predatory Behavior ; }, abstract = {Ecological communities are undeniably diverse, both in terms of the species that compose them as well as the type of interactions that link species to each other. Despite this long recognition of the coexistence of multiple interaction types in nature, little is known about the consequences of this diversity for community functioning. In the ongoing context of global change and increasing species extinction rates, it seems crucial to improve our understanding of the drivers of the relationship between species diversity and ecosystem functioning. Here, using a multispecies dynamical model of ecological communities including various interaction types (e.g. competition for space, predator interference, recruitment facilitation in addition to feeding), we studied the role of the presence and the intensity of these interactions for species diversity, community functioning (biomass and production) and the relationship between diversity and functioning.Taken jointly, the diverse interactions have significant effects on species diversity, whose amplitude and sign depend on the type of interactions involved and their relative abundance. They however consistently increase the slope of the relationship between diversity and functioning, suggesting that species losses might have stronger effects on community functioning than expected when ignoring the diversity of interaction types and focusing on feeding interactions only.}, }
@article {pmid31446647, year = {2019}, author = {Lemos, LN and Medeiros, JD and Dini-Andreote, F and Fernandes, GR and Varani, AM and Oliveira, G and Pylro, VS}, title = {Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle.}, journal = {Molecular ecology}, volume = {28}, number = {18}, pages = {4259-4271}, doi = {10.1111/mec.15208}, pmid = {31446647}, issn = {1365-294X}, mesh = {Bacteria/*genetics ; Base Sequence ; Gene Regulatory Networks ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microbiota/genetics ; Mining ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; }, abstract = {The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co-metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.}, }
@article {pmid31433524, year = {2019}, author = {Eccles, KM and Pauli, BD and Chan, HM}, title = {The Use of Geographic Information Systems for Spatial Ecological Risk Assessments: An Example from the Athabasca Oil Sands Area in Canada.}, journal = {Environmental toxicology and chemistry}, volume = {38}, number = {12}, pages = {2797-2810}, doi = {10.1002/etc.4577}, pmid = {31433524}, issn = {1552-8618}, support = {//Canada Research Chairs/International ; Joint Oil Sands Monitoring Program//Environment and Climate Change Canada/International ; CREATE grant//Natural Sciences and Engineering Research Council of Canada/International ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Animals ; Canada ; Charadriiformes/growth &amp; development ; Cluster Analysis ; Ecotoxicology ; Environmental Monitoring/*methods ; Environmental Pollutants/analysis ; Geographic Information Systems ; Mercury/analysis ; Oil and Gas Fields/*chemistry ; Ovum/chemistry/metabolism ; Plants/chemistry/metabolism ; Swallows ; }, abstract = {There is an acknowledged need in ecotoxicology for methods that integrate spatial analyses in risk assessment. This has resulted in the emergence of landscape ecotoxicology, a subdiscipline of ecotoxicology. However, landscape ecotoxicology has yet to become common practice in risk assessment due to the underdevelopment of techniques and a lack of standardized methods. In the present study, we demonstrate how geographic information systems (GISs) can serve as a standardized platform to integrate data, assess spatial patterns of ecotoxicological data for multiple species, and assess relationships between chemical mixture exposures and effects on biota for landscape ecotoxicological risks assessment. We use data collected under the Joint Oil Sands Monitoring Program in the Athabasca Oil Sands Region in Alberta, Canada. This dataset is composed of concentrations of contaminants including metals and polycyclic aromatic compounds, and health endpoints measured in 1100 biological samples, including tree swallows, amphibians, gull and tern eggs, plants, and mammals. We present 3 examples using a GIS as a platform and geospatial analysis to: 1) integrate data and assess spatial patterns of contaminant exposure in the region, 2) assess spatial patterns of exposures to complex mixtures, and 3) examine patterns of exposures and responses across the landscape. We summarize the methods used in the present study into a workflow for ease of use. The GIS methods allow researchers to identify hot spots of contamination, use georeferenced monitoring data to derive quantitative exposure-response relationships, and assess complex exposures with more realism. Environ Toxicol Chem 2019;38:2797-2810. © 2019 SETAC.}, }
@article {pmid31418863, year = {2019}, author = {Serbin, SP and Wu, J and Ely, KS and Kruger, EL and Townsend, PA and Meng, R and Wolfe, BT and Chlus, A and Wang, Z and Rogers, A}, title = {From the Arctic to the tropics: multibiome prediction of leaf mass per area using leaf reflectance.}, journal = {The New phytologist}, volume = {224}, number = {4}, pages = {1557-1568}, doi = {10.1111/nph.16123}, pmid = {31418863}, issn = {1469-8137}, support = {WIS01809//U.S. Department of Agriculture/International ; NNX08AV07H/NASA/NASA/United States ; NNX12AQ28G/NASA/NASA/United States ; 1638720//National Science Foundation/International ; DE-SC0012704//Biological and Environmental Research/International ; NNX08AV07H/NASA/NASA/United States ; NNX12AQ28G/NASA/NASA/United States ; }, mesh = {Arctic Regions ; Databases, Factual ; Ecosystem ; *Models, Biological ; Models, Statistical ; Plant Leaves/*chemistry/*physiology ; Spatio-Temporal Analysis ; Spectrum Analysis/methods ; Tropical Climate ; }, abstract = {Leaf mass per area (LMA) is a key plant trait, reflecting tradeoffs between leaf photosynthetic function, longevity, and structural investment. Capturing spatial and temporal variability in LMA has been a long-standing goal of ecological research and is an essential component for advancing Earth system models. Despite the substantial variation in LMA within and across Earth's biomes, an efficient, globally generalizable approach to predict LMA is still lacking. We explored the capacity to predict LMA from leaf spectra across much of the global LMA trait space, with values ranging from 17 to 393 g m-2 . Our dataset contained leaves from a wide range of biomes from the high Arctic to the tropics, included broad- and needleleaf species, and upper- and lower-canopy (i.e. sun and shade) growth environments. Here we demonstrate the capacity to rapidly estimate LMA using only spectral measurements across a wide range of species, leaf age and canopy position from diverse biomes. Our model captures LMA variability with high accuracy and low error (R2 = 0.89; root mean square error (RMSE) = 15.45 g m-2). Our finding highlights the fact that the leaf economics spectrum is mirrored by the leaf optical spectrum, paving the way for this technology to predict the diversity of LMA in ecosystems across global biomes.}, }
@article {pmid31418215, year = {2019}, author = {Wang, QL and Han, YJ and Zhang, LP and Feng, C and Wang, MT}, title = {[GIS-based ecological climate suitability regionalization for Cordyceps sinensis in Shiqu County, Sichuan Province, China.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {7}, pages = {2137-2144}, doi = {10.13287/j.1001-9332.201907.022}, pmid = {31418215}, issn = {1001-9332}, mesh = {China ; Climate ; *Cordyceps ; Ecology ; *Geographic Information Systems ; Soil ; }, abstract = {Based on the biological characteristics of Cordyceps sinensis, combined with the spatial and temporal distribution characteristics of local agro-climatic resources and the investigation data of C. sinensis resources, we investigated the ecological climate suitability regionalization and the spatial distribution of C. sinensis in Shiqu County using mathematical statistics analysis, optimization method and GIS spatial analysis. We used altitude, mean annual temperature, mean annual precipitation, vegetation, and soil as the leading indicators and topographic gradient as the auxiliary indicators, as the main basis for the suitability zoning of C. sinensis resources. The results showed that C. sinensis grew in most of the townships in Shiqu County, with their distribution areas being fragmented and scattered, showing sporadic patches and blocks. They were mainly distributed in east and west parts of the county and in the Zhaqu River basin in the central part. The suitable distribution area for C. sinensis in Shiqu was 4000-4700 m above sea level, with mean annual temperature of -2.5-3 ℃ and mean annual precipitation of 550-850 mm. The growth environment was generally alpine mea-dow and subalpine meadow with good hydrophobicity and slope of 15°-50°. The suitable growth environment and meteorological conditions were beneficial to the growth and development of feeding plants and bat moths. The unsuitable area was in the high mountain area above the river wide valley area, pastoral area, wetland, or snowline.}, }
@article {pmid31397053, year = {2019}, author = {Liu, Y and Schwalm, CR and Samuels-Crow, KE and Ogle, K}, title = {Ecological memory of daily carbon exchange across the globe and its importance in drylands.}, journal = {Ecology letters}, volume = {22}, number = {11}, pages = {1806-1816}, doi = {10.1111/ele.13363}, pmid = {31397053}, issn = {1461-0248}, support = {DBI#1458867//NSF/ ; DE-AC05-00OR22725//DOE/ ; }, mesh = {*Carbon ; Carbon Cycle ; Carbon Dioxide ; Ecology ; *Ecosystem ; }, abstract = {How do antecedent (past) conditions influence land-carbon dynamics after those conditions no longer persist? In particular, quantifying such memory effects associated with the influence of past environmental (exogenous) and biological (endogenous) conditions is crucial for understanding and predicting the carbon cycle. Here we show, using data from 42 eddy covariance sites across six major biomes, that ecological memory-decomposed into environmental and biological memory components-of daily net carbon exchange (NEE) is critical for understanding the land-carbon metabolism, especially in drylands for which memory explains ~ 32% of the variation in NEE. The strong environmental memory in drylands was primarily driven by short- and long-term moisture status. Moreover, the strength of environmental memory scales with increasing water stress. This universal scaling relationship, emerging within and among major biomes, suggests a potential adaptive response to water limitation. Our findings underscore the necessity of considering ecological memory in experiments, observations and modelling.}, }
@article {pmid31350429, year = {2019}, author = {Stewart, FEC and Darlington, S and Volpe, JP and McAdie, M and Fisher, JT}, title = {Corridors best facilitate functional connectivity across a protected area network.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10852}, doi = {10.1038/s41598-019-47067-x}, pmid = {31350429}, issn = {2045-2322}, mesh = {*Animal Migration ; Animals ; Biodiversity ; Canada ; Conservation of Natural Resources/*methods ; Ecology/methods ; *Ecosystem ; Geographic Information Systems ; Locomotion ; Mustelidae/*physiology ; *Natural Resources ; }, abstract = {Biologging data allow animal ecologists to directly measure species' fine-scale spatiotemporal responses to environments, such as movement - critical for our understanding of biodiversity declines in the Anthropocene. Animal movement between resource patches is a behavioral expression of multiple ecological processes that affect individual fitness. Protected area (PA) networks are a tool used to conserve biodiversity by sustaining habitat patches across vast heterogeneous landscapes. However, our ability to design PA networks that conserve biodiversity relies on our accurate understanding of animal movement and functional connectivity; this understanding is rarely tested in real-world situations due to the large geographic expanse of most PA networks. Using a tractable PA network mesocosm, we employ cutting-edge biologging technology to analyze animal movement decisions in response to a highly heterogeneous landscape. We analyze these data to test, in a novel way, three common hypotheses about functional connectivity - structural corridors, least cost paths, and stepping stones. Consistently, animals moved along structurally self-similar corridors. In reference to the Aichi 2020 Biodiversity Targets, relying on species to &quot;stepping stone&quot; across habitat remnants may not achieve protected area network conservation objectives.}, }
@article {pmid31344542, year = {2019}, author = {Saedpanah, S and Amanollahi, J}, title = {Environmental pollution and geo-ecological risk assessment of the Qhorveh mining area in western Iran.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {253}, number = {}, pages = {811-820}, doi = {10.1016/j.envpol.2019.07.049}, pmid = {31344542}, issn = {1873-6424}, mesh = {Ecology ; Environment ; Environmental Monitoring/*methods ; Environmental Pollution/*statistics &amp; numerical data ; Geographic Information Systems ; Iran ; *Mining ; Risk Assessment ; Soil ; Soil Pollutants/analysis ; }, abstract = {In order to evaluate the effect of mining activity on the environment of the Qhorveh mining area in the west of Iran, the geological, ecological and environmental data, related to social development and regional economic status, were used. The geological data included seven sub-indices, such as vegetation coverage, land utilization type, and fault activity; ecological data, with two sub-indices, such as degree of ecological environment recovery; and finally, environmental data, with three sub-indices, such as soil and dust pollutions. These were selected based on the literature and expert opinion which were utilized for environmental pollution and geo-ecological (EPGE) risk assessment of the study site. Remote sensing (RS) image, field sampling, digital elevation map, and data retrieved from different government agencies were used to generate layers for the sub-indices in the geographic information system (GIS) environment. In addition, the analytical hierarchy process (AHP) method was used to determine the weight of sub-indices. Five levels consisting of best, good, middle, poor and worst were used to describe the EPGE risk assessment of the Qhorveh mining area. Results showed that worst and poor levels of EPGE risk are in the east and northeast of the study area where the gold and pumice mines are located while best and good levels of EPGE risk are in its center where the stone mines are located. According to the results of this research, the EPGE risk assessment of the Qhorveh mining area is affected by the environmental pollution index with its highest weight (0.3908). It can be concluded that the integration of the RS, GIS and AHP methods proposed in this study improved the evaluation quality of EPGE risk assessment.}, }
@article {pmid31330063, year = {2019}, author = {Fountain-Jones, NM and Machado, G and Carver, S and Packer, C and Recamonde-Mendoza, M and Craft, ME}, title = {How to make more from exposure data? An integrated machine learning pipeline to predict pathogen exposure.}, journal = {The Journal of animal ecology}, volume = {88}, number = {10}, pages = {1447-1461}, doi = {10.1111/1365-2656.13076}, pmid = {31330063}, issn = {1365-2656}, mesh = {Animals ; Animals, Wild ; *Distemper Virus, Canine ; Ecology ; *Lions ; Machine Learning ; }, abstract = {Predicting infectious disease dynamics is a central challenge in disease ecology. Models that can assess which individuals are most at risk of being exposed to a pathogen not only provide valuable insights into disease transmission and dynamics but can also guide management interventions. Constructing such models for wild animal populations, however, is particularly challenging; often only serological data are available on a subset of individuals and nonlinear relationships between variables are common. Here we provide a guide to the latest advances in statistical machine learning to construct pathogen-risk models that automatically incorporate complex nonlinear relationships with minimal statistical assumptions from ecological data with missing data. Our approach compares multiple machine learning algorithms in a unified environment to find the model with the best predictive performance and uses game theory to better interpret results. We apply this framework on two major pathogens that infect African lions: canine distemper virus (CDV) and feline parvovirus. Our modelling approach provided enhanced predictive performance compared to more traditional approaches, as well as new insights into disease risks in a wild population. We were able to efficiently capture and visualize strong nonlinear patterns, as well as model complex interactions between variables in shaping exposure risk from CDV and feline parvovirus. For example, we found that lions were more likely to be exposed to CDV at a young age but only in low rainfall years. When combined with our data calibration approach, our framework helped us to answer questions about risk of pathogen exposure that are difficult to address with previous methods. Our framework not only has the potential to aid in predicting disease risk in animal populations, but also can be used to build robust predictive models suitable for other ecological applications such as modelling species distribution or diversity patterns.}, }
@article {pmid31318965, year = {2019}, author = {Flórián, N and Ladányi, M and Ittzés, A and Kröel-Dulay, G and Ónodi, G and Mucsi, M and Szili-Kovács, T and Gergócs, V and Dányi, L and Dombos, M}, title = {Effects of single and repeated drought on soil microarthropods in a semi-arid ecosystem depend more on timing and duration than drought severity.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219975}, pmid = {31318965}, issn = {1932-6203}, mesh = {Animals ; *Arthropods ; *Biodiversity ; Biomass ; *Droughts ; *Ecosystem ; Soil/chemistry/*parasitology ; }, abstract = {Soil moisture is one of the most important factors affecting soil biota. In arid and semi-arid ecosystems, soil mesofauna is adapted to temporary drought events, but, until now, we have had a limited understanding of the impacts of the different magnitudes and frequencies of drought predicted to occur according to future climate change scenarios. The present study focuses on how springtails and mites respond to simulated repeated drought events of different magnitudes in a field experiment in a Hungarian semi-arid sand steppe. Changes in soil arthropod activities were monitored with soil trapping over two years in a sandy soil. In the first year (2014), we applied an extreme drought pretreatment, and in the consecutive year, we applied less devastating treatments (severe drought, moderate drought, water addition) to these sites. In the first year, the extreme drought pretreatment tended to have a negative effect (either significantly or not significantly) on the capture of all Collembola groups, whereas all mite groups increased in activity density. However, in the consecutive year, between the extreme drought and control treatments, we only detected differences in soil microbial biomass. In the cases of severe drought, moderate drought and water addition, we did not find considerable changes across the microarthropods, except in the case of epedaphic Collembola. In the cases of the water addition and drought treatments, the duration and timing of the manipulation seemed to be more important for soil mesofauna than their severity (i.e., the level of soil moisture decrease). We suggest that in these extreme habitats, soil mesofauna are able to survive extreme conditions, and their populations recover rapidly, but they may not be able to cope with very long drought periods.}, }
@article {pmid31310429, year = {2019}, author = {di Porcia E Brugnera, M and Meunier, F and Longo, M and Krishna Moorthy, SM and De Deurwaerder, H and Schnitzer, SA and Bonal, D and Faybishenko, B and Verbeeck, H}, title = {Modeling the impact of liana infestation on the demography and carbon cycle of tropical forests.}, journal = {Global change biology}, volume = {25}, number = {11}, pages = {3767-3780}, pmid = {31310429}, issn = {1365-2486}, mesh = {Carbon Cycle ; Demography ; *Ecosystem ; Forests ; Panama ; Trees ; *Tropical Climate ; }, abstract = {There is mounting empirical evidence that lianas affect the carbon cycle of tropical forests. However, no single vegetation model takes into account this growth form, although such efforts could greatly improve the predictions of carbon dynamics in tropical forests. In this study, we incorporated a novel mechanistic representation of lianas in a dynamic global vegetation model (the Ecosystem Demography Model). We developed a liana-specific plant functional type and mechanisms representing liana-tree interactions (such as light competition, liana-specific allometries, and attachment to host trees) and parameterized them according to a comprehensive literature meta-analysis. We tested the model for an old-growth forest (Paracou, French Guiana) and a secondary forest (Gigante Peninsula, Panama). The resulting model simulations captured many features of the two forests characterized by different levels of liana infestation as revealed by a systematic comparison of the model outputs with empirical data, including local census data from forest inventories, eddy flux tower data, and terrestrial laser scanner-derived forest vertical structure. The inclusion of lianas in the simulations reduced the secondary forest net productivity by up to 0.46 tC ha-1 year-1 , which corresponds to a limited relative reduction of 2.6% in comparison with a reference simulation without lianas. However, this resulted in significantly reduced accumulated above-ground biomass after 70 years of regrowth by up to 20 tC /ha (19% of the reference simulation). Ultimately, the simulated negative impact of lianas on the total biomass was almost completely cancelled out when the forest reached an old-growth successional stage. Our findings suggest that lianas negatively influence the forest potential carbon sink strength, especially for young, disturbed, liana-rich sites. In light of the critical role that lianas play in the profound changes currently experienced by tropical forests, this new model provides a robust numerical tool to forecast the impact of lianas on tropical forest carbon sinks.}, }
@article {pmid31295663, year = {2019}, author = {Pitacco, V and Reizopoulou, S and Sfriso, A and Sfriso, A and Mistri, M and Munari, C}, title = {The difficulty of disentangling natural from anthropogenic forcing factors makes the evaluation of ecological quality problematic: A case study from Adriatic lagoons.}, journal = {Marine environmental research}, volume = {150}, number = {}, pages = {104756}, doi = {10.1016/j.marenvres.2019.104756}, pmid = {31295663}, issn = {1879-0291}, mesh = {Animals ; Ecology ; *Ecosystem ; *Environmental Monitoring ; Invertebrates ; Wetlands ; }, abstract = {The complex and dynamic nature of transitional ecosystems pose problems for the assessment of the Ecological Quality Status required by the European Water Framework Directive (WFD; 2000/60/EC). In six Adriatic lagoons, Ecological Quality Status was studied by comparing a biotic index based on macrophytes (MaQI), and three indices based on invertebrates (M-AMBI, M-bAMBI, and ISD). Ecological Status evaluated though MaQI and ISD resulted in quite degraded ecosystems (moderate/poor/bad), with only opportunistic algae and macrobenthic communities dominated by small size classes. Those results were supported by physico-chemical parameters, indicating high nutrients inputs, and anthropogenic pressures related with agriculture and fishery activities. Ecological Status obtained with M-AMBI and M-bAMBI was higher, with some sites reaching even the &quot;good&quot; status. The best response to anthropogenic pressures, in terms of a pressure index, was obtained by M-AMBI and M-bAMBI. Nevertheless, the response of used metrics (such as AMBI and bAMBI) to environmental variables not related to anthropogenic impact, and the high heterogeneity of physical-chemical conditions within lagoons, represent potential problems for the correct evaluation of Ecological Status of transitional waters. When different metrics give different responses it becomes a problem for managers who cannot easily make a decision on the remedial measures. The disagreement among indices arose because of the different response of biological elements to different stressors, and because the different indices based on macroinvertebrates focused on different aspects of the community, providing complementary information. So urge the need to find alternative approaches for a correct assessment of Ecological Status, with the combination of different biological elements, and considering the development of new indices (e.g. M-bAMBI) or refinement of the existing ones.}, }
@article {pmid31290101, year = {2019}, author = {Tian, D and Yan, Z and Ma, S and Ding, Y and Luo, Y and Chen, Y and Du, E and Han, W and Kovacs, ED and Shen, H and Hu, H and Kattge, J and Schmid, B and Fang, J}, title = {Family-level leaf nitrogen and phosphorus stoichiometry of global terrestrial plants.}, journal = {Science China. Life sciences}, volume = {62}, number = {8}, pages = {1047-1057}, doi = {10.1007/s11427-019-9584-1}, pmid = {31290101}, issn = {1869-1889}, mesh = {Databases, Factual ; Ecosystem ; Models, Statistical ; Nitrogen/*metabolism ; Phosphorus/*metabolism ; Photosynthesis ; Phylogeny ; Plant Leaves/*chemistry/*metabolism ; Plants/*metabolism ; Soil ; Stereoisomerism ; Temperature ; }, abstract = {Leaf nitrogen (N) and phosphorus (P) concentrations are critical for photosynthesis, growth, reproduction and other ecological processes of plants. Previous studies on large-scale biogeographic patterns of leaf N and P stoichiometric relationships were mostly conducted using data pooled across taxa, while family/genus-level analyses are rarely reported. Here, we examined global patterns of family-specific leaf N and P stoichiometry using a global data set of 12,716 paired leaf N and P records which includes 204 families, 1,305 genera, and 3,420 species. After determining the minimum size of samples (i.e., 35 records), we analyzed leaf N and P concentrations, N:P ratios and N∼P scaling relationships of plants for 62 families with 11,440 records. The numeric values of leaf N and P stoichiometry varied significantly across families and showed diverse trends along gradients of mean annual temperature (MAT) and mean annual precipitation (MAP). The leaf N and P concentrations and N:P ratios of 62 families ranged from 6.11 to 30.30 mg g-1, 0.27 to 2.17 mg g-1, and 10.20 to 35.40, respectively. Approximately 1/3-1/2 of the families (22-35 of 62) showed a decrease in leaf N and P concentrations and N:P ratios with increasing MAT or MAP, while the remainder either did not show a significant trend or presented the opposite pattern. Family-specific leaf N∼P scaling exponents did not converge to a certain empirical value, with a range of 0.307-0.991 for 54 out of 62 families which indicated a significant N∼P scaling relationship. Our results for the first time revealed large variation in the family-level leaf N and P stoichiometry of global terrestrial plants and that the stoichiometric relationships for at least one-third of the families were not consistent with the global trends reported previously. The numeric values of the family-specific leaf N and P stoichiometry documented in the current study provide critical synthetic parameters for biogeographic modeling and for further studies on the physiological and ecological mechanisms underlying the nutrient use strategies of plants from different phylogenetic taxa.}, }
@article {pmid31286860, year = {2019}, author = {Meola, M and Rifa, E and Shani, N and Delbès, C and Berthoud, H and Chassard, C}, title = {DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {560}, pmid = {31286860}, issn = {1471-2164}, mesh = {Classification/*methods ; Dairy Products/*microbiology ; *Databases, Genetic ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.<br><br>RESULTS: We provide a manually curated database composed of 10'290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.}, }
@article {pmid31285584, year = {2019}, author = {Edwards, RA and Vega, AA and Norman, HM and Ohaeri, M and Levi, K and Dinsdale, EA and Cinek, O and Aziz, RK and McNair, K and Barr, JJ and Bibby, K and Brouns, SJJ and Cazares, A and de Jonge, PA and Desnues, C and Díaz Muñoz, SL and Fineran, PC and Kurilshikov, A and Lavigne, R and Mazankova, K and McCarthy, DT and Nobrega, FL and Reyes Muñoz, A and Tapia, G and Trefault, N and Tyakht, AV and Vinuesa, P and Wagemans, J and Zhernakova, A and Aarestrup, FM and Ahmadov, G and Alassaf, A and Anton, J and Asangba, A and Billings, EK and Cantu, VA and Carlton, JM and Cazares, D and Cho, GS and Condeff, T and Cortés, P and Cranfield, M and Cuevas, DA and De la Iglesia, R and Decewicz, P and Doane, MP and Dominy, NJ and Dziewit, L and Elwasila, BM and Eren, AM and Franz, C and Fu, J and Garcia-Aljaro, C and Ghedin, E and Gulino, KM and Haggerty, JM and Head, SR and Hendriksen, RS and Hill, C and Hyöty, H and Ilina, EN and Irwin, MT and Jeffries, TC and Jofre, J and Junge, RE and Kelley, ST and Khan Mirzaei, M and Kowalewski, M and Kumaresan, D and Leigh, SR and Lipson, D and Lisitsyna, ES and Llagostera, M and Maritz, JM and Marr, LC and McCann, A and Molshanski-Mor, S and Monteiro, S and Moreira-Grez, B and Morris, M and Mugisha, L and Muniesa, M and Neve, H and Nguyen, NP and Nigro, OD and Nilsson, AS and O'Connell, T and Odeh, R and Oliver, A and Piuri, M and Prussin Ii, AJ and Qimron, U and Quan, ZX and Rainetova, P and Ramírez-Rojas, A and Raya, R and Reasor, K and Rice, GAO and Rossi, A and Santos, R and Shimashita, J and Stachler, EN and Stene, LC and Strain, R and Stumpf, R and Torres, PJ and Twaddle, A and Ugochi Ibekwe, M and Villagra, N and Wandro, S and White, B and Whiteley, A and Whiteson, KL and Wijmenga, C and Zambrano, MM and Zschach, H and Dutilh, BE}, title = {Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.}, journal = {Nature microbiology}, volume = {4}, number = {10}, pages = {1727-1736}, doi = {10.1038/s41564-019-0494-6}, pmid = {31285584}, issn = {2058-5276}, support = {K99 AI119401/AI/NIAID NIH HHS/United States ; T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/classification/*genetics ; Bacteroidetes/classification/genetics/virology ; *Biological Coevolution ; DNA, Viral/genetics ; Feces/virology ; Female ; *Gastrointestinal Microbiome ; Genetic Variation ; Humans ; Male ; Phylogeny ; Phylogeography ; Primates/virology ; }, abstract = {Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.}, }
@article {pmid31278668, year = {2019}, author = {Watson, AK and Lannes, R and Pathmanathan, JS and Méheust, R and Karkar, S and Colson, P and Corel, E and Lopez, P and Bapteste, E}, title = {The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {271-308}, doi = {10.1007/978-1-4939-9074-0_9}, pmid = {31278668}, issn = {1940-6029}, mesh = {Biodiversity ; Biological Evolution ; Computational Biology/methods ; Ecosystem ; Evolution, Molecular ; Gene Ontology ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Multigene Family ; }, abstract = {In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.}, }
@article {pmid31278639, year = {2019}, author = {Ha, S and Yang, Z}, title = {Evaluation for landscape aesthetic value of the Natural World Heritage Site.}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {8}, pages = {483}, pmid = {31278639}, issn = {1573-2959}, support = {2016YFC0503306//Department of Science and Technology for Social Development/ ; }, mesh = {China ; *Conservation of Natural Resources ; Decision Making ; Environmental Monitoring/*methods ; *Esthetics ; Geographic Information Systems ; Lakes ; Public Opinion ; Rivers ; Wetlands ; }, abstract = {The landscape aesthetic value (LAV) is one essential component of outstanding universal value (OUV) for a Natural World Heritage Site (NWHS). In the identification of LAV, there is the subjectivity of methodology suggested by IUCN in the operation manual, and the expert-led evaluation is insufficient for reflecting all observers' opinions. This study focuses on establishing a universal system combining the subjectivity and objectivity, the experts' and the public's opinions to evaluate the LAV of an NWHS. We used the NWHS criteria, the ecological environment, and the viewing experience as established indicators; nine metrics were applied as corresponding layers respectively to map and give a final spatial evaluation based on the ArcGIS overlay analysis with their comprehensive weights from 3 groups of decision makers. In order to verify the rationality of our model, the LAV of a case study in Bayanbulak of NWHS Xinjiang Tianshan has been evaluated. It is demonstrated that central region of Bayanbulak with unique landscape that taking rivers, lakes, and swamps as base interlacing with wetland meadows has particularly high LAV; it basically shows a concentric circle-like distribution feature that LAV decreases from inside to outside and is consistent with practical protection status. This study responds to the UNESCO's request to monitor and evaluate the OUV of the NWHS; we believe results can provide a useful reference for the planning and decision-making of relevant scenic spots.}, }
@article {pmid31269286, year = {2019}, author = {Kienzler, A and Connors, KA and Bonnell, M and Barron, MG and Beasley, A and Inglis, CG and Norberg-King, TJ and Martin, T and Sanderson, H and Vallotton, N and Wilson, P and Embry, MR}, title = {Mode of Action Classifications in the EnviroTox Database: Development and Implementation of a Consensus MOA Classification.}, journal = {Environmental toxicology and chemistry}, volume = {38}, number = {10}, pages = {2294-2304}, pmid = {31269286}, issn = {1552-8618}, mesh = {Animals ; *Consensus ; Databases, Factual ; *Ecotoxicology ; Fishes/physiology ; Invertebrates/physiology ; Risk Assessment ; Toxicity Tests, Acute ; }, abstract = {Multiple mode of action (MOA) frameworks have been developed in aquatic ecotoxicology, mainly based on fish toxicity. These frameworks provide information on a key determinant of chemical toxicity, but the MOA categories and level of specificity remain unique to each of the classification schemes. The present study aimed to develop a consensus MOA assignment within EnviroTox, a curated in vivo aquatic toxicity database, based on the following MOA classification schemes: Verhaar (modified) framework, Assessment Tool for Evaluating Risk, Toxicity Estimation Software Tool, and OASIS. The MOA classifications from each scheme were first collapsed into one of 3 categories: non-specifically acting (i.e., narcosis), specifically acting, or nonclassifiable. Consensus rules were developed based on the degree of concordance among the 4 individual MOA classifications to attribute a consensus MOA to each chemical. A confidence rank was also assigned to the consensus MOA classification based on the degree of consensus. Overall, 40% of the chemicals were classified as narcotics, 17% as specifically acting, and 43% as unclassified. Sixty percent of chemicals had a medium to high consensus MOA assignment. When compared to empirical acute toxicity data, the general trend of specifically acting chemicals being more toxic is clearly observed for both fish and invertebrates but not for algae. EnviroTox is the first approach to establishing a high-level consensus across 4 computationally and structurally distinct MOA classification schemes. This consensus MOA classification provides both a transparent understanding of the variation between MOA classification schemes and an added certainty of the MOA assignment. In terms of regulatory relevance, a reliable understanding of MOA can provide information that can be useful for the prioritization (ranking) and risk assessment of chemicals. Environ Toxicol Chem 2019;38:2294-2304. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.}, }
@article {pmid31265463, year = {2019}, author = {Ruess, J and Pleška, M and Guet, CC and Tkačik, G}, title = {Molecular noise of innate immunity shapes bacteria-phage ecologies.}, journal = {PLoS computational biology}, volume = {15}, number = {7}, pages = {e1007168}, pmid = {31265463}, issn = {1553-7358}, mesh = {Bacteria/*immunology/*virology ; Bacteriophages/*immunology ; Computational Biology ; DNA Restriction-Modification Enzymes/immunology ; Ecosystem ; Immunity, Innate ; Microbial Consortia/immunology ; Models, Biological ; Models, Immunological ; Single-Cell Analysis ; Stochastic Processes ; }, abstract = {Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems.}, }
@article {pmid31251341, year = {2019}, author = {Pepin, KM and Pedersen, K and Wan, XF and Cunningham, FL and Webb, CT and Wilber, MQ}, title = {Individual-Level Antibody Dynamics Reveal Potential Drivers of Influenza A Seasonality in Wild Pig Populations.}, journal = {Integrative and comparative biology}, volume = {59}, number = {5}, pages = {1231-1242}, pmid = {31251341}, issn = {1557-7023}, support = {R01 AI116744/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antibodies, Viral/*blood ; Influenza A virus/*physiology ; Introduced Species ; Orthomyxoviridae Infections/immunology/*veterinary/virology ; Seasons ; Swine ; Swine Diseases/*immunology/virology ; United States ; }, abstract = {Swine are important in the ecology of influenza A virus (IAV) globally. Understanding the ecological role of wild pigs in IAV ecology has been limited because surveillance in wild pigs is often for antibodies (serosurveillance) rather than IAVs, as in humans and domestic swine. As IAV antibodies can persist long after an infection, serosurveillance data are not necessarily indicative of current infection risk. However, antibody responses to IAV infections cause a predictable antibody response, thus time of infection can be inferred from antibody levels in serological samples, enabling identification of risk factors of infection at estimated times of infection. Recent work demonstrates that these quantitative antibody methods (QAMs) can accurately recover infection dates, even when individual-level variation in antibody curves is moderately high. Also, the methodology can be implemented in a survival analysis (SA) framework to reduce bias from opportunistic sampling. Here we integrated QAMs and SA and applied this novel QAM-SA framework to understand the dynamics of IAV infection risk in wild pigs seasonally and spatially, and identify risk factors. We used national-scale IAV serosurveillance data from 15 US states. We found that infection risk was highest during January-March (54% of 61 estimated peaks), with 24% of estimated peaks occurring from May to July, and some low-level of infection risk occurring year-round. Time-varying IAV infection risk in wild pigs was positively correlated with humidity and IAV infection trends in domestic swine and humans, and did not show wave-like spatial spread of infection among states, nor more similar levels of infection risk among states with more similar meteorological conditions. Effects of host sex on IAV infection risk in wild pigs were generally not significant. Because most of the variation in infection risk was explained by state-level factors or infection risk at long-distances, our results suggested that predicting IAV infection risk in wild pigs is complicated by local ecological factors and potentially long-distance translocation of infection. In addition to revealing factors of IAV infection risk in wild pigs, our framework is broadly applicable for quantifying risk factors of disease transmission using opportunistic serosurveillance sampling, a common methodology in wildlife disease surveillance. Future research on the factors that determine individual-level antibody kinetics will facilitate the design of serosurveillance systems that can extract more accurate estimates of time-varying disease risk from quantitative antibody data.}, }
@article {pmid31246974, year = {2019}, author = {Michalska-Smith, MJ and Allesina, S}, title = {Telling ecological networks apart by their structure: A computational challenge.}, journal = {PLoS computational biology}, volume = {15}, number = {6}, pages = {e1007076}, pmid = {31246974}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Ecology/*methods ; *Ecosystem ; Machine Learning ; *Models, Biological ; *Symbiosis ; }, abstract = {Ecologists have been compiling ecological networks for over a century, detailing the interactions between species in a variety of ecosystems. To this end, they have built networks for mutualistic (e.g., pollination, seed dispersal) as well as antagonistic (e.g., herbivory, parasitism) interactions. The type of interaction being represented is believed to be reflected in the structure of the network, which would differ substantially between mutualistic and antagonistic networks. Here, we put this notion to the test by attempting to determine the type of interaction represented in a network based solely on its structure. We find that, although it is easy to separate different kinds of nonecological networks, ecological networks display much structural variation, making it difficult to distinguish between mutualistic and antagonistic interactions. We therefore frame the problem as a challenge for the community of scientists interested in computational biology and machine learning. We discuss the features a good solution to this problem should possess and the obstacles that need to be overcome to achieve this goal.}, }
@article {pmid31240840, year = {2019}, author = {Bastille-Rousseau, G and Wittemyer, G}, title = {Leveraging multidimensional heterogeneity in resource selection to define movement tactics of animals.}, journal = {Ecology letters}, volume = {22}, number = {9}, pages = {1417-1427}, doi = {10.1111/ele.13327}, pmid = {31240840}, issn = {1461-0248}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Behavior, Animal ; *Ecosystem ; *Elephants ; Geographic Information Systems ; Kenya ; *Motor Activity ; }, abstract = {Increasing interest in the complexity, variation and drivers of movement-related behaviours promise new insight into fundamental components of ecology. Resolving the multidimensionality of spatially explicit behaviour remains a challenge for investigating tactics and their relation to niche construction, but high-resolution movement data are providing unprecedented understanding of the diversity of spatially explicit behaviours. We introduce a framework for investigating individual variation in movement-defined resource selection that integrates the behavioural and ecological niche concepts. We apply it to long-term tracking data of 115 African elephants (Loxodonta africana), illustrating how a behavioural hypervolume can be defined based on differences between individuals and their ecological settings, and applied to explore population heterogeneity. While normative movement behaviour is frequently used to characterise population behaviour, we demonstrate the value of leveraging heterogeneity in the behaviour to gain greater insight into population structure and the mechanisms driving space-use tactics.}, }
@article {pmid31215647, year = {2019}, author = {Mencuccini, M and Rosas, T and Rowland, L and Choat, B and Cornelissen, H and Jansen, S and Kramer, K and Lapenis, A and Manzoni, S and Niinemets, Ü and Reich, P and Schrodt, F and Soudzilovskaia, N and Wright, IJ and Martínez-Vilalta, J}, title = {Leaf economics and plant hydraulics drive leaf : wood area ratios.}, journal = {The New phytologist}, volume = {224}, number = {4}, pages = {1544-1556}, doi = {10.1111/nph.15998}, pmid = {31215647}, issn = {1469-8137}, mesh = {Databases, Factual ; Plant Leaves/*physiology ; Trees/physiology ; Water/metabolism ; Wood/*physiology ; Xylem/physiology ; }, abstract = {Biomass and area ratios between leaves, stems and roots regulate many physiological and ecological processes. The Huber value Hv (sapwood area/leaf area ratio) is central to plant water balance and drought responses. However, its coordination with key plant functional traits is poorly understood, and prevents developing trait-based prediction models. Based on theoretical arguments, we hypothesise that global patterns in Hv of terminal woody branches can be predicted from variables related to plant trait spectra, that is plant hydraulics and size and leaf economics. Using a global compilation of 1135 species-averaged Hv , we show that Hv varies over three orders of magnitude. Higher Hv are seen in short small-leaved low-specific leaf area (SLA) shrubs with low Ks in arid relative to tall large-leaved high-SLA trees with high Ks in moist environments. All traits depend on climate but climatic correlations are stronger for explanatory traits than Hv . Negative isometry is found between Hv and Ks , suggesting a compensation to maintain hydraulic supply to leaves across species. This work identifies the major global drivers of branch sapwood/leaf area ratios. Our approach based on widely available traits facilitates the development of accurate models of above-ground biomass allocation and helps predict vegetation responses to drought.}, }
@article {pmid31188063, year = {2019}, author = {Laudadio, I and Fulci, V and Stronati, L and Carissimi, C}, title = {Next-Generation Metagenomics: Methodological Challenges and Opportunities.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {7}, pages = {327-333}, doi = {10.1089/omi.2019.0073}, pmid = {31188063}, issn = {1557-8100}, mesh = {Animals ; Big Data ; Biodiversity ; Computational Biology/methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiological Techniques ; Microbiology/trends ; Microbiota ; }, abstract = {Metagenomics is not only one of the newest omics system science technologies but also one that has arguably the broadest set of applications and impacts globally. Metagenomics has found vast utility not only in environmental sciences, ecology, and public health but also in clinical medicine and looking into the future, in planetary health. In line with the One Health concept, metagenomics solicits collaboration between molecular biologists, geneticists, microbiologists, clinicians, computational biologists, plant biologists, veterinarians, and other health care professionals. Almost every ecological niche of our planet hosts an extremely diverse community of organisms that are still poorly characterized. Detailed characterization of the features of such communities is instrumental to our comprehension of ecological, biological, and clinical complexity. This expert review article evaluates how metagenomics is improving our knowledge of microbiota composition from environmental to human samples. Furthermore, we offer an analysis of the common technical and methodological challenges and potential pitfalls arising from metagenomics approaches, such as metagenomics study design, data processing, and interpretation. All in all, at this critical juncture of further growth of the metagenomics field, it is time to critically reflect on the lessons learned and the future prospects of next-generation metagenomics science, technology, and conceivable applications, particularly from the standpoint of a metagenomics methodology perspective.}, }
@article {pmid31173423, year = {2019}, author = {Norton, BA and Bending, GD and Clark, R and Corstanje, R and Dunnett, N and Evans, KL and Grafius, DR and Gravestock, E and Grice, SM and Harris, JA and Hilton, S and Hoyle, H and Lim, E and Mercer, TG and Pawlett, M and Pescott, OL and Richards, JP and Southon, GE and Warren, PH}, title = {Urban meadows as an alternative to short mown grassland: effects of composition and height on biodiversity.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {29}, number = {6}, pages = {e01946}, pmid = {31173423}, issn = {1051-0761}, mesh = {*Biodiversity ; Ecosystem ; *Grassland ; Plants ; Soil ; }, abstract = {There are increasing calls to provide greenspace in urban areas, yet the ecological quality, as well as quantity, of greenspace is important. Short mown grassland designed for recreational use is the dominant form of urban greenspace in temperate regions but requires considerable maintenance and typically provides limited habitat value for most taxa. Alternatives are increasingly proposed, but the biodiversity potential of these is not well understood. In a replicated experiment across six public urban greenspaces, we used nine different perennial meadow plantings to quantify the relative roles of floristic diversity and height of sown meadows on the richness and composition of three taxonomic groups: plants, invertebrates, and soil microbes. We found that all meadow treatments were colonized by plant species not sown in the plots, suggesting that establishing sown meadows does not preclude further locally determined grassland development if management is appropriate. Colonizing species were rarer in taller and more diverse plots, indicating competition may limit invasion rates. Urban meadow treatments contained invertebrate and microbial communities that differed from mown grassland. Invertebrate taxa responded to changes in both height and richness of meadow vegetation, but most orders were more abundant where vegetation height was longer than mown grassland. Order richness also increased in longer vegetation and Coleoptera family richness increased with plant diversity in summer. Microbial community composition seems sensitive to plant species composition at the soil surface (0-10 cm), but in deeper soils (11-20 cm) community variation was most responsive to plant height, with bacteria and fungi responding differently. In addition to improving local residents' site satisfaction, native perennial meadow plantings can produce biologically diverse grasslands that support richer and more abundant invertebrate communities, and restructured plant, invertebrate, and soil microbial communities compared with short mown grassland. Our results suggest that diversification of urban greenspace by planting urban meadows in place of some mown amenity grassland is likely to generate substantial biodiversity benefits, with a mosaic of meadow types likely to maximize such benefits.}, }
@article {pmid31163047, year = {2019}, author = {Kaczensky, P and Khaliun, S and Payne, J and Boldgiv, B and Buuveibaatar, B and Walzer, C}, title = {Through the eye of a Gobi khulan - Application of camera collars for ecological research of far-ranging species in remote and highly variable ecosystems.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0217772}, pmid = {31163047}, issn = {1932-6203}, mesh = {Animals ; Behavior, Animal/physiology ; Circadian Rhythm/physiology ; *Ecosystem ; Equidae/*physiology ; *Geographic Information Systems ; Geography ; Humans ; Image Processing, Computer-Assisted ; Livestock ; Mongolia ; Photography/*instrumentation ; Rain ; *Remote Sensing Technology ; Species Specificity ; Water ; }, abstract = {The Mongolian Gobi-Eastern Steppe Ecosystem is one of the largest remaining natural drylands and home to a unique assemblage of migratory ungulates. Connectivity and integrity of this ecosystem are at risk if increasing human activities are not carefully planned and regulated. The Gobi part supports the largest remaining population of the Asiatic wild ass (Equus hemionus; locally called &quot;khulan&quot;). Individual khulan roam over areas of thousands of square kilometers and the scale of their movements is among the largest described for terrestrial mammals, making them particularly difficult to monitor. Although GPS satellite telemetry makes it possible to track animals in near-real time and remote sensing provides environmental data at the landscape scale, remotely collected data also harbors the risk of missing important abiotic or biotic environmental variables or life history events. We tested the potential of animal born camera systems (&quot;camera collars&quot;) to improve our understanding of the drivers and limitations of khulan movements. Deployment of a camera collar on an adult khulan mare resulted in 7,881 images over a one-year period. Over half of the images showed other khulan and 1,630 images showed enough of the collared khulan to classify the behaviour of the animals seen into several main categories. These khulan images provided us with: i) new insights into important life history events and grouping dynamics, ii) allowed us to calculate time budgets for many more animals than the collared khulan alone, and iii) provided us with a training dataset for calibrating data from accelerometer and tilt sensors in the collar. The images also allowed to document khulan behaviour near infrastructure and to obtain a day-time encounter rate between a specific khulan with semi-nomadic herders and their livestock. Lastly, the images allowed us to ground truth the availability of water by: i) confirming waterpoints predicted from other analyses, ii) detecting new waterpoints, and iii) compare precipitation records for rain and snow from landscape scale climate products with those documented by the camera collar. We discuss the added value of deploying camera collars on a subset of animals in remote, highly variable ecosystems for research and conservation.}, }
@article {pmid31150382, year = {2019}, author = {Boza, G and Worsley, SF and Yu, DW and Scheuring, I}, title = {Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability.}, journal = {PLoS computational biology}, volume = {15}, number = {5}, pages = {e1007109}, pmid = {31150382}, issn = {1553-7358}, mesh = {Animals ; Anti-Bacterial Agents/biosynthesis ; Computational Biology ; Ecosystem ; Host Microbial Interactions/*physiology ; Microbiota/*physiology ; Models, Biological ; Symbiosis/physiology ; }, abstract = {Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine 'private resources' with the ecological phenomenon known as 'community bistability' to favour some microbial strains over others. We briefly review evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotics to suppress non-beneficial, competitor strains, and (iii) provide resources that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. The faster early growth of preferred strains, combined with the phenomenon of 'community bistability,' allows those strains to continue to dominate the microbiome even after the private resource is withdrawn or made public. This is because after a beneficial colony reaches a sufficiently large size, it can resist invasion by parasites without further private support from the host. We further explicitly model localized microbial interactions and diffusion dynamics, and we show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that there is a wide range of parameters under which hosts can promote the assembly of a self-sustaining defensive microbiome. This in turn supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.}, }
@article {pmid31138696, year = {2019}, author = {Xu, L and Stige, LC and Leirs, H and Neerinckx, S and Gage, KL and Yang, R and Liu, Q and Bramanti, B and Dean, KR and Tang, H and Sun, Z and Stenseth, NC and Zhang, Z}, title = {Historical and genomic data reveal the influencing factors on global transmission velocity of plague during the Third Pandemic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {24}, pages = {11833-11838}, pmid = {31138696}, issn = {1091-6490}, mesh = {Animals ; Climate Change ; Databases, Factual ; Genome, Bacterial/*genetics ; Genomics/methods ; Humans ; Pandemics/*statistics &amp; numerical data ; Plague/*genetics/*transmission ; Virulence/*genetics ; Yersinia pestis/genetics ; }, abstract = {Quantitative knowledge about which natural and anthropogenic factors influence the global spread of plague remains sparse. We estimated the worldwide spreading velocity of plague during the Third Pandemic, using more than 200 years of extensive human plague case records and genomic data, and analyzed the association of spatiotemporal environmental factors with spreading velocity. Here, we show that two lineages, 2.MED and 1.ORI3, spread significantly faster than others, possibly reflecting differences among strains in transmission mechanisms and virulence. Plague spread fastest in regions with low population density and high proportion of pasture- or forestland, findings that should be taken into account for effective plague monitoring and control. Temperature exhibited a nonlinear, U-shaped association with spread speed, with a minimum around 20 °C, while precipitation showed a positive association. Our results suggest that global warming may accelerate plague spread in warm, tropical regions and that the projected increased precipitation in the Northern Hemisphere may increase plague spread in relevant regions.}, }
@article {pmid31133727, year = {2019}, author = {Piross, IS and Harnos, A and Rózsa, L}, title = {Rensch's rule in avian lice: contradictory allometric trends for sexual size dimorphism.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7908}, doi = {10.1038/s41598-019-44370-5}, pmid = {31133727}, issn = {2045-2322}, mesh = {Animals ; Birds/anatomy &amp; histology/*parasitology ; *Body Size ; Female ; Host-Parasite Interactions ; Male ; Parasites/*anatomy &amp; histology/classification/genetics ; Phthiraptera/*anatomy &amp; histology/classification/genetics ; Phylogeny ; *Sex Characteristics ; }, abstract = {Rensch's rule (RR) postulates that in comparisons across closely related species, male body size relative to female size increases with the average size of the species. This holds true in several vertebrate and also in certain free-living invertebrate taxa. Here, we document the validity of RR in avian lice using three families (Philopteridae, Menoponidae, and Ricinidae). Using published data on the body length of 989 louse species, subspecies, or distinct intraspecific lineages, we applied phylogenetic reduced major axis regression to analyse the body size of females vs. males while accounting for phylogenetic non-independence. Our results indicate that philopterid and menoponid lice follow RR, while ricinids exhibit the opposite pattern. In the case of philopterids and menoponids, we argue that larger-bodied bird species tend to host lice that are both larger in size and more abundant. Thus, sexual selection acting on males makes them relatively larger, and this is stronger than fecundity selection acting on females. Ricinids exhibit converse RR, likely because fecundity selection is stronger in their case.}, }
@article {pmid31128642, year = {2019}, author = {Blažek, J and Zukal, J and Bandouchova, H and Berková, H and Kovacova, V and Martínková, N and Pikula, J and Řehák, Z and Škrabánek, P and Bartonička, T}, title = {Numerous cold arousals and rare arousal cascades as a hibernation strategy in European Myotis bats.}, journal = {Journal of thermal biology}, volume = {82}, number = {}, pages = {150-156}, doi = {10.1016/j.jtherbio.2019.04.002}, pmid = {31128642}, issn = {0306-4565}, mesh = {Animals ; Arousal ; Behavior, Animal ; Body Temperature ; Chiroptera/*physiology ; Cold Temperature ; *Hibernation ; Seasons ; Torpor ; }, abstract = {Hibernating bats optimise the duration of torpor bouts and arousals in relation to hibernaculum microclimatic conditions and fat reserves. Clustering has significant physiological and ecological benefits, promoting successful hibernation of individuals. Such aggregations may help maintain optimal temperatures, allowing better energy utilisation than in solitarily bats. However, aroused bats in a cluster could conceivably disturb those still hibernating, starting an energy-demanding arousal process. Our study was conducted over two winters in two different hibernacula (cave and mine) in the Czech Republic, where Greater mouse-eared bats (Myotis myotis) have previously been diagnosed with white-nose syndrome. In 118 arousal episodes we recorded 193 individual arousals in which a warming phase was observed, 135 (69.9%) being cold arousals, where bats ceased increasing their body temperatures at ≤ 10 °C. The remaining arousals were standard normothermic arousals, where body (fur) surface temperatures reached > 20 °C. Cold arousals occurred during the mid- and late hibernation periods, suggesting they were a response to disturbance by a neighbour in the same cluster. Arousal cascades, where bats aroused in series, were rare (12.7%) and reached a maximum in mid-January. Our data suggest that Myotis bats prolong their torpor bouts using numerous cold arousals but few arousal cascades. Upon arrival of a bat, the clustered bats show tolerance to disturbing by conspecifics.}, }
@article {pmid31112783, year = {2019}, author = {Liu, YY and Jin, WT and Wei, XX and Wang, XQ}, title = {Cryptic speciation in the Chinese white pine (Pinus armandii): Implications for the high species diversity of conifers in the Hengduan Mountains, a global biodiversity hotspot.}, journal = {Molecular phylogenetics and evolution}, volume = {138}, number = {}, pages = {114-125}, doi = {10.1016/j.ympev.2019.05.015}, pmid = {31112783}, issn = {1095-9513}, mesh = {Alleles ; Base Sequence ; *Biodiversity ; Cell Nucleus/genetics ; China ; Databases, Genetic ; Gene Dosage ; Genes, Plant ; *Genetic Speciation ; Genetics, Population ; Geography ; Phylogeny ; Pinus/*genetics ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; RNA, Messenger/genetics/metabolism ; Species Specificity ; Transcriptome/genetics ; }, abstract = {Conifers are the largest and ecologically and economically most important component group of the gymnosperms. Despite their slow rate of molecular evolution, rapid and recent diversification was unexpectedly prevalent in this ancient group in the Hengduan Mountains, a world's biodiversity hotspot and gymnosperm diversity center in Southwest China. In this study, we investigated the underlying mechanisms and disentangled the interactions of geography and ecology in speciation and evolution in Pinus armandii, an important forest tree species endemic to China, by integrating analyses of population transcriptomics, population genetics and ecological niche modeling. Many lines of evidence suggest that cryptic speciation has occurred in P. armandii. During the process, geologically induced formation of Mount Gongga and other massive peaks might trigger the initial vicariance isolation of the northern and southern subdivisions, and ecologically based selection then reinforced their differentiation and local adaptation. Our ecological niche analysis and earlier reciprocal transplant experiments in P. armandii provided convincing evidences for the critical role of ecology in the process of speciation. These findings suggest that both geography and ecology contributed significantly to the abundance of very recent and rapid species divergences, which promoted the rising of the extremely high conifer diversity in the Hengduan Mountains.}, }
@article {pmid31086738, year = {2019}, author = {Warwick-Dugdale, J and Solonenko, N and Moore, K and Chittick, L and Gregory, AC and Allen, MJ and Sullivan, MB and Temperton, B}, title = {Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6800}, pmid = {31086738}, issn = {2167-8359}, abstract = {Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.}, }
@article {pmid31073136, year = {2019}, author = {Bátori, Z and Vojtkó, A and Maák, IE and Lőrinczi, G and Farkas, T and Kántor, N and Tanács, E and Kiss, PJ and Juhász, O and Módra, G and Tölgyesi, C and Erdős, L and Aguilon, DJ and Keppel, G}, title = {Karst dolines provide diverse microhabitats for different functional groups in multiple phyla.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7176}, doi = {10.1038/s41598-019-43603-x}, pmid = {31073136}, issn = {2045-2322}, mesh = {Animals ; Ants/*physiology ; Biodiversity ; Climate ; Ecosystem ; Humidity ; Hungary ; Temperature ; Tracheophyta/*physiology ; }, abstract = {Fine-scale topographic complexity creates important microclimates that can facilitate species to grow outside their main distributional range and increase biodiversity locally. Enclosed depressions in karst landscapes ('dolines') are topographically complex environments which produce microclimates that are drier and warmer (equator-facing slopes) and cooler and moister (pole-facing slopes and depression bottoms) than the surrounding climate. We show that the distribution patterns of functional groups for organisms in two different phyla, Arthropoda (ants) and Tracheophyta (vascular plants), mirror this variation of microclimate. We found that north-facing slopes and bottoms of solution dolines in northern Hungary provided key habitats for ant and plant species associated with cooler and/or moister conditions. Contrarily, south-facing slopes of dolines provided key habitats for species associated with warmer and/or drier conditions. Species occurring on the surrounding plateau were associated with intermediate conditions. We conclude that karst dolines provide a diversity of microclimatic habitats that may facilitate the persistence of taxa with diverse environmental preferences, indicating these dolines to be potential safe havens for multiple phyla under local and global climate oscillations.}, }
@article {pmid31071155, year = {2019}, author = {Hofman, MPG and Hayward, MW and Heim, M and Marchand, P and Rolandsen, CM and Mattisson, J and Urbano, F and Heurich, M and Mysterud, A and Melzheimer, J and Morellet, N and Voigt, U and Allen, BL and Gehr, B and Rouco, C and Ullmann, W and Holand, Ø and Jørgensen, NH and Steinheim, G and Cagnacci, F and Kroeschel, M and Kaczensky, P and Buuveibaatar, B and Payne, JC and Palmegiani, I and Jerina, K and Kjellander, P and Johansson, Ö and LaPoint, S and Bayrakcismith, R and Linnell, JDC and Zaccaroni, M and Jorge, MLS and Oshima, JEF and Songhurst, A and Fischer, C and Mc Bride, RT and Thompson, JJ and Streif, S and Sandfort, R and Bonenfant, C and Drouilly, M and Klapproth, M and Zinner, D and Yarnell, R and Stronza, A and Wilmott, L and Meisingset, E and Thaker, M and Vanak, AT and Nicoloso, S and Graeber, R and Said, S and Boudreau, MR and Devlin, A and Hoogesteijn, R and May-Junior, JA and Nifong, JC and Odden, J and Quigley, HB and Tortato, F and Parker, DM and Caso, A and Perrine, J and Tellaeche, C and Zieba, F and Zwijacz-Kozica, T and Appel, CL and Axsom, I and Bean, WT and Cristescu, B and Périquet, S and Teichman, KJ and Karpanty, S and Licoppe, A and Menges, V and Black, K and Scheppers, TL and Schai-Braun, SC and Azevedo, FC and Lemos, FG and Payne, A and Swanepoel, LH and Weckworth, BV and Berger, A and Bertassoni, A and McCulloch, G and Šustr, P and Athreya, V and Bockmuhl, D and Casaer, J and Ekori, A and Melovski, D and Richard-Hansen, C and van de Vyver, D and Reyna-Hurtado, R and Robardet, E and Selva, N and Sergiel, A and Farhadinia, MS and Sunde, P and Portas, R and Ambarli, H and Berzins, R and Kappeler, PM and Mann, GK and Pyritz, L and Bissett, C and Grant, T and Steinmetz, R and Swedell, L and Welch, RJ and Armenteras, D and Bidder, OR and González, TM and Rosenblatt, A and Kachel, S and Balkenhol, N}, title = {Right on track? Performance of satellite telemetry in terrestrial wildlife research.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216223}, pmid = {31071155}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Animals, Wild/*physiology ; *Ecosystem ; *Environmental Monitoring ; *Geographic Information Systems ; *Spacecraft ; *Telemetry ; }, abstract = {Satellite telemetry is an increasingly utilized technology in wildlife research, and current devices can track individual animal movements at unprecedented spatial and temporal resolutions. However, as we enter the golden age of satellite telemetry, we need an in-depth understanding of the main technological, species-specific and environmental factors that determine the success and failure of satellite tracking devices across species and habitats. Here, we assess the relative influence of such factors on the ability of satellite telemetry units to provide the expected amount and quality of data by analyzing data from over 3,000 devices deployed on 62 terrestrial species in 167 projects worldwide. We evaluate the success rate in obtaining GPS fixes as well as in transferring these fixes to the user and we evaluate failure rates. Average fix success and data transfer rates were high and were generally better predicted by species and unit characteristics, while environmental characteristics influenced the variability of performance. However, 48% of the unit deployments ended prematurely, half of them due to technical failure. Nonetheless, this study shows that the performance of satellite telemetry applications has shown improvements over time, and based on our findings, we provide further recommendations for both users and manufacturers.}, }
@article {pmid31067326, year = {2019}, author = {Fitak, RR and Antonides, JD and Baitchman, EJ and Bonaccorso, E and Braun, J and Kubiski, S and Chiu, E and Fagre, AC and Gagne, RB and Lee, JS and Malmberg, JL and Stenglein, MD and Dusek, RJ and Forgacs, D and Fountain-Jones, NM and Gilbertson, MLJ and Worsley-Tonks, KEL and Funk, WC and Trumbo, DR and Ghersi, BM and Grimaldi, W and Heisel, SE and Jardine, CM and Kamath, PL and Karmacharya, D and Kozakiewicz, CP and Kraberger, S and Loisel, DA and McDonald, C and Miller, S and O'Rourke, D and Ott-Conn, CN and Páez-Vacas, M and Peel, AJ and Turner, WC and VanAcker, MC and VandeWoude, S and Pecon-Slattery, J}, title = {The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise.}, journal = {The Journal of heredity}, volume = {110}, number = {3}, pages = {261-274}, doi = {10.1093/jhered/esz001}, pmid = {31067326}, issn = {1465-7333}, mesh = {Animal Diseases/epidemiology/*etiology/transmission ; Animals ; *Animals, Wild ; Biodiversity ; Biological Evolution ; Computational Biology/methods ; Disease Susceptibility ; Ecology ; Environment ; Genome ; *Genomics/methods ; Host-Pathogen Interactions/genetics ; Humans ; *Research ; }, abstract = {The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented &quot;Big Data&quot; tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural &quot;Genomics of Disease in Wildlife&quot; workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) &quot;Improving communication,&quot; 2) &quot;Methodological and analytical advancements,&quot; 3) &quot;Translation into practice,&quot; 4) &quot;Integrating landscape ecology and genomics,&quot; and 5) &quot;Emerging new questions.&quot; Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.}, }
@article {pmid31056485, year = {2019}, author = {Švec, P and Hönig, V and Zubriková, D and Wittmann, M and Pfister, K and Grubhoffer, L}, title = {The use of multi-criteria evaluation for the selection of study plots for monitoring of I. ricinus ticks - Example from Central Europe.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {4}, pages = {905-910}, doi = {10.1016/j.ttbdis.2019.04.014}, pmid = {31056485}, issn = {1877-9603}, mesh = {Altitude ; Animals ; Borrelia burgdorferi/isolation &amp; purification ; *Ecosystem ; Encephalitis Viruses, Tick-Borne/isolation &amp; purification ; Female ; Geographic Information Systems ; Geography ; Ixodes/*physiology ; Male ; Sampling Studies ; Tick-Borne Diseases/*epidemiology ; }, abstract = {Research projects in the field of eco-epidemiology of tick-borne diseases often require extensive sampling of arthropod vectors in the field. The aim of our study was to use geographical information systems (GIS) to select appropriate sampling sites of Ixodes ricinus ticks in central European habitat for further ecological studies of vector-borne pathogens (tick-borne encephalitis virus and Borrelia burgdorferi sensu lato). The model area was the Czech-German borderland (the region of South Bohemia and two regions in Germany: the Upper Palatinate and Lower Bavaria) where numerous human tick-borne encephalitis cases are reported annually. We prepared the sampling site design as a multi-criteria evaluation (MCE) task. In the GIS environment, we conducted MCE with a set of environmental, socio-economic and epidemiological data (altitude, vegetation cover, number of tick-borne encephalitis cases recorded in the past, tourist activity). The MCE classified the surveyed area into two classes: suitable for tick collection and unsuitable for tick collection. Subsequently, 50 tick sampling sites were randomly selected in the suitable area: 30 in South Bohemia (Czech Republic) and 20 in the Upper Palatinate and Lower Bavaria regions (Bavaria, Germany). The sampling sites were identified and surveyed in the field. The presence of ticks was confirmed by flagging at each of the selected plots. The described MCE system represents a versatile tool for semi-randomized design of tick sampling sites for research projects in the field of tick-borne pathogen ecology as well as for tick-borne pathogen surveillance programs run by local health authorities.}, }
@article {pmid31042745, year = {2019}, author = {Niku, J and Brooks, W and Herliansyah, R and Hui, FKC and Taskinen, S and Warton, DI}, title = {Efficient estimation of generalized linear latent variable models.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216129}, pmid = {31042745}, issn = {1932-6203}, mesh = {Algorithms ; Computer Simulation ; Data Interpretation, Statistical ; Likelihood Functions ; *Linear Models ; *Multivariate Analysis ; Software ; }, abstract = {Generalized linear latent variable models (GLLVM) are popular tools for modeling multivariate, correlated responses. Such data are often encountered, for instance, in ecological studies, where presence-absences, counts, or biomass of interacting species are collected from a set of sites. Until very recently, the main challenge in fitting GLLVMs has been the lack of computationally efficient estimation methods. For likelihood based estimation, several closed form approximations for the marginal likelihood of GLLVMs have been proposed, but their efficient implementations have been lacking in the literature. To fill this gap, we show in this paper how to obtain computationally convenient estimation algorithms based on a combination of either the Laplace approximation method or variational approximation method, and automatic optimization techniques implemented in R software. An extensive set of simulation studies is used to assess the performances of different methods, from which it is shown that the variational approximation method used in conjunction with automatic optimization offers a powerful tool for estimation.}, }
@article {pmid31031001, year = {2019}, author = {Gregory, AC and Zayed, AA and Conceição-Neto, N and Temperton, B and Bolduc, B and Alberti, A and Ardyna, M and Arkhipova, K and Carmichael, M and Cruaud, C and Dimier, C and Domínguez-Huerta, G and Ferland, J and Kandels, S and Liu, Y and Marec, C and Pesant, S and Picheral, M and Pisarev, S and Poulain, J and Tremblay, JÉ and Vik, D and ,  and Babin, M and Bowler, C and Culley, AI and de Vargas, C and Dutilh, BE and Iudicone, D and Karp-Boss, L and Roux, S and Sunagawa, S and Wincker, P and Sullivan, MB}, title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole.}, journal = {Cell}, volume = {177}, number = {5}, pages = {1109-1123.e14}, pmid = {31031001}, issn = {1097-4172}, support = {T32 AI112542/AI/NIAID NIH HHS/United States ; }, mesh = {Aquatic Organisms/*genetics ; *Biodiversity ; DNA Viruses/*genetics ; DNA, Viral/*genetics ; *Metagenome ; *Water Microbiology ; }, abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.}, }
@article {pmid31026273, year = {2019}, author = {Park, DS and Akuffo, AA and Muench, DE and Grimes, HL and Epling-Burnette, PK and Maini, PK and Anderson, ARA and Bonsall, MB}, title = {Clonal hematopoiesis of indeterminate potential and its impact on patient trajectories after stem cell transplantation.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006913}, pmid = {31026273}, issn = {1553-7358}, support = {R01 HL122661/HL/NHLBI NIH HHS/United States ; U54 CA193489/CA/NCI NIH HHS/United States ; P30 CA076292/CA/NCI NIH HHS/United States ; U01 CA232382/CA/NCI NIH HHS/United States ; I01 CX000114/CX/CSRD VA/United States ; }, mesh = {Animals ; Computational Biology ; Hematopoiesis/*physiology ; *Hematopoietic Stem Cells/cytology/physiology ; Humans ; Mice ; *Models, Biological ; Stem Cell Transplantation/*statistics &amp; numerical data ; }, abstract = {Clonal hematopoiesis of indeterminate potential (CHIP) is a recently identified process where older patients accumulate distinct subclones defined by recurring somatic mutations in hematopoietic stem cells. CHIP's implications for stem cell transplantation have been harder to identify due to the high degree of mutational heterogeneity that is present within the genetically distinct subclones. In order to gain a better understanding of CHIP and the impact of clonal dynamics on transplantation outcomes, we created a mathematical model of clonal competition dynamics. Our analyses highlight the importance of understanding competition intensity between healthy and mutant clones. Importantly, we highlight the risk that CHIP poses in leading to dominance of precancerous mutant clones and the risk of donor derived leukemia. Furthermore, we estimate the degree of competition intensity and bone marrow niche decline in mice during aging by using our modeling framework. Together, our work highlights the importance of better characterizing the ecological and clonal composition in hematopoietic donor populations at the time of stem cell transplantation.}, }
@article {pmid31024153, year = {2019}, author = {Jensen, EL and Clement, R and Kosta, A and Maberly, SC and Gontero, B}, title = {A new widespread subclass of carbonic anhydrase in marine phytoplankton.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2094-2106}, doi = {10.1038/s41396-019-0426-8}, pmid = {31024153}, issn = {1751-7370}, mesh = {Amino Acid Sequence ; Carbon/*metabolism ; Carbon Dioxide/*metabolism ; Carbonic Anhydrases/*genetics/metabolism ; Chloroplasts/enzymology/ultrastructure ; Coenzymes ; Databases, Nucleic Acid ; Diatoms/*enzymology/genetics/ultrastructure ; Geography ; Microscopy, Electron, Transmission ; Oceans and Seas ; Photosynthesis ; Phylogeny ; Phytoplankton/*enzymology/genetics/ultrastructure ; Sequence Alignment ; }, abstract = {Most aquatic photoautotrophs depend on CO2-concentrating mechanisms (CCMs) to maintain productivity at ambient concentrations of CO2, and carbonic anhydrase (CA) plays a key role in these processes. Here we present different lines of evidence showing that the protein LCIP63, identified in the marine diatom Thalassiosira pseudonana, is a CA. However, sequence analysis showed that it has a low identity with any known CA and therefore belongs to a new subclass that we designate as iota-CA. Moreover, LCIP63 unusually prefers Mn2+ to Zn2+ as a cofactor, which is potentially of ecological relevance since Mn2+ is more abundant than Zn2+ in the ocean. LCIP63 is located in the chloroplast and only expressed at low concentrations of CO2. When overexpressed using biolistic transformation, the rate of photosynthesis at limiting concentrations of dissolved inorganic carbon increased, confirming its role in the CCM. LCIP63 homologs are present in the five other sequenced diatoms and in other algae, bacteria, and archaea. Thus LCIP63 is phylogenetically widespread but overlooked. Analysis of the Tara Oceans database confirmed this and showed that LCIP63 is widely distributed in marine environments and is therefore likely to play an important role in global biogeochemical carbon cycling.}, }
@article {pmid31024020, year = {2019}, author = {Milleret, C and Ordiz, A and Sanz-Pérez, A and Uzal, A and Carricondo-Sanchez, D and Eriksen, A and Sand, H and Wabakken, P and Wikenros, C and Åkesson, M and Zimmermann, B}, title = {Testing the influence of habitat experienced during the natal phase on habitat selection later in life in Scandinavian wolves.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6526}, doi = {10.1038/s41598-019-42835-1}, pmid = {31024020}, issn = {2045-2322}, mesh = {Animals ; Behavior ; *Ecosystem ; Geographic Information Systems ; Geography ; Humans ; Models, Theoretical ; Principal Component Analysis ; Scandinavian and Nordic Countries ; Wolves/*physiology ; }, abstract = {Natal habitat preference induction (NHPI) occurs when characteristics of the natal habitat influence the future habitat selection of an animal. However, the influence of NHPI after the dispersal phase has received remarkably little attention. We tested whether exposure to humans in the natal habitat helps understand why some adult wolves Canis lupus may approach human settlements more than other conspecifics, a question of both ecological and management interest. We quantified habitat selection patterns within home ranges using resource selection functions and GPS data from 21 wolf pairs in Scandinavia. We identified the natal territory of each wolf with genetic parental assignment, and we used human-related characteristics within the natal territory to estimate the degree of anthropogenic influence in the early life of each wolf. When the female of the adult wolf pair was born in an area with a high degree of anthropogenic influence, the wolf pair tended to select areas further away from humans, compared to wolf pairs from natal territories with a low degree of anthropogenic influence. Yet the pattern was statistically weak, we suggest that our methodological approach can be useful in other systems to better understand NHPI and to inform management about human-wildlife interactions.}, }
@article {pmid31024009, year = {2019}, author = {Rund, SSC and Braak, K and Cator, L and Copas, K and Emrich, SJ and Giraldo-Calderón, GI and Johansson, MA and Heydari, N and Hobern, D and Kelly, SA and Lawson, D and Lord, C and MacCallum, RM and Roche, DG and Ryan, SJ and Schigel, D and Vandegrift, K and Watts, M and Zaspel, JM and Pawar, S}, title = {MIReAD, a minimum information standard for reporting arthropod abundance data.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {40}, doi = {10.1038/s41597-019-0042-5}, pmid = {31024009}, issn = {2052-4463}, support = {BB/N013573/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/International ; HHSN272201400029C/AI/NIAID NIH HHS/United States ; R01 AI136035/AI/NIAID NIH HHS/United States ; U01 CK000510/CK/NCEZID CDC HHS/United States ; R01 AI122284/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Arthropods/physiology ; Biodiversity ; Ecosystem ; Information Dissemination ; Information Storage and Retrieval/*standards ; Population Dynamics ; }, abstract = {Arthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the &quot;FAIR,&quot; (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests.}, }
@article {pmid31007605, year = {2019}, author = {Thomas, HJD and Myers-Smith, IH and Bjorkman, AD and Elmendorf, SC and Blok, D and Cornelissen, JHC and Forbes, BC and Hollister, RD and Normand, S and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Wilmking, M and Wipf, S and Cornwell, WK and Kattge, J and Goetz, SJ and Guay, KC and Alatalo, JM and Anadon-Rosell, A and Angers-Blondin, S and Berner, LT and Björk, RG and Buchwal, A and Buras, A and Carbognani, M and Christie, K and Siegwart Collier, L and Cooper, EJ and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Heijmans, MMPD and Hermanutz, L and Hudson, JMG and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Johnstone, JF and Kaarlejärvi, E and Kulonen, A and Lamarque, LJ and Lévesque, E and Little, CJ 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 Petraglia, A and Rumpf, SB and Semenchuk, PR and Soudzilovskaia, NA and Spasojevic, MJ and Speed, JDM and Tape, KD and Te Beest, M and Tomaselli, M and Trant, A and Treier, UA and Venn, S and Vowles, T and Weijers, S and Zamin, T and Atkin, OK and Bahn, M and Blonder, B and Campetella, G and Cerabolini, BEL and Chapin Iii, FS and Dainese, M and de Vries, FT and Díaz, S and Green, W and Jackson, RB and Manning, P and Niinemets, Ü and Ozinga, WA and Peñuelas, J and Reich, PB and Schamp, B and Sheremetev, S and van Bodegom, PM}, title = {Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome.}, journal = {Global ecology and biogeography : a journal of macroecology}, volume = {28}, number = {2}, pages = {78-95}, pmid = {31007605}, issn = {1466-822X}, abstract = {Aim: Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits.<br><br>Location: Tundra biome.<br><br>Time period: Data collected between 1964 and 2016.<br><br>Major taxa studied: 295 tundra vascular plant species.<br><br>Methods: We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits.<br><br>Results: Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression.<br><br>Main conclusions: Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra vegetation change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insights for ecological prediction and modelling.}, }
@article {pmid31002569, year = {2019}, author = {Memarzadeh, M and Boettiger, C}, title = {Resolving the Measurement Uncertainty Paradox in Ecological Management.}, journal = {The American naturalist}, volume = {193}, number = {5}, pages = {645-660}, doi = {10.1086/702704}, pmid = {31002569}, issn = {1537-5323}, mesh = {*Conservation of Natural Resources ; *Decision Support Techniques ; Ecology/*methods ; *Fisheries ; *Uncertainty ; }, abstract = {Ecological management and decision-making typically focus on uncertainty about the future, but surprisingly little is known about how to account for uncertainty of the present: that is, the realities of having only partial or imperfect measurements. Our primary paradigms for handling decisions under uncertainty-the precautionary principle and optimal control-have so far given contradictory results. This paradox is best illustrated in the example of fisheries management, where many ideas that guide thinking about ecological decision-making were first developed. We find that simplistic optimal control approaches have repeatedly concluded that a manager should increase catch quotas when faced with greater uncertainty about the fish biomass. Current best practices take a more precautionary approach, decreasing catch quotas by a fixed amount to account for uncertainty. Using comparisons to both simulated and historical catch data, we find that neither approach is sufficient to avoid stock collapses under moderate observational uncertainty. Using partially observed Markov decision process (POMDP) methods, we demonstrate how this paradox arises from flaws in the standard theory, which contributes to overexploitation of fisheries and increased probability of economic and ecological collapse. In contrast, we find that POMDP-based management avoids such overexploitation while also generating higher economic value. These results have significant implications for how we handle uncertainty in both fisheries and ecological management more generally.}, }
@article {pmid30980778, year = {2019}, author = {Bay, RA and Taylor, EB and Schluter, D}, title = {Parallel introgression and selection on introduced alleles in a native species.}, journal = {Molecular ecology}, volume = {28}, number = {11}, pages = {2802-2813}, doi = {10.1111/mec.15097}, pmid = {30980778}, issn = {1365-294X}, mesh = {*Alleles ; Animals ; Canada ; Gene Frequency/genetics ; Gene Ontology ; Geography ; *Inbreeding ; Oncorhynchus/genetics ; Polymorphism, Single Nucleotide/genetics ; *Selection, Genetic ; Species Specificity ; United States ; }, abstract = {As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that the degree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome-wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.}, }
@article {pmid30973867, year = {2019}, author = {Stone, L and Simberloff, D and Artzy-Randrup, Y}, title = {Network motifs and their origins.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006749}, pmid = {30973867}, issn = {1553-7358}, mesh = {Computational Biology ; Ecosystem ; Gene Regulatory Networks ; Humans ; Models, Biological ; Neural Networks, Computer ; Social Networking ; *Systems Biology ; }, abstract = {Modern network science is a new and exciting research field that has transformed the study of complex systems over the last 2 decades. Of particular interest is the identification of small &quot;network motifs&quot; that might be embedded in a larger network and that indicate the presence of evolutionary design principles or have an overly influential role on system-wide dynamics. Motifs are patterns of interconnections, or subgraphs, that appear in an observed network significantly more often than in compatible randomized networks. The concept of network motifs was introduced into Systems Biology by Milo, Alon and colleagues in 2002, quickly revolutionized the field, and it has had a huge impact in wider scientific domains ever since. Here, we argue that the same concept and tools for the detection of motifs were well known in the ecological literature decades into the last century, a fact that is generally not recognized. We review the early history of network motifs, their evolution in the mathematics literature, and their recent rediscoveries.}, }
@article {pmid30928035, year = {2019}, author = {Louro, R and Santos-Silva, C and Nobre, T}, title = {What is in a name? Terfezia classification revisited.}, journal = {Fungal biology}, volume = {123}, number = {4}, pages = {267-273}, doi = {10.1016/j.funbio.2019.01.003}, pmid = {30928035}, issn = {1878-6146}, mesh = {Ascomycota/*classification/*genetics/growth &amp; development ; Computational Biology ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; *Phylogeny ; *Terminology as Topic ; }, abstract = {Desert truffles (mycorrhizal hypogeous Ascomycota) are found in arid and semi-arid areas of the globe and have great ecological and economic importance. Terfezia is undoubtedly the most diversified of all desert truffle genera, but its taxonomy is far from resolved. Specifically, the large number of newly described species plus the high intraspecific morphological variability observed within some Terfezia lineages as rendered the use of molecular techniques mandatory for specimen's discrimination. But the subsequent increasing amount of sequence data produced also a huge number of undescribed taxa that required determination. We compiled and used the public available ITS data on Terfezia spp. on the custom-curated UNITE database to reconstruct the genus phylogeny. We found at least 17 distinct lineages within the genus and successfully resolved some of the more pressing taxonomic issues, namely the T. leptoderma/olbiensis complex and some misapplied synonymy. Based on this resolved phylogeny, and motivated by the recent new described species, we proposed an identification key to Terfezia genus highlighting the importance of morphological and ecological characterization.}, }
@article {pmid30927270, year = {2019}, author = {Fletcher, RJ and Hefley, TJ and Robertson, EP and Zuckerberg, B and McCleery, RA and Dorazio, RM}, title = {A practical guide for combining data to model species distributions.}, journal = {Ecology}, volume = {100}, number = {6}, pages = {e02710}, doi = {10.1002/ecy.2710}, pmid = {30927270}, issn = {1939-9170}, mesh = {Animals ; *Birds ; *Ecology ; Information Storage and Retrieval ; }, abstract = {Understanding and accurately modeling species distributions lies at the heart of many problems in ecology, evolution, and conservation. Multiple sources of data are increasingly available for modeling species distributions, such as data from citizen science programs, atlases, museums, and planned surveys. Yet reliably combining data sources can be challenging because data sources can vary considerably in their design, gradients covered, and potential sampling biases. We review, synthesize, and illustrate recent developments in combining multiple sources of data for species distribution modeling. We identify five ways in which multiple sources of data are typically combined for modeling species distributions. These approaches vary in their ability to accommodate sampling design, bias, and uncertainty when quantifying environmental relationships in species distribution models. Many of the challenges for combining data are solved through the prudent use of integrated species distribution models: models that simultaneously combine different data sources on species locations to quantify environmental relationships for explaining species distribution. We illustrate these approaches using planned survey data on 24 species of birds coupled with opportunistically collected eBird data in the southeastern United States. This example illustrates some of the benefits of data integration, such as increased precision in environmental relationships, greater predictive accuracy, and accounting for sample bias. Yet it also illustrates challenges of combining data sources with vastly different sampling methodologies and amounts of data. We provide one solution to this challenge through the use of weighted joint likelihoods. Weighted joint likelihoods provide a means to emphasize data sources based on different criteria (e.g., sample size), and we find that weighting improves predictions for all species considered. We conclude by providing practical guidance on combining multiple sources of data for modeling species distributions.}, }
@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}, 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 = {568}, number = {7750}, pages = {88-92}, doi = {10.1038/s41586-019-1048-z}, pmid = {30918402}, issn = {1476-4687}, mesh = {Agriculture/*statistics &amp; numerical data ; *Altitude ; Animals ; *Biodiversity ; *Ecosystem ; Humidity ; Microbiology ; Plants ; Rain ; Tanzania ; Temperature ; *Tropical Climate ; }, 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 {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}, mesh = {Acclimatization ; Animals ; Arthropods/*drug effects/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; *Epigenesis, Genetic ; *Gene Expression Regulation ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Insecticides/*adverse effects ; Pyrethrins/*adverse effects ; Reproduction/drug effects ; Soil ; }, 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 {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 = {25}, number = {6}, pages = {1922-1940}, doi = {10.1111/gcb.14619}, pmid = {30884039}, issn = {1365-2486}, mesh = {*Climate Change ; Ecosystem ; Plant Development ; Plant Leaves/physiology ; *Plant Physiological Phenomena ; Seasons ; Temperature ; }, 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 modeling 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 complicate the modeling 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 modeling, and on the scaling of phenology from species to landscape-level.}, }
@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}, pmid = {30883574}, issn = {1932-6203}, mesh = {*Climate Change ; Ecosystem ; *Models, Biological ; Temperature ; }, 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 {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}, 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 {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}, 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 {pmid30832740, year = {2019}, author = {Song, W and Wemheuer, B and Zhang, S and Steensen, K and Thomas, T}, title = {MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {36}, pmid = {30832740}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Databases, Genetic ; Drug Resistance, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Soil Microbiology ; }, abstract = {BACKGROUND: Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level.<br><br>RESULTS: Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms.<br><br>CONCLUSION: MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .}, }
@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 = {}, pmid = {30832282}, issn = {1660-4601}, mesh = {Biodiversity ; China ; Cities ; *City Planning ; *Conservation of Natural Resources ; *Ecosystem ; Humans ; *Mining ; }, 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 {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 = {}, 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 {pmid30739152, year = {2019}, author = {Robinson, KF and Fuller, AK and Stedman, RC and Siemer, WF and Decker, DJ}, title = {Integration of social and ecological sciences for natural resource decision making: challenges and opportunities.}, journal = {Environmental management}, volume = {63}, number = {5}, pages = {565-573}, pmid = {30739152}, issn = {1432-1009}, support = {WE-173-G//New York Federal Aid in Wildlife Restoration Grant/International ; }, mesh = {*Conservation of Natural Resources ; Decision Making ; Decision Support Techniques ; *Ecology ; Humans ; Natural Resources ; }, abstract = {The last 25 years have witnessed growing recognition that natural resource management decisions depend as much on understanding humans and their social interactions as on understanding the interactions between non-human organisms and their environment. Decision science provides a framework for integrating ecological and social factors into a decision, but challenges to integration remain. The decision-analytic framework elicits values and preferences to help articulate objectives, and then evaluates the outcomes of alternative management actions to achieve these objectives. Integrating social science into these steps can be hindered by failing to include social scientists as more than stakeholder-process facilitators, assuming that specific decision-analytic skills are commonplace for social scientists, misperceptions of social data as inherently qualitative, timescale mismatches for iterating through decision analysis and collecting relevant social data, difficulties in predicting human behavior, and failures of institutions to recognize the importance of this integration. We engage these challenges, and suggest solutions to them, helping move forward the integration of social and biological/ecological knowledge and considerations in decision-making.}, }
@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}, 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 {pmid30714190, year = {2019}, author = {Connors, KA and Beasley, A and Barron, MG and Belanger, SE and Bonnell, M and Brill, JL and de Zwart, D and Kienzler, A and Krailler, J and Otter, R and Phillips, JL and Embry, MR}, title = {Creation of a Curated Aquatic Toxicology Database: EnviroTox.}, journal = {Environmental toxicology and chemistry}, volume = {38}, number = {5}, pages = {1062-1073}, pmid = {30714190}, issn = {1552-8618}, support = {//Health and Environmental Sciences Institute Animal Alternatives in Environmental Risk Assessment Technical Committee/International ; }, mesh = {Animals ; Aquatic Organisms/drug effects ; *Databases, Factual ; *Ecotoxicology ; Risk Assessment ; Toxicity Tests, Acute ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Flexible, rapid, and predictive approaches that do not require the use of large numbers of vertebrate test animals are needed because the chemical universe remains largely untested for potential hazards. Development of robust new approach methodologies and nontesting approaches requires the use of existing information via curated, integrated data sets. The ecological threshold of toxicological concern (ecoTTC) represents one such new approach methodology that can predict a conservative de minimis toxicity value for chemicals with little or no information available. For the creation of an ecoTTC tool, a large, diverse environmental data set was developed from multiple sources, with harmonization, characterization, and information quality assessment steps to ensure that the information could be effectively organized and mined. The resulting EnviroTox database contains 91 217 aquatic toxicity records representing 1563 species and 4016 unique Chemical Abstracts Service numbers and is a robust, curated database containing high-quality aquatic toxicity studies that are traceable to the original information source. Chemical-specific information is also linked to each record and includes physico-chemical information, chemical descriptors, and mode of action classifications. Toxicity data are associated with the physico-chemical data, mode of action classifications, and curated taxonomic information for the organisms tested. The EnviroTox platform also includes 3 analysis tools: a predicted-no-effect concentration calculator, an ecoTTC distribution tool, and a chemical toxicity distribution tool. Although the EnviroTox database and tools were originally developed to support ecoTTC analysis and development, they have broader applicability to the field of ecological risk assessment. Environ Toxicol Chem 2019;9999:1-12. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.}, }
@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 = {35}, number = {4}, pages = {277-281}, doi = {10.1016/j.pt.2019.01.003}, pmid = {30713051}, issn = {1471-5007}, mesh = {*Biostatistics ; Parasitology/*methods ; *Software ; }, 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 {pmid30703281, year = {2019}, author = {Gill, BA and Musili, PM and Kurukura, S and Hassan, AA and Goheen, JR and Kress, WJ and Kuzmina, M and Pringle, RM and Kartzinel, TR}, title = {Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {838-846}, doi = {10.1111/1755-0998.13001}, pmid = {30703281}, issn = {1755-0998}, support = {//The Nature Conservancy/ ; DEB-1355122//National Science Foundation/ ; DEB-1457679//National Science Foundation/ ; DEB-1556728//National Science Foundation/ ; IOS-1656527//National Science Foundation/ ; Natural Sciences and Engineering Council Research Tools and Instruments Grant//National Science Foundation/ ; }, mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/*genetics ; DNA, Ribosomal Spacer ; *Databases, Genetic ; Grassland ; Kenya ; *Phylogeny ; Plant Proteins/genetics ; Plants/*classification/*genetics ; }, abstract = {Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA-barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL-F, trnH-psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%. We evaluated the ability of these markers, singly and in combination, to delimit species by calculating intra- and interspecific genetic distances. We further estimated a plant community phylogeny and demonstrated its utility by testing if evolutionary relatedness could predict the tendency of members of the Mpala plant community to have or lack &quot;barcode gaps&quot;, defined as disparities between the maximum intra- and minimum interspecific genetic distances. We found barcode gaps for 72%-89% of taxa depending on the marker or markers used. With the exception of the markers rbcL and ITS, we found that evolutionary relatedness was an important predictor of barcode-gap presence or absence for all of the markers in combination and for matK, trnL-F, and trnH-psbA individually. This plant DNA barcode library and community phylogeny will be a valuable resource for future investigations.}, }
@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}, pmid = {30695030}, issn = {1545-7885}, mesh = {Animals ; Big Data ; Computational Biology/methods ; Data Curation/*methods/*trends ; Humans ; Publications ; Reproducibility of Results ; Software ; Workflow ; }, 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 {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 {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}, pmid = {30651533}, issn = {2041-1723}, mesh = {Autotrophic Processes ; Biomass ; Biota/*physiology ; Energy Metabolism/*physiology ; Forests ; *Models, Biological ; Phytoplankton/*physiology ; Trees/*physiology ; }, 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 {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}, pmid = {30625219}, issn = {1932-6203}, mesh = {Altitude ; Animals ; Biodiversity ; Czech Republic ; Ecosystem ; Expert Systems ; Female ; Fuzzy Logic ; Male ; *Mobile Applications ; *Odonata/anatomy &amp; histology/classification ; Seasons ; Volunteers ; }, 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 {pmid30589896, year = {2018}, author = {Shimamoto, CY and Padial, AA and da Rosa, CM and Marques, MCM}, title = {Restoration of ecosystem services in tropical forests: A global meta-analysis.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208523}, pmid = {30589896}, issn = {1932-6203}, mesh = {Carbon/chemistry ; Databases, Factual ; Ecology ; *Ecosystem ; *Environmental Restoration and Remediation ; *Forests ; Soil/chemistry ; Tropical Climate ; }, abstract = {To reverse the effects of deforestation, tropical areas have expanded restoration efforts in recent years. As ecological restoration positively affects the structure and function of degraded ecosystems, understanding to what extent restoration recovers ecosystem services (ES) is an important step in directing large-scale restoration actions. We evaluated the effect of restoration in increasing the provision of ES in tropical forests. We performed a global meta-analysis of ecological indicators of the ES provided in restored areas, degraded areas and reference ecosystems. We tested for the effects of different restoration strategies, different types of degradation and for the effects of restoration over time. Overall, restoration actions contributed to a significant increase in levels of ecological indicators of ES (carbon pool, soil attributes and biodiversity protection) compared to disturbed areas. Among the restoration strategies, the natural regeneration was the most effective. Biodiversity protection and carbon recovered better than soil attributes. All other restoration strategies recovered ES to a substantially lesser degree, and reforestation with exotics decreased the ES of areas degraded by agriculture. In areas degraded by pasture, restoration was more effective in recovering the biodiversity protection, whereas in areas degraded by agriculture, the restoration recovered mainly the carbon pool. Our results show that by choosing the correct strategy, restoration can recover much of the ES lost by the degradation of tropical forests. These results should be considered for large-scale conservation and management efforts for this biome.}, }
@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}, 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 {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}, 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 {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}, mesh = {Brazil ; Carbon Sequestration ; Conservation of Natural Resources/*economics ; Cost-Benefit Analysis ; *Ecosystem ; }, 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 {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}, pmid = {30565882}, issn = {1755-0998}, support = {//Alfred P. Sloan Foundation/ ; 100956/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; DBI-1262645//National Science Foundation/ ; SS/05/01//Predator Free 2050/ ; R21AI130635/NH/NIH HHS/United States ; //College of Agriculture and Life Sciences, Cornell University/ ; R01 GM127418/GM/NIGMS NIH HHS/United States ; R21 AI130635/AI/NIAID NIH HHS/United States ; R01GM127418/NH/NIH HHS/United States ; }, 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 {pmid30540766, year = {2018}, author = {Taff, CC and Freeman-Gallant, CR and Streby, HM and Kramer, GR}, title = {Geolocator deployment reduces return rate, alters selection, and impacts demography in a small songbird.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207783}, pmid = {30540766}, issn = {1932-6203}, mesh = {Animal Migration/physiology ; Animals ; Behavior, Animal/physiology ; Breeding ; Conservation of Natural Resources/methods ; Demography/*methods ; Ecology/instrumentation/methods ; Geographic Information Systems/*instrumentation/trends ; Reproduction ; Seasons ; Songbirds/physiology ; }, abstract = {In the past few years, miniature light-level geolocators have been developed for tracking wild bird species that were previously too small to track during their full annual cycle. Geolocators offer an exciting opportunity to study the full annual cycle for many species. However, the potential detrimental effects of carrying geolocators are still poorly understood, especially for small-bodied birds. Here, we deployed light-level geolocators on common yellowthroat warblers (Geothlypis trichas). Over two years, we monitored return rates and neighborhood demography for 40 warblers carrying a geolocator and 20 reference birds that did not carry a geolocator. We compared the two groups with long-term data from 108 unmanipulated birds breeding at the same location in previous and subsequent years. Overall, we found that individuals carrying a geolocator were less likely to return to the study site in the following year (21% to 33% returned, depending on inclusion criteria) than either contemporaneous controls (55%) or long-term controls (55%). Among birds marked with geolocators, we also detected viability selection for greater wing length, whereas this pattern was not present in control birds. Finally, in each year after geolocator deployment, inexperienced breeders colonized vacant territories and this demographic effect persisted for two years after deployment. Sexual selection and ornamentation are strongly age-dependent in this system, and behavioral data collected after geolocator deployment is likely to differ systematically from natural conditions. Clearly geolocators will continue to be useful tools, but we suggest that future studies should carefully consider the potential for biased returns and the ecological validity of behavioral data collected from geolocator marked populations.}, }
@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 = {2019}, 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 = {100}, number = {2}, pages = {e02568}, pmid = {30499218}, issn = {0012-9658}, support = {GBMF4563//Gordon and Betty Moore Foundation/International ; //University of Florida Biodiversity Institute Graduate Research Fellowship/International ; }, mesh = {*Climate Change ; Longitudinal Studies ; *Models, Theoretical ; Seasons ; }, 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 potential trade-offs related to spatial scale, observer variance, and interannual variability. Here we explored this issue with phenology by comparing models built using data from the large-scale, citizen science USA National Phenology Network (USA-NPN) 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 data set. 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 data sets 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 chosen. Predictions for USA-NPN data had the lowest error when 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 data set can integrate parameters over a large spatial scale while those using an LTER data set can only estimate parameters for a single location. Accordingly, the choice of data set 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 data sets, 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 that integrate the strengths of both data sets.}, }
@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/International ; }, mesh = {Adult ; Afghan Campaign 2001- ; Exposure to Violence/psychology ; Female ; Humans ; Iraq War, 2003-2011 ; Longitudinal Studies ; Male ; *Resilience, Psychological ; Sex Factors ; Sex Offenses/psychology ; Social Environment ; Stress Disorders, Post-Traumatic/etiology/*psychology ; Surveys and Questionnaires ; United States/epidemiology ; Veterans/*psychology ; }, 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 {pmid30419993, year = {2019}, author = {Lozano-Jaramillo, M and Bastiaansen, JWM and Dessie, T and Komen, H}, title = {Use of geographic information system tools to predict animal breed suitability for different agro-ecological zones.}, journal = {Animal : an international journal of animal bioscience}, volume = {13}, number = {7}, pages = {1536-1543}, pmid = {30419993}, issn = {1751-732X}, mesh = {Animal Husbandry/instrumentation/*methods ; Animals ; Breeding/methods ; *Chickens ; *Environment ; Ethiopia ; Geographic Information Systems/*statistics &amp; numerical data ; }, abstract = {Predicting breed-specific environmental suitability has been problematic in livestock production. Native breeds have low productivity but are thought to be more robust to perform under local conditions than exotic breeds. Attempts to introduce genetically improved exotic breeds are generally unsuccessful, mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to determine its suitability to different locations. Here, we present a methodology to predict the suitability of breeds for different agro-ecological zones using Geographic Information Systems tools and predictive habitat distribution models. This methodology was tested on the current distribution of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Cross-validation results show this methodology to be effective in predicting breed suitability for specific environmental conditions. Furthermore, the model predicts suitable areas of the country where the breeds could be introduced. The specific climatic parameters that explained the potential distribution of each of the breeds were similar to the environment from which the breeds originated. This novel methodology finds application in livestock programs, allowing for a more informed decision when designing breeding programs and introduction programs, and increases our understanding of the role of the environment in livestock productivity.}, }
@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 {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}, 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 {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 = {U54 MD012388/MD/NIMHD NIH HHS/United States ; U54MD012388/MD/NIMHD NIH HHS/United States ; }, mesh = {Adult ; Female ; *Health Status Disparities ; Health Surveys ; Humans ; Male ; Morbidity ; *Prisoners ; Prisons ; *Social Determinants of Health ; 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 {pmid30409881, year = {2018}, author = {Kubelka, V and Šálek, M and Tomkovich, P and Végvári, Z and Freckleton, RP and Székely, T}, title = {Global pattern of nest predation is disrupted by climate change in shorebirds.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6415}, pages = {680-683}, doi = {10.1126/science.aat8695}, pmid = {30409881}, issn = {1095-9203}, mesh = {Animals ; Birds/*physiology ; *Climate Change ; Databases, Factual ; Nesting Behavior/*physiology ; Predatory Behavior/*physiology ; }, abstract = {Ongoing climate change is thought to disrupt trophic relationships, with consequences for complex interspecific interactions, yet the effects of climate change on species interactions are poorly understood, and such effects have not been documented at a global scale. Using a single database of 38,191 nests from 237 populations, we found that shorebirds have experienced a worldwide increase in nest predation over the past 70 years. Historically, there existed a latitudinal gradient in nest predation, with the highest rates in the tropics; however, this pattern has been recently reversed in the Northern Hemisphere, most notably in the Arctic. This increased nest predation is consistent with climate-induced shifts in predator-prey relationships.}, }
@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 Sillero, C 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 ; }, mesh = {Animals ; *Biological Evolution ; Canidae/*genetics ; *Gene Flow ; *Hybridization, Genetic ; *Phylogeny ; }, 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 {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 {pmid30269352, year = {2019}, author = {Saatkamp, A and Cochrane, A and Commander, L and Guja, LK and Jimenez-Alfaro, B and Larson, J and Nicotra, A and Poschlod, P and Silveira, FAO and Cross, AT and Dalziell, EL and Dickie, J and Erickson, TE and Fidelis, A and Fuchs, A and Golos, PJ and Hope, M and Lewandrowski, W and Merritt, DJ and Miller, BP and Miller, RG and Offord, CA and Ooi, MKJ and Satyanti, A and Sommerville, KD and Tangney, R and Tomlinson, S and Turner, S and Walck, JL}, title = {A research agenda for seed-trait functional ecology.}, journal = {The New phytologist}, volume = {221}, number = {4}, pages = {1764-1775}, doi = {10.1111/nph.15502}, pmid = {30269352}, issn = {1469-8137}, support = {R-90470-01//Commonwealth Scientific and Industrial Research Organisation/International ; }, mesh = {Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; Germination/*physiology ; Seed Dispersal/*physiology ; Seedlings/physiology ; Seeds/*physiology ; }, abstract = {Trait-based approaches have improved our understanding of plant evolution, community assembly and ecosystem functioning. A major challenge for the upcoming decades is to understand the functions and evolution of early life-history traits, across levels of organization and ecological strategies. Although a variety of seed traits are critical for dispersal, persistence, germination timing and seedling establishment, only seed mass has been considered systematically. Here we suggest broadening the range of morphological, physiological and biochemical seed traits to add new understanding on plant niches, population dynamics and community assembly. The diversity of seed traits and functions provides an important challenge that will require international collaboration in three areas of research. First, we present a conceptual framework for a seed ecological spectrum that builds upon current understanding of plant niches. We then lay the foundation for a seed-trait functional network, the establishment of which will underpin and facilitate trait-based inferences. Finally, we anticipate novel insights and challenges associated with incorporating diverse seed traits into predictive evolutionary ecology, community ecology and applied ecology. If the community invests in standardized seed-trait collection and the implementation of rigorous databases, major strides can be made at this exciting frontier of functional ecology.}, }
@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}, mesh = {Biometry ; Geographic Mapping ; *Global Warming ; Humidity ; Phenotype ; *Plant Physiological Phenomena ; Plants/*anatomy &amp; histology ; Soil/chemistry ; Spatio-Temporal Analysis ; Temperature ; *Tundra ; Water/analysis ; }, 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 {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 {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 {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}, mesh = {Evolution, Molecular ; Fungi/*genetics/*metabolism ; *Genome, Fungal ; Metabolic Networks and Pathways ; *Multigene Family ; *Phylogeny ; }, 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 = {2019}, 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 = {27}, number = {1}, pages = {51-63}, doi = {10.1016/j.tim.2018.08.006}, pmid = {30181062}, issn = {1878-4380}, mesh = {Bacteria/genetics/*virology ; Bacteriophages/genetics/*growth &amp; development ; *Host Specificity ; }, 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 {pmid30157296, year = {2018}, author = {Benedetti-Cecchi, L and Bulleri, F and Dal Bello, M and Maggi, E and Ravaglioli, C and Rindi, L}, title = {Hybrid datasets: integrating observations with experiments in the era of macroecology and big data.}, journal = {Ecology}, volume = {99}, number = {12}, pages = {2654-2666}, doi = {10.1002/ecy.2504}, pmid = {30157296}, issn = {0012-9658}, support = {PRA_2017_19//Università di Pisa/International ; RBFR12RXWL//Italian Ministry for Education, University and Research through project HI-BEF/International ; }, mesh = {*Big Data ; Ecology ; *Ecosystem ; Research ; }, abstract = {Understanding how increasing human domination of the biosphere affects life on earth is a critical research challenge. This task is facilitated by the increasing availability of open-source data repositories, which allow ecologists to address scientific questions at unprecedented spatial and temporal scales. Large datasets are mostly observational, so they may have limited ability to uncover causal relations among variables. Experiments are better suited at attributing causation, but they are often limited in scope. We propose hybrid datasets, resulting from the integration of observational with experimental data, as an approach to leverage the scope and ability to attribute causality in ecological studies. We show how the analysis of hybrid datasets with emerging techniques in time series analysis (Convergent Cross-mapping) and macroecology (Joint Species Distribution Models) can generate novel insights into causal effects of abiotic and biotic processes that would be difficult to achieve otherwise. We illustrate these principles with two case studies in marine ecosystems and discuss the potential to generalize across environments, species and ecological processes. If used wisely, the analysis of hybrid datasets may become the standard approach for research goals that seek causal explanations for large-scale ecological phenomena.}, }
@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}, mesh = {Acclimatization ; Carbon Sequestration ; *Climate Change ; *Ecosystem ; Environmental Monitoring/methods ; Seasons ; Spacecraft ; *Temperature ; Tibet ; Water ; }, 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}, mesh = {*Animal Distribution ; Animals ; Datasets as Topic ; Geography ; Insecta/*physiology ; Introduced Species/*statistics &amp; numerical data ; *Models, Biological ; *Plants ; Population Dynamics/statistics &amp; numerical data ; }, 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 {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 {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 {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 ; }, mesh = {Altitude ; Animals ; Bayes Theorem ; *Biodiversity ; Birds/*physiology ; Climate ; *Ecosystem ; Feeding Behavior ; Flowers/*physiology ; Fruit ; Insecta/*physiology ; Phylogeny ; Plants ; Research Design ; Species Specificity ; *Symbiosis ; Tanzania ; }, 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 {pmid30084019, year = {2018}, author = {Potgieter, LJ and Gaertner, M and Irlich, UM and O'Farrell, PJ and Stafford, L and Vogt, H and Richardson, DM}, title = {Managing Urban Plant Invasions: a Multi-Criteria Prioritization Approach.}, journal = {Environmental management}, volume = {62}, number = {6}, pages = {1168-1185}, pmid = {30084019}, issn = {1432-1009}, support = {85417//National Research Foundation/International ; }, mesh = {Agriculture ; Biodiversity ; Cities ; *Decision Support Techniques ; Ecology ; *Ecosystem ; Geographic Information Systems ; Introduced Species/*statistics &amp; numerical data ; *Plant Development ; South Africa ; }, abstract = {Alien plant invasions in urban areas can have considerable impact on biodiversity and ecosystem services (ES). Managing urban plant invasions is particularly challenging given the complex interactions between ecological, economic and social elements that exist in the urban milieu. Strategic landscape-scale insights are crucial for guiding management, as are tactical site-scale perspectives to plan and coordinate control efforts on the ground. Integrating these requirements to enhance management efficiency is a major challenge. Decision-support models have considerable potential for guiding and informing management strategies when problems are complex. This study uses multi-criteria decision tools to develop a prioritization framework for managing invasive alien plants (IAPs) in urban areas at landscape and local scales. We used the Analytic Hierarchy Process (AHP; a multi-criteria decision support model) to develop and rank criteria for prioritising IAP management in the City of Cape Town (CoCT), South Africa. Located within a global biodiversity hotspot, Cape Town has a long history of alien plant introductions and a complex socio-political make-up, creating a useful system to explore the challenges associated with managing urban plant invasions. To guide the prioritization of areas for IAP management across the CoCT, a stakeholder workshop was held to identify a goal and criteria for consideration, and to assess the relative importance given to each criterion in IAP management. Workshop attendees were drawn from multiple disciplines involved with different aspects of IAP research and management: government departments, scientists and researchers, and managers with a diverse set of skills and interests. We selected spatial datasets and applied our multi-criteria decision analysis in a Geographic Information System (GIS) to develop a landscape-scale prioritization map. To address issues relevant in an urban setting, we also modified an existing IAP management framework to develop a tactical (site-level) prioritization scheme for guiding on-the-ground control operations. High-priority sites for IAP management were identified at landscape- and local scales across the study area. Factors related to safety and security emerged as pivotal features for setting spatially-explicit priorities for management. The approach applied in this study can be useful for managers in all urban settings to guide the selection and prioritization of areas for IAP management.}, }
@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 {pmid30060110, year = {2018}, author = {Doering, JA and Lee, S and Kristiansen, K and Evenseth, L and Barron, MG and Sylte, I and LaLone, CA}, title = {In Silico Site-Directed Mutagenesis Informs Species-Specific Predictions of Chemical Susceptibility Derived From the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Tool.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {166}, number = {1}, pages = {131-145}, pmid = {30060110}, issn = {1096-0929}, support = {EPA999999//Intramural EPA/United States ; }, mesh = {Acetylcholinesterase/*genetics ; Amino Acid Sequence ; Amino Acids/*genetics ; Animals ; Computational Biology/*methods ; Computer Simulation ; Hazardous Substances/toxicity ; Humans ; Molecular Docking Simulation ; *Mutagenesis, Site-Directed ; Receptors, Steroid/*genetics ; Sequence Alignment ; Species Specificity ; Toxicity Tests/*methods ; }, abstract = {Chemical hazard assessment requires extrapolation of information from model organisms to all species of concern. The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed as a rapid, cost-effective method to aid cross-species extrapolation of susceptibility to chemicals acting on specific protein targets through evaluation of protein structural similarities and differences. The greatest resolution for extrapolation of chemical susceptibility across species involves comparisons of individual amino acid residues at key positions involved in protein-chemical interactions. However, a lack of understanding of whether specific amino acid substitutions among species at key positions in proteins affect interaction with chemicals made manual interpretation of alignments time consuming and potentially inconsistent. Therefore, this study used in silico site-directed mutagenesis coupled with docking simulations of computational models for acetylcholinesterase (AChE) and ecdysone receptor (EcR) to investigate how specific amino acid substitutions impact protein-chemical interaction. This study found that computationally derived substitutions in identities of key amino acids caused no change in protein-chemical interaction if residues share the same side chain functional properties and have comparable molecular dimensions, while differences in these characteristics can change protein-chemical interaction. These findings were considered in the development of capabilities for automatically generated species-specific predictions of chemical susceptibility in SeqAPASS. These predictions for AChE and EcR were shown to agree with SeqAPASS predictions comparing the primary sequence and functional domain sequence of proteins for more than 90% of the investigated species, but also identified dramatic species-specific differences in chemical susceptibility that align with results from standard toxicity tests. These results provide a compelling line of evidence for use of SeqAPASS in deriving screening level, species-specific, susceptibility predictions across broad taxonomic groups for application to human and ecological hazard assessment.}, }
@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 {pmid30054531, year = {2018}, author = {Simões, T and Novais, SC and Natal-da-Luz, T and Devreese, B and de Boer, T and Roelofs, D and Sousa, JP and van Straalen, NM and Lemos, MFL}, title = {An integrative omics approach to unravel toxicity mechanisms of environmental chemicals: effects of a formulated herbicide.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11376}, pmid = {30054531}, issn = {2045-2322}, support = {SFRH/BPD/94500/2013//Ministry of Education and Science | Funda&amp;#x00E7;&amp;#x00E3;o para a Ci&amp;#x00EA;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/International ; SFRH/BPD/110943/2015//Ministry of Education and Science | Funda&amp;#x00E7;&amp;#x00E3;o para a Ci&amp;#x00EA;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/International ; PTDC/AGR-PRO/3496/2012//Ministry of Education and Science | Funda&amp;#x00E7;&amp;#x00E3;o para a Ci&amp;#x00EA;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/International ; UID/MAR/04292/2013//Ministry of Education and Science | Funda&amp;#x00E7;&amp;#x00E3;o para a Ci&amp;#x00EA;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/International ; 604305//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/International ; }, mesh = {Animals ; Arthropods/drug effects/genetics ; Environmental Pollutants/*toxicity ; Gene Expression Regulation/drug effects ; Gene Ontology ; Gene Regulatory Networks/drug effects ; Genomics/*methods ; Herbicides/*toxicity ; RNA, Messenger/genetics/metabolism ; Reproduction/drug effects ; Survival Analysis ; *Toxicity Tests ; Transcriptome/genetics ; }, abstract = {The use of integrative molecular approaches can aid in a comprehensive understanding of the effects of toxicants at different levels of biological organization, also supporting risk assessment. The present study aims to unravel the toxicity mechanisms of a widely used herbicide to the arthropod Folsomia candida exposed in a natural soil, by linking effects on reproduction, proteomics and genome-wide gene expression. The EC50 effects on reproduction over 4 weeks was 4.63 mg glyphosate/kg of soil. The formulation included a polyethoxylated tallowamine as an adjuvant, which at 50% effect on reproduction had an estimated concentration of 0.87-1.49 mg/kg of soil. No effects were observed on survival and reproduction when using the isolated active substance, pointing the toxicity of the formulated product to the co-formulant instead of the active ingredient, glyphosate. RNA sequencing and shotgun proteomics were applied to assess differential transcript and protein expressions between exposed and control organisms in time, respectively. Specific functional categories at protein and transcriptome levels were concordant with each other, despite overall limited correlations between datasets. The exposure to this formulation affected normal cellular respiration and lipid metabolism, inducing oxidative stress and leading to impairment in biological life cycle mechanisms such as molting and reproduction.}, }
@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}, doi = {10.1016/S0140-6736(18)31224-8}, 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 {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 {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 {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 {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 = {2019}, 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 = {48}, number = {3}, pages = {251-263}, pmid = {29981010}, issn = {1654-7209}, support = {1639529//National Science Foundation/ ; }, mesh = {Cities ; Decision Making ; *Ecology ; Food ; Humans ; *Water ; }, 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 {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 {pmid29934651, year = {2018}, author = {Lane, BA and Sandoval-Solis, S and Stein, ED and Yarnell, SM and Pasternack, GB and Dahlke, HE}, title = {Beyond Metrics? The Role of Hydrologic Baseline Archetypes in Environmental Water Management.}, journal = {Environmental management}, volume = {62}, number = {4}, pages = {678-693}, pmid = {29934651}, issn = {1432-1009}, mesh = {California ; *Climate Change ; Conservation of Water Resources/*methods ; Databases, Factual ; Environmental Monitoring/*methods ; Humans ; *Hydrology ; Rivers ; Water Movements ; Water Resources/*supply &amp; distribution ; Water Supply/standards/*statistics &amp; numerical data ; }, abstract = {Balancing ecological and human water needs often requires characterizing key aspects of the natural flow regime and then predicting ecological response to flow alterations. Flow metrics are generally relied upon to characterize long-term average statistical properties of the natural flow regime (hydrologic baseline conditions). However, some key aspects of hydrologic baseline conditions may be better understood through more complete consideration of continuous patterns of daily, seasonal, and inter-annual variability than through summary metrics. Here we propose the additional use of high-resolution dimensionless archetypes of regional stream classes to improve understanding of baseline hydrologic conditions and inform regional environmental flows assessments. In an application to California, we describe the development and analysis of hydrologic baseline archetypes to characterize patterns of flow variability within and between stream classes. We then assess the utility of archetypes to provide context for common flow metrics and improve understanding of linkages between aquatic patterns and processes and their hydrologic controls. Results indicate that these archetypes may offer a distinct and complementary tool for researching mechanistic flow-ecology relationships, assessing regional patterns for streamflow management, or understanding impacts of changing climate.}, }
@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 = {R35 GM124774/GM/NIGMS NIH HHS/United States ; 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 {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 {pmid29855518, year = {2018}, author = {Grüss, A and Biggs, C and Heyman, WD and Erisman, B}, title = {Prioritizing monitoring and conservation efforts for fish spawning aggregations in the U.S. Gulf of Mexico.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8473}, doi = {10.1038/s41598-018-26898-0}, pmid = {29855518}, issn = {2045-2322}, mesh = {Animals ; *Conservation of Water Resources ; Databases, Factual ; Ecosystem ; Fishes/*physiology ; Gulf of Mexico ; Linear Models ; United States ; }, abstract = {In the U.S. Gulf of Mexico (U.S. GOM), the identification and characterization of transient fish spawning aggregation (FSA) sites is recognized as a regional priority for conservation, but progress is hindered by a lack of understanding of FSA distributions for most exploited species. We employed information compiled in regional databases on FSAs and monitoring for the U.S. GOM to fit species distribution models and produce maps showing the areas likely to host single- and multi-species transient FSA sites. Our results revealed two distinct regions of the U.S. GOM for prioritizing monitoring and conservation efforts for transient FSAs: the coastal waters surrounding major bay systems, particularly those of Texas and Louisiana, and portions of the continental shelf edge (the Flower Garden Banks area and the West Florida shelf edge). The next step would be to locate and characterize actual transient FSA sites in the U.S. GOM by surveying within the areas we identified.}, }
@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}, mesh = {*Biota ; *Ecosystem ; Prevalence ; }, 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 {pmid29736767, year = {2018}, author = {Hale, BW}, title = {Mapping Potential Environmental Impacts from Tourists Using Data from Social Media: A Case Study in the Westfjords of Iceland.}, journal = {Environmental management}, volume = {62}, number = {3}, pages = {446-457}, pmid = {29736767}, issn = {1432-1009}, support = {IZK0Z2_171645//Swiss National Science Foundation/Switzerland ; }, mesh = {Ecology ; *Environment ; Estuaries ; Geographic Information Systems ; Humans ; Iceland ; *Social Media ; *Travel ; }, abstract = {With tourism increasing in remote regions, it is important to be able to estimate potential environmental impacts from the tourists in order to plan and manage natural areas. This study combines measures of ecological sensitivity with data from publicly available geotagged photographs posted on the social media site Flickr to assess the vulnerability of the locations frequented by foreign tourists in the Westfjords region of Iceland between 2014 and 2016. The results suggest that tourists cluster primarily around six hotspots that represented some of the major known tourist destinations of the region. Although tourists generally frequented areas with lower ecological sensitivity and rarely went far beyond the main roads, one of the hotspots was in an area of higher ecological sensitivity. Further, tourists also appeared to have higher intensity stays when they entered areas of higher ecological sensitivity. Overall, these findings highlight the usefulness of combining data from social media in assessing potential environmental impacts of tourism. However, natural resource managers should be aware of limitations in the use of such data.}, }
@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 {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}, mesh = {Animal Welfare/*standards ; Animals ; Aquaculture/*standards ; Biomedical Research/standards ; European Union ; *Fishes ; Laboratory Animal Science/*standards ; }, 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 {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 {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 ; T32 AI007528/AI/NIAID 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 {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 {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 {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 = {UL1 TR001409/TR/NCATS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; DP2 GM123485/GM/NIGMS NIH HHS/United States ; R35 GM122547/GM/NIGMS NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; R01 GM089753/GM/NIGMS NIH HHS/United States ; R21 CA220398/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Biomedical Research/methods/*trends ; Biomedical Technology/*trends ; Decision Making ; Deep Learning/*trends ; Delivery of Health Care/methods/trends ; Disease/genetics ; Drug Design ; Electronic Health Records/trends ; Humans ; Terminology as Topic ; }, 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 {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 {pmid29599464, year = {2018}, author = {Muška, M and Tušer, M and Frouzová, J and Mrkvička, T and Ricard, D and Seďa, J and Morelli, F and Kubečka, J}, title = {Real-time distribution of pelagic fish: combining hydroacoustics, GIS and spatial modelling at a fine spatial scale.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5381}, pmid = {29599464}, issn = {2045-2322}, mesh = {Acoustics ; Animals ; Ecosystem ; Environmental Monitoring ; Fishes/*physiology ; Geographic Information Systems ; Population Dynamics ; *Spatial Analysis ; }, abstract = {Understanding spatial distribution of organisms in heterogeneous environment remains one of the chief issues in ecology. Spatial organization of freshwater fish was investigated predominantly on large-scale, neglecting important local conditions and ecological processes. However, small-scale processes are of an essential importance for individual habitat preferences and hence structuring trophic cascades and species coexistence. In this work, we analysed the real-time spatial distribution of pelagic freshwater fish in the Římov Reservoir (Czechia) observed by hydroacoustics in relation to important environmental predictors during 48 hours at 3-h interval. Effect of diurnal cycle was revealed of highest significance in all spatial models with inverse trends between fish distribution and predictors in day and night in general. Our findings highlighted daytime pelagic fish distribution as highly aggregated, with general fish preferences for central, deep and highly illuminated areas, whereas nighttime distribution was more disperse and fish preferred nearshore steep sloped areas with higher depth. This turnover suggests prominent movements of significant part of fish assemblage between pelagic and nearshore areas on a diel basis. In conclusion, hydroacoustics, GIS and spatial modelling proved as valuable tool for predicting local fish distribution and elucidate its drivers, which has far reaching implications for understanding freshwater ecosystem functioning.}, }
@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}, mesh = {*Biological Evolution ; Ecology ; Phenotype ; *Plant Leaves ; Plant Physiological Phenomena ; Plants ; }, 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 {pmid29491180, year = {2018}, author = {Reeves, DB and Magaret, AS and Greninger, AL and Johnston, C and Schiffer, JT}, title = {Model-based estimation of superinfection prevalence from limited datasets.}, journal = {Journal of the Royal Society, Interface}, volume = {15}, number = {139}, pages = {}, pmid = {29491180}, issn = {1742-5662}, mesh = {*Databases, Factual ; Female ; HIV Infections/*epidemiology ; *HIV-1 ; Herpes Genitalis/*epidemiology ; *Herpesvirus 2, Human ; Humans ; Male ; *Models, Biological ; Prevalence ; Superinfection/*epidemiology ; }, abstract = {Humans can be infected sequentially by different strains of the same virus. Estimating the prevalence of so-called 'superinfection' for a particular pathogen is vital because superinfection implies a failure of immunologic memory against a given virus despite past exposure, which may signal challenges for future vaccine development. Increasingly, viral deep sequencing and phylogenetic inference can discriminate distinct strains within a host. Yet, a population-level study may misrepresent the true prevalence of superinfection for several reasons. First, certain infections such as herpes simplex virus (HSV-2) only reactivate single strains, making multiple samples necessary to detect superinfection. Second, the number of samples collected in a study may be fewer than the actual number of independently acquired strains within a single person. Third, detecting strains that are relatively less abundant can be difficult, even for other infections such as HIV-1 where deep sequencing may identify multiple strains simultaneously. Here we develop a model of superinfection inspired by ecology. We define an infected individual's richness as the number of infecting strains and use ecological evenness to quantify the relative strain abundances. The model uses an EM methodology to infer the true prevalence of superinfection from limited clinical datasets. Simulation studies with known true prevalence are used to contrast our EM method to a standard (naive) calculation. While varying richness, evenness and sampling we quantify the accuracy and precision of our method. The EM method outperforms in all cases, particularly when sampling is low, and richness or unevenness is high. Here, sensitivity to our assumptions about clinical data is considered. The simulation studies also provide insight into optimal study designs; estimates of prevalence improve equally by enrolling more participants or gathering more samples per person. Finally, we apply our method to data from published studies of HSV-2 and HIV-1 superinfection.}, }
@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 {pmid29431888, year = {2018}, author = {Hackett, SC and Bonsall, MB}, title = {Management of a stage-structured insect pest: an application of approximate optimization.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {28}, number = {4}, pages = {938-952}, doi = {10.1002/eap.1700}, pmid = {29431888}, issn = {1051-0761}, support = {BB/H01814X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Ceratitis capitata ; *Decision Support Techniques ; Female ; Insecticides/*economics ; Male ; Models, Biological ; Pest Control, Biological/*economics ; }, abstract = {Ecological decision problems frequently require the optimization of a sequence of actions over time where actions may have both immediate and downstream effects. Dynamic programming can solve such problems only if the dimensionality is sufficiently low. Approximate dynamic programming (ADP) provides a suite of methods applicable to problems of arbitrary complexity at the expense of guaranteed optimality. The most easily generalized method is the look-ahead policy: a brute-force algorithm that identifies reasonable actions by constructing and solving a series of temporally truncated approximations of the full problem over a defined planning horizon. We develop and apply this approach to a pest management problem inspired by the Mediterranean fruit fly, Ceratitis capitata. The model aims to minimize the cumulative costs of management actions and medfly-induced losses over a single 16-week season. The medfly population is stage-structured and grows continuously while management decisions are made at discrete, weekly intervals. For each week, the model chooses between inaction, insecticide application, or one of six sterile insect release ratios. Look-ahead policy performance is evaluated over a range of planning horizons, two levels of crop susceptibility to medfly and three levels of pesticide persistence. In all cases, the actions proposed by the look-ahead policy are contrasted to those of a myopic policy that minimizes costs over only the current week. We find that look-ahead policies always out-performed a myopic policy and decision quality is sensitive to the temporal distribution of costs relative to the planning horizon: it is beneficial to extend the planning horizon when it excludes pertinent costs. However, longer planning horizons may reduce decision quality when major costs are resolved imminently. ADP methods such as the look-ahead-policy-based approach developed here render questions intractable to dynamic programming amenable to inference but should be applied carefully as their flexibility comes at the expense of guaranteed optimality. However, given the complexity of many ecological management problems, the capacity to propose a strategy that is &quot;good enough&quot; using a more representative problem formulation may be preferable to an optimal strategy derived from a simplified model.}, }
@article {pmid29426939, year = {2018}, author = {Sablok, G and Hayward, RJ and Davey, PA and Santos, RP and Schliep, M and Larkum, A and Pernice, M and Dolferus, R and Ralph, PJ}, title = {SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2749}, pmid = {29426939}, issn = {2045-2322}, mesh = {Aquatic Organisms/*classification/*genetics ; *Databases, Genetic ; Marine Biology ; Phylogeny ; Plants/*classification/*genetics ; Transcriptome/genetics ; }, abstract = {Seagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php .}, }
@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 {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 {pmid29332298, year = {2018}, author = {Garay, J and Cressman, R and Móri, TF and Varga, T}, title = {The ESS and replicator equation in matrix games under time constraints.}, journal = {Journal of mathematical biology}, volume = {76}, number = {7}, pages = {1951-1973}, pmid = {29332298}, issn = {1432-1416}, support = {K 108615//Hungarian National Research, Development and Innovation Office NKFIH/International ; GINOP 2.3.2-15-2016-00057//Hungarian National Research, Development and Innovation Office NKFIH/International ; 690817//Horizon 2020: The EU Framework Programme for Research and Innovation, Marie Skłodowska-Curie Actions/International ; 690817//Horizon 2020: The EU Framework Programme for Research and Innovation, Marie Skłodowska-Curie Actions/International ; }, mesh = {Animals ; *Biological Evolution ; Computational Biology ; Ecosystem ; *Game Theory ; Humans ; Mathematical Concepts ; *Models, Biological ; Mutation ; Phenotype ; Population Dynamics ; Time Factors ; }, abstract = {Recently, we introduced the class of matrix games under time constraints and characterized the concept of (monomorphic) evolutionarily stable strategy (ESS) in them. We are now interested in how the ESS is related to the existence and stability of equilibria for polymorphic populations. We point out that, although the ESS may no longer be a polymorphic equilibrium, there is a connection between them. Specifically, the polymorphic state at which the average strategy of the active individuals in the population is equal to the ESS is an equilibrium of the polymorphic model. Moreover, in the case when there are only two pure strategies, a polymorphic equilibrium is locally asymptotically stable under the replicator equation for the pure-strategy polymorphic model if and only if it corresponds to an ESS. Finally, we prove that a strict Nash equilibrium is a pure-strategy ESS that is a locally asymptotically stable equilibrium of the replicator equation in n-strategy time-constrained matrix games.}, }
@article {pmid29318843, year = {2017}, author = {Xiao, JL and Zhang, XB and Liu, YC and Li, M and Li, B and Shan, YQ and Qu, XB}, title = {[Quality of Schisandrae Chinensis Fructus regionalization based on GIS technology].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {22}, pages = {4408-4413}, doi = {10.19540/j.cnki.cjcmm.2017.0192}, pmid = {29318843}, issn = {1001-5302}, mesh = {China ; Drugs, Chinese Herbal/*standards ; Fruit/chemistry ; *Geographic Information Systems ; Plants, Medicinal/chemistry ; Quality Control ; Schisandra/*chemistry ; }, abstract = {This paper is aims to clarify the spatial distribution of high quality medicinal materials Schisandrae Chinensis Fructus. Based on investigation and field investigation, the samples and distribution information of Schisandrae Chinensis Fructus were collected. Based on the data of four kinds of lignin chemical constituents, ecological environment factors and spatial distribution data of Schisandrae Chinensis Fructus, using GIS technology, maximum information entropy model and SPSS statistical analysis method for regionalizing the quality of Schisandrae Chinensis Fructus. The results showed that Schisandrae Chinensis Fructus was mainly distributed in the northeast of Liaoning, east of Jilin, east of Heilongjiang. The content of schisandrin was higher in the samples from northeastern part of Jilin province and the northeastern part of Liaoning province, The content of deoxyschizandrin was higher in the samples from middle of Jilin province and northeastern Hebei province, where the content of schisandrin B was higher in the samples from Jilin area, The higher schisantherin A sample were from southeast of Jilin and northeast of Liaoning. Considering the content of four components in Schisandrae Chinensis Fructus, the quality of Schisandrae Chinensis Fructus was concentrated in the southeast of Jilin and the northeastern part of Liaoning.}, }
@article {pmid29318840, year = {2017}, author = {Dong, YB and Luo, Y and Zhu, C and Peng, WF and Xu, XL and Fang, QM}, title = {[Application of remote sensing and GIS in study of suitability distribution of Swertia mussotii, a Tibetan medicine in Sichuan province].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {22}, pages = {4387-4394}, doi = {10.19540/j.cnki.cjcmm.2017.0189}, pmid = {29318840}, issn = {1001-5302}, mesh = {China ; Ecology ; *Geographic Information Systems ; Medicine, Tibetan Traditional ; *Plant Dispersal ; Plants, Medicinal/growth &amp; development ; *Remote Sensing Technology ; Swertia/*growth &amp; development ; }, abstract = {Swertia mussotii is a kind of rare medicinal materials, the relevant researches are mainly concentrated on its medicinal efficacy and medicinal value till now, researches of adaptive distribution by applying remote sensing and GIS are relatively less. This study is to analyze the adaptive distribution of S.mussotii in Sichuan province by applying remote sensing and GIS technology, and provide scientific basis for the protection and development of wild resources, artificial cultivation and adjustment of Chinese medicine industrial distribution in Sichuan province. Based on literature review and ecological factors such as altitude, annual precipitation and annual average temperature, this study extracted ecological factors, overlay analysis in GIS, as well as combining GPS field validation data by means of remote sensing and GIS, discusses the adaptive distribution of SMF sin Sichuan province. ①The area of adaptive distribution of S. mussotii in Sichuan province is 1 543.749 km², mainly in Dege county, Ganzi county, Daofu county, Kangding county, Barkam, Jinchuan county, Xiaojin county, Danba county, Daocheng county, Xiangcheng county, Xinlong county, Aba county, Muli county and other counties and cities, accounts for about 7.25% in total area. ② Combining statistical information and field validation, this study found that S. mussotii adaptive distribution gained by remote sensing and GIS is in conformity with its actual distribution. The study shows that remote sensing and GIS technology are feasible to obtain the S. mussotii adaptive distribution, they can further be applied to studies on adaptive distributions of other rare Chinese medicinal herb.}, }
@article {pmid29318837, year = {2017}, author = {Wu, XJ and Zhang, XB and Guo, LP and Yu, Y and Huang, LQ}, title = {[Study on distribution division of Codonopsis Radix].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {22}, pages = {4368-4372}, doi = {10.19540/j.cnki.cjcmm.2017.0186}, pmid = {29318837}, issn = {1001-5302}, mesh = {Altitude ; China ; Codonopsis/*growth &amp; development ; Ecology ; Geographic Information Systems ; *Plant Dispersal ; Plants, Medicinal/*growth &amp; development ; }, abstract = {This paper is aimed to clarify the distribution of Codonopsis Radix in China and search the main ecological factors that affect the suitability distribution. Through literature reading, National Specimen Information Infrastructure researching, field investigation and general survey of Chinese medicine resources, the distribution information was acquired. The MaxEnt model and ArcGIS technology were applied to analyze the main environmental factors influencing the suitability of Codonopsis Radix with integrated 55 environmental factors. The results showed the precipitation and altitude were the major factors impacting the ecology suitable of Codonopsis Radix. The ecological suitable region of C. pilosula was mainly concentrated in south Gansu, Shanxi, Shanxi, Ningxia and, and the ecological suitable region of C. pilosula var. modesta was mainly concentrated in south Gansu, northwest Guizhou, northeast Sichuan, and the ecological suitable region of C. tangshen was mainly concentrated in west Hubei, east Chongqing, middle Sichuan. Combined with the investigation and cultivation of Codonopsis Radix distribution information, the results of ecological suitability of Codonopsis Radix were verified. The ecological suitability distribution result of Codonopsis Radix was consistent with each species actual distribution, which could provide scientific basis for carrying out the rational cultivation of Codonopsis Radix.}, }
@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 {pmid29247477, year = {2018}, author = {Haas, TC and Ferreira, SM}, title = {Finding politically feasible conservation policies: the case of wildlife trafficking.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {28}, number = {2}, pages = {473-494}, doi = {10.1002/eap.1662}, pmid = {29247477}, issn = {1051-0761}, mesh = {Animals ; Commerce ; Conservation of Natural Resources/*legislation &amp; jurisprudence ; *Decision Support Techniques ; *Perissodactyla ; Politics ; Population Dynamics ; South Africa ; Uncertainty ; }, abstract = {Conservation management is of increasing importance in ecology as most ecosystems nowadays are essentially managed ecosystems. Conservation managers work within a political-ecological system when they develop and attempt to implement a conservation plan that is designed to meet particular conservation goals. In this article, we develop a decision support tool that can identify a conservation policy for a managed wildlife population that is both sustainable and politically feasible. Part of our tool consists of a simulation model composed of interacting influence diagrams. We build, fit, and use our tool on the case of rhino horn trafficking between South Africa and Asia. Using these diagrams, we show how a rhino poacher's belief system can be modified by such a policy and locate it in a perceived risks-benefits space before and after policy implementation. We statistically fit our model to observations on group actions and rhino abundance. We then use this fitted model to compute a politically feasible conservation policy.}, }
@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 {pmid29171224, year = {2017}, author = {Zhang, F and Chen, SQ and Wang, LL and Zhang, T and Zhang, XB and Zhu, SD}, title = {[Study on ecological suitability regionalization of Corni Fructus based on Maxent and ArcGIS model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {16}, pages = {3078-3083}, doi = {10.19540/j.cnki.cjcmm.20170714.017}, pmid = {29171224}, issn = {1001-5302}, mesh = {China ; Climate ; Cornus/*growth &amp; development ; Ecology ; Geographic Information Systems ; Plants, Medicinal/*growth &amp; development ; Soil ; }, abstract = {Through planting regionalization the scientific basis for planting area of high-quality medicinal materials was predicted. Through interview investigation and field survey, the distribution information of Corni Fructus in China was collected,and 89 sampling point from 14 producing areas were collected. Climate and topography of Corni Fructus were analyzed, the ecological adaptability of study was conducted based on ArcGIS and Maxent. Different suitability grade at potential areas and regionalization map were formulated. There are nine ecological factors affecting the growth of Corni Fructus, for example precipitation in November and March and vegetation type. The results showed that the most suitable habitats are Henan, Shaanxi, Zhejiang, Chongqing, Hubei, Sichuan, Anhui, Hunan and Shandong province. Using the spatial analysis method,the study not only illustrates the most suitable for the surroundings of Corni Fructus,but also provides a scientific reference for wild resource tending, introduction and cultivation, and artificial planting base and directing production layout.}, }
@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 = {R01 HG005220/HG/NHGRI NIH HHS/United States ; T32 GM074897/GM/NIGMS NIH HHS/United States ; U54 DE023798/DE/NIDCR 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}, mesh = {Animals ; Biodiversity ; *Environmental Restoration and Remediation ; *Forests ; Meta-Analysis as Topic ; Plants/metabolism ; }, 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 {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 {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 {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 {pmid29097776, year = {2017}, author = {Iquebal, MA and Jaiswal, S and Mahato, AK and Jayaswal, PK and Angadi, UB and Kumar, N and Sharma, N and Singh, AK and Srivastav, M and Prakash, J and Singh, SK and Khan, K and Mishra, RK and Rajan, S and Bajpai, A and Sandhya, BS and Nischita, P and Ravishankar, KV and Dinesh, MR and Rai, A and Kumar, D and Sharma, TR and Singh, NK}, title = {MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14968}, pmid = {29097776}, issn = {2045-2322}, mesh = {Databases, Genetic ; Fruit/genetics ; Genome, Plant ; Genomics ; Internet ; Mangifera/*genetics ; *Phylogeny ; Phylogeography ; *Polymorphism, Single Nucleotide ; }, abstract = {Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.}, }
@article {pmid29095369, year = {2019}, author = {Vest, JR and Menachemi, N}, title = {A population ecology perspective on the functioning and future of health information organizations.}, journal = {Health care management review}, volume = {44}, number = {4}, pages = {344-355}, doi = {10.1097/HMR.0000000000000185}, pmid = {29095369}, issn = {1550-5030}, mesh = {*Commerce ; *Efficiency, Organizational ; Electronic Health Records ; *Health Information Exchange ; Humans ; Interviews as Topic ; Models, Theoretical ; Qualitative Research ; }, abstract = {BACKGROUND: Increasingly, health care providers need to exchange information to meet policy expectations and business needs. A variety of health information organizations (HIOs) provide services to facilitate health information exchange (HIE). However, the future of these organizations is unclear.<br><br>PURPOSE: The aim of this study was to explore the environmental context, potential futures, and survivability of community HIOs, enterprise HIEs, and electronic health record vendor-mediated exchange using the population ecology theory.<br><br>APPROACH: Qualitative interviews with 33 key informants representing each type of HIE organization were analyzed using template analysis.<br><br>RESULTS: Community HIOs, enterprise HIEs, and electronic health record vendors exhibited a high degree of competition for resources, especially in the area of exchange infrastructure services. Competition resulted in closures in some areas. In response to environmental pressures, each organizational type was endeavoring to differentiate its services and unique use case, as well as pursing symbiotic relationships or attempting resource partitioning.<br><br>CONCLUSION: HIOs compete for similar resources and are reacting to environmental pressures to better position themselves for continued survival and success. Our ecological research perspective helps move the discourse away from situation of a single exchange organization type toward a view of the broader dynamics and relationships of all organizations involved in facilitating HIE activities.<br><br>PRACTICE IMPLICATIONS: HIOs are attempting to partition the environment and differentiate services. HIE options should not be construed as an &quot;either/or&quot; decision, but one where multiple and complementary participation may be required.}, }
@article {pmid29094363, year = {2018}, author = {Glynou, K and Nam, B and Thines, M and Maciá-Vicente, JG}, title = {Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species.}, journal = {The New phytologist}, volume = {217}, number = {3}, pages = {1190-1202}, doi = {10.1111/nph.14873}, pmid = {29094363}, issn = {1469-8137}, mesh = {Ascomycota/*physiology ; Biodiversity ; Databases, Genetic ; Endophytes/*physiology ; Microbiota ; Molecular Sequence Annotation ; Mycorrhizae/*physiology ; Sequence Analysis, DNA ; }, abstract = {There is increasing knowledge on the diversity of root-endophytic fungi, but limited information on their lifestyles and dependence on hosts hampers our understanding of their ecological functions. We compared diversity and biogeographical patterns of cultivable and noncultivable root endophytes to assess whether their occurrence is determined by distinct ecological factors. The endophytic diversity in roots of nonmycorrhizal Microthlaspi spp. growing across Europe was assessed using high-throughput sequencing (HTS) and compared with a previous dataset based on cultivation of endophytes from the same root samples. HTS revealed a large fungal richness undetected by cultivation, but which largely comprised taxa with restricted distributions and/or low representation of sequence reads. Both datasets coincided in a consistent high representation of widespread endophytes within orders Pleosporales, Hypocreales and Helotiales, as well as similar associations of community structure with spatial and environmental conditions. Likewise, distributions of particular endophytes inferred by HTS agreed with cultivation data in suggesting individual ecological preferences. Our findings support that Microthlaspi spp. roots are colonized mostly by saprotrophic and likely facultative endophytes, and that differential niche preferences and distribution ranges among fungi importantly drive the assembly of root-endophytic communities.}, }
@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 &amp; development ; China ; *Climate ; *Ecology ; Geographic Information Systems ; Plant Dispersal ; Plants, Medicinal/*growth &amp; 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 {pmid29087435, year = {2018}, author = {Piccolo, BD and Wankhade, UD and Chintapalli, SV and Bhattacharyya, S and Chunqiao, L and Shankar, K}, title = {Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {6}, pages = {1050-1052}, pmid = {29087435}, issn = {1367-4811}, support = {UL1 TR001449/TR/NCATS NIH HHS/United States ; }, mesh = {*Data Interpretation, Statistical ; *Ecosystem ; Microbiological Techniques ; Microbiology ; Programming Languages ; Sequence Analysis ; *Software ; }, abstract = {Summary: Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive.<br><br>DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed.<br><br>Contact: bdpiccolo@uams.edu.}, }
@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}, doi = {10.1016/j.scitotenv.2017.08.301}, 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 {pmid28922513, year = {2018}, author = {Gray, S and Voinov, A and Paolisso, M and Jordan, R and BenDor, T and Bommel, P and Glynn, P and Hedelin, B and Hubacek, K and Introne, J and Kolagani, N and Laursen, B and Prell, C and Schmitt Olabisi, L and Singer, A and Sterling, E and Zellner, M}, title = {Purpose, processes, partnerships, and products: four Ps to advance participatory socio-environmental modeling.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {28}, number = {1}, pages = {46-61}, doi = {10.1002/eap.1627}, pmid = {28922513}, issn = {1051-0761}, mesh = {Animals ; Cameroon ; *Community Participation ; *Conservation of Natural Resources ; Environment ; Geographic Information Systems ; Humans ; India ; *Models, Theoretical ; Social Environment ; Zambia ; }, abstract = {Including stakeholders in environmental model building and analysis is an increasingly popular approach to understanding ecological change. This is because stakeholders often hold valuable knowledge about socio-environmental dynamics and collaborative forms of modeling produce important boundary objects used to collectively reason about environmental problems. Although the number of participatory modeling (PM) case studies and the number of researchers adopting these approaches has grown in recent years, the lack of standardized reporting and limited reproducibility have prevented PM's establishment and advancement as a cohesive field of study. We suggest a four-dimensional framework (4P) that includes reporting on dimensions of (1) the Purpose for selecting a PM approach (the why); (2) the Process by which the public was involved in model building or evaluation (the how); (3) the Partnerships formed (the who); and (4) the Products that resulted from these efforts (the what). We highlight four case studies that use common PM software-based approaches (fuzzy cognitive mapping, agent-based modeling, system dynamics, and participatory geospatial modeling) to understand human-environment interactions and the consequences of ecological changes, including bushmeat hunting in Tanzania and Cameroon, agricultural production and deforestation in Zambia, and groundwater management in India. We demonstrate how standardizing communication about PM case studies can lead to innovation and new insights about model-based reasoning in support of ecological policy development. We suggest that our 4P framework and reporting approach provides a way for new hypotheses to be identified and tested in the growing field of PM.}, }
@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 {pmid28904348, year = {2017}, author = {Liu, S and Hao, H and Lu, X and Zhao, X and Wang, Y and Zhang, Y and Xie, Z and Wang, R}, title = {Transcriptome profiling of genes involved in induced systemic salt tolerance conferred by Bacillus amyloliquefaciens FZB42 in Arabidopsis thaliana.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10795}, pmid = {28904348}, issn = {2045-2322}, mesh = {Arabidopsis/*microbiology/*physiology ; *Bacillus amyloliquefaciens ; Computational Biology/methods ; Energy Metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Plant Development/genetics ; Reproducibility of Results ; Salinity ; Salt Tolerance/*genetics ; Soil/chemistry ; Stress, Physiological/genetics ; *Transcriptome ; }, abstract = {Plant growth-promoting Bacillus amyloliquefaciens FZB42 induces systemic salt tolerance in Arabidopsis and enhances the fresh and dry weight. However, the underlying molecular mechanism that allows plants to respond to FZB42 and exhibit salt tolerance is largely unknown. Therefore, we performed large-scale transcriptome sequencing of Arabidopsis shoot tissues grown under salt stress with or without FZB42 inoculation by using Illumina sequencing to identify the key genes and pathways with important roles during this interaction. In total, 1461 genes were differentially expressed (FZB42-inoculated versus non-inoculated samples) at 0 mM NaCl, of which 953 were upregulated and 508 downregulated, while 1288 genes were differentially expressed at 100 mM NaCl, of which 1024 were upregulated and 264 were downregulated. Transcripts associated with photosynthesis, auxin-related, SOS scavenging, Na+ translocation, and osmoprotectant synthesis, such as trehalose and proline, were differentially expressed by FZB42 inoculation, which reduced the susceptibility to salt and facilitated salt adaptation. Meanwhile, etr1-3, eto1, jar1-1, and abi4-102 hormone-related mutants demonstrated that FZB42 might induce plant salt tolerance via activating plants ET/JA signaling but not ABA-dependent pathway. The results here characterize the plant transcriptome under salt stress with plant growth-promoting bacteria inoculation, thereby providing insights into the molecular mechanisms responsible for induced salt tolerance.}, }
@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 {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 &quot;Candidatus Prosthecochloris korallensis&quot; was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows &quot;Ca. P. korallensis&quot; belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals &quot;Ca. P. korallensis&quot; 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 &quot;Ca. P. korallensis&quot; is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: &quot;Ca. P. korallensis&quot; might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide &quot;Ca. P. korallensis&quot; with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.}, }
@article {pmid28833890, year = {2017}, author = {Scales, KL and Hazen, EL and Maxwell, SM and Dewar, H and Kohin, S and Jacox, MG and Edwards, CA and Briscoe, DK and Crowder, LB and Lewison, RL and Bograd, SJ}, title = {Fit to predict? Eco-informatics for predicting the catchability of a pelagic fish in near real time.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {27}, number = {8}, pages = {2313-2329}, doi = {10.1002/eap.1610}, pmid = {28833890}, issn = {1051-0761}, mesh = {Animals ; California ; Computational Biology ; Ecology ; *Fisheries ; *Fishes ; Models, Biological ; Pacific Ocean ; Remote Sensing Technology/*methods ; }, abstract = {The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing eco-informatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 yr (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of occurrence (presence-absence) and catchability (total catch per gillnet set) of broadbill swordfish Xiphias gladius in the California Current System. Using freely available environmental data sets and open source software, we explore the physical drivers of regional swordfish distribution. Comparing models built upon remotely sensed data sets with those built upon a data-assimilative configuration of the Regional Ocean Modelling System (ROMS), we explore trade-offs in model construction, and address how physical data can affect predictive performance and operational capacity. Swordfish catchability was found to be highest in deeper waters (>1,500 m) with surface temperatures in the 14-20°C range, isothermal layer depth (ILD) of 20-40 m, positive sea surface height (SSH) anomalies, and during the new moon (<20% lunar illumination). We observed a greater influence of mesoscale variability (SSH, wind speed, isothermal layer depth, eddy kinetic energy) in driving swordfish catchability (total catch) than was evident in predicting the relative probability of presence (presence-absence), confirming the utility of generating spatiotemporally dynamic predictions. Data-assimilative ROMS circumvent the limitations of satellite remote sensing in providing physical data fields for species distribution models (e.g., cloud cover, variable resolution, subsurface data), and facilitate broad-scale prediction of dynamic species distributions in near real time.}, }
@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}, mesh = {Animals ; Bias ; Humans ; Parasites/*growth &amp; development ; Parasitic Diseases/*parasitology ; Parasitology/*methods ; Sample Size ; }, 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}, mesh = {Animal Distribution/*physiology ; Animals ; *Biodiversity ; Environmental Monitoring/*methods ; Models, Biological ; }, 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 ; }, mesh = {Animals ; Conserved Sequence ; Daphnia/*genetics ; Gene Expression Regulation ; *Gene Regulatory Networks ; Genome ; Genotype ; Multigene Family ; *Transcription, Genetic ; }, 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 {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 {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}, support = {/WT_/Wellcome Trust/United Kingdom ; }, 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 {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 {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 {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}, support = {P 23949/FWF_/Austrian Science Fund FWF/Austria ; }, 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}, mesh = {*Animal Communication ; Animals ; *Odorants ; *Predatory Behavior ; *Research ; }, 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}, doi = {10.1890/14-2200}, 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 ; K23 HL130641/HL/NHLBI NIH HHS/United States ; L30 HL120241/HL/NHLBI NIH HHS/United States ; I01 CX000911/CX/CSRD VA/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, MTP and Wolf, JBW}, 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//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}, doi = {10.1890/14-2080.1}, 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