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Bibliography on: Ecological Informatics

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ESP: PubMed Auto Bibliography 15 Nov 2018 at 01:36 Created: 

Ecological Informatics

Wikipedia: Ecological Informatics Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are National Science Foundation Datanet projects, DataONE and Data Conservancy.

Created with PubMed® Query: "ecology OR ecological" and ("data management" or informatics) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2018-11-14
CmpDate: 2018-11-14

Wang S, Loreau M, Arnoldi JF, et al (2017)

An invariability-area relationship sheds new light on the spatial scaling of ecological stability.

Nature communications, 8:15211 pii:ncomms15211.

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.

RevDate: 2018-11-12

Mazel F, Davis KM, Loudon A, et al (2018)

Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.

mSystems, 3(5): pii:mSystems00097-18.

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 "phylosymbiosis." 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.

RevDate: 2018-11-10

Trotter RT, Lininger MR, Camplain R, et al (2018)

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.

International journal of environmental research and public health, 15(11): pii:ijerph15112500.

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, "Health Disparities in Jail Populations." 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.

RevDate: 2018-11-08
CmpDate: 2018-11-08

Couger MB, Arévalo L, P Campbell (2018)

A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations.

G3 (Bethesda, Md.), 8(7):2145-2152 pii:g3.118.200318.

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.

RevDate: 2018-11-02
CmpDate: 2018-11-02

Chen F, Zhang J, Chen J, et al (2018)

realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta).

Database : the journal of biological databases and curation, 2018:.

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 ( 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:

RevDate: 2018-11-02
CmpDate: 2018-11-02

Wayland MT, JC Chubb (2016)

A new R package and web application for detecting bilateral asymmetry in parasitic infections.

Folia parasitologica, 63:.

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 ( and a web application ( 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.

RevDate: 2018-10-31
CmpDate: 2018-10-31

Xu XH, Lv ZQ, Zhou XY, et al (2017)

Drought prediction and sustainable development of the ecological environment.

Environmental science and pollution research international, 24(35):26974-26982.

In the 1990s ecological early warning research began with the aim of elucidating the effect of drought in dry regions of the world. Drought has been a prevalent natural disaster, ravaging the Yun'nan province of China for over 5 years since 2009. Due to the extensive range, depth and devastating losses, the drought has reached a once-in-a-century severity. Yun'nan province suffered particularly badly from the drought, which took its toll on both the ecological environment and the sustainable economic development of the province. We chose to study Pu'er city in Yun'nun province for this research, and analysed the drought traits of Pu'er city utilizing geographic information technology. We applied the Mann-Kendall test for trend, linear tendency estimation and percentage of precipitation anomalies, as well as using combinations of monthly data searches of meteorological reports from 1980-2010. The results showed that except for a small rise in spring precipitation, the overall rainfall of Pu'er city showed a decreasing trend. The results of this study can provide an adequate and reliable theoretical basis and technological methods for use in government decision making, and promote research into early warning ecology.

RevDate: 2018-10-29
CmpDate: 2018-10-29

Ridding LE, Redhead JW, Oliver TH, et al (2018)

The importance of landscape characteristics for the delivery of cultural ecosystem services.

Journal of environmental management, 206:1145-1154.

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.

RevDate: 2018-10-29
CmpDate: 2018-10-29

He L, Shen J, Y Zhang (2018)

Ecological vulnerability assessment for ecological conservation and environmental management.

Journal of environmental management, 206:1115-1125.

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.

RevDate: 2018-10-25
CmpDate: 2018-10-25

Stephens PR, Pappalardo P, Huang S, et al (2017)

Global Mammal Parasite Database version 2.0.

Ecology, 98(5):1476.

Illuminating the ecological and evolutionary dynamics of parasites is one of the most pressing issues facing modern science, and is critical for basic science, the global economy, and human health. Extremely important to this effort are data on the disease-causing organisms of wild animal hosts (including viruses, bacteria, protozoa, helminths, arthropods, and fungi). Here we present an updated version of the Global Mammal Parasite Database, a database of the parasites of wild ungulates (artiodactyls and perissodactyls), carnivores, and primates, and make it available for download as complete flat files. The updated database has more than 24,000 entries in the main data file alone, representing data from over 2700 literature sources. We include data on sampling method and sample sizes when reported, as well as both "reported" and "corrected" (i.e., standardized) binomials for each host and parasite species. Also included are current higher taxonomies and data on transmission modes used by the majority of species of parasites in the database. In the associated metadata we describe the methods used to identify sources and extract data from the primary literature, how entries were checked for errors, methods used to georeference entries, and how host and parasite taxonomies were standardized across the database. We also provide definitions of the data fields in each of the four files that users can download.

RevDate: 2018-10-23
CmpDate: 2018-10-23

Gibb H, Dunn RR, Sanders NJ, et al (2017)

A global database of ant species abundances.

Ecology, 98(3):883-884.

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.

RevDate: 2018-10-22

Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, et al (2018)

Interspecific Gene Flow Shaped the Evolution of the Genus Canis.

Current biology : CB pii:S0960-9822(18)31125-4 [Epub ahead of print].

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 "ghost" basal canid lineage.

RevDate: 2018-10-18
CmpDate: 2018-10-18

Byrne SL, Erthmann PØ, Agerbirk N, et al (2017)

The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry.

Scientific reports, 7:40728 pii:srep40728.

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 "dead-end" 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.

RevDate: 2018-10-12
CmpDate: 2018-10-12

Djikanović V, Skorić S, Spasić S, et al (2018)

Ecological risk assessment for different macrophytes and fish species in reservoirs using biota-sediment accumulation factors as a useful tool.

Environmental pollution (Barking, Essex : 1987), 241:1167-1174.

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.

RevDate: 2018-10-09
CmpDate: 2018-10-09

Klimešová J, Danihelka J, Chrtek J, et al (2017)

CLO-PLA: a database of clonal and bud-bank traits of the Central European flora.

Ecology, 98(4):1179.

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.

RevDate: 2018-10-03
CmpDate: 2018-10-03

Kim HS, Lee BY, Han J, et al (2018)

The genome of the freshwater monogonont rotifer Brachionus calyciflorus.

Molecular ecology resources, 18(3):646-655.

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.

RevDate: 2018-09-27

Bjorkman AD, Myers-Smith IH, Elmendorf SC, et al (2018)

Plant functional trait change across a warming tundra biome.

Nature pii:10.1038/s41586-018-0563-7 [Epub ahead of print].

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.

RevDate: 2018-09-18
CmpDate: 2018-09-18

Tumolo BB, MB Flinn (2017)

Top-down effects of an invasive omnivore: detection in long-term monitoring of large-river reservoir chlorophyll-a.

Oecologia, 185(2):293-303.

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.

RevDate: 2018-09-10
CmpDate: 2018-09-10

Wang Q, Xiong X, Wang X, et al (2018)

Suckling Piglet Intestinal Enterocyte Nutrient Metabolism Changes.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 48(5):2103-2113.

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.

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.

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.

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.

RevDate: 2018-09-08

Rokas A, Wisecaver JH, AL Lind (2018)

The birth, evolution and death of metabolic gene clusters in fungi.

Nature reviews. Microbiology pii:10.1038/s41579-018-0075-3 [Epub ahead of print].

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.

RevDate: 2018-09-05

de Jonge PA, Nobrega FL, Brouns SJJ, et al (2018)

Molecular and Evolutionary Determinants of Bacteriophage Host Range.

Trends in microbiology pii:S0966-842X(18)30178-1 [Epub ahead of print].

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.

RevDate: 2018-09-04
CmpDate: 2018-09-04

Muscente AD, Prabhu A, Zhong H, et al (2018)

Quantifying ecological impacts of mass extinctions with network analysis of fossil communities.

Proceedings of the National Academy of Sciences of the United States of America, 115(20):5217-5222.

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.

RevDate: 2018-08-29

An S, Zhu X, Shen M, et al (2018)

Mismatch in elevational shifts between satellite observed vegetation greenness and temperature isolines during 2000-2016 on the Tibetan Plateau.

Global change biology [Epub ahead of print].

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. This article is protected by copyright. All rights reserved.

RevDate: 2018-08-27

Dornelas M, Antão LH, Moyes F, et al (2018)

BioTIME: A database of biodiversity time series for the Anthropocene.

Global ecology and biogeography : a journal of macroecology, 27(7):760-786.

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.

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.

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).

Time period and grain: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

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.

Software format: .csv and .SQL.

RevDate: 2018-08-21
CmpDate: 2018-08-21

Zhang Q, Zeng FL, Zhang DF, et al (2016)

[Ecology suitability regions and ecological characteristics of Panax notoginseng (Burk.) F.H. Chen based on maximum entropy model].

Yao xue xue bao = Acta pharmaceutica Sinica, 51(10):1629-1637.

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.

RevDate: 2018-08-20
CmpDate: 2018-08-20

Martin RW, Waits ER, CT Nietch (2018)

Empirically-based modeling and mapping to consider the co-occurrence of ecological receptors and stressors.

The Science of the total environment, 613-614:1228-1239.

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.

RevDate: 2018-08-15

Liebhold AM, Yamanaka T, Roques A, et al (2018)

Plant diversity drives global patterns of insect invasions.

Scientific reports, 8(1):12095 pii:10.1038/s41598-018-30605-4.

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.

RevDate: 2018-08-15
CmpDate: 2018-08-15

Chen S, Wang W, Xu W, et al (2018)

Plant diversity enhances productivity and soil carbon storage.

Proceedings of the National Academy of Sciences of the United States of America, 115(16):4027-4032.

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.

RevDate: 2018-08-10

Albrecht J, Classen A, Vollstädt MGR, et al (2018)

Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient.

Nature communications, 9(1):3177 pii:10.1038/s41467-018-05610-w.

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.

RevDate: 2018-08-01
CmpDate: 2018-08-01

Zachar I, Szilágyi A, Számadó S, et al (2018)

Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection.

Proceedings of the National Academy of Sciences of the United States of America, 115(7):E1504-E1510.

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.

RevDate: 2018-07-31
CmpDate: 2018-07-31

Soranno PA, Bacon LC, Beauchene M, et al (2017)

LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes.

GigaScience, 6(12):1-22.

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.

RevDate: 2018-07-26

Bird SM, R King (2018)

Multiple Systems Estimation (or Capture-Recapture Estimation) to Inform Public Policy.

Annual review of statistics and its application, 5:95-118.

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 "capture-shy" 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: "period" definition; "case" 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 "cases" across different lists; demographic or other information about the "case" 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.

RevDate: 2018-07-18

Longbottom J, Shearer FM, Devine M, et al (2018)

Vulnerability to snakebite envenoming: a global mapping of hotspots.

Lancet (London, England) pii:S0140-6736(18)31224-8 [Epub ahead of print].

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.

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.

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.

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.

FUNDING: Bill & Melinda Gates Foundation.

RevDate: 2018-07-07

Lant C, Baggio J, Konar M, et al (2018)

The U.S. food-energy-water system: A blueprint to fill the mesoscale gap for science and decision-making.

Ambio pii:10.1007/s13280-018-1077-0 [Epub ahead of print].

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.

RevDate: 2018-06-15
CmpDate: 2018-06-15

Mirtl M, T Borer E, Djukic I, et al (2018)

Genesis, goals and achievements of Long-Term Ecological Research at the global scale: A critical review of ILTER and future directions.

The Science of the total environment, 626:1439-1462.

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.

RevDate: 2018-06-13
CmpDate: 2018-06-13

Dick J, Orenstein DE, Holzer JM, et al (2018)

What is socio-ecological research delivering? A literature survey across 25 international LTSER platforms.

The Science of the total environment, 622-623:1225-1240.

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.

RevDate: 2018-06-26

Snell Taylor SJ, Evans BS, White EP, et al (2018)

The prevalence and impact of transient species in ecological communities.

Ecology [Epub ahead of print].

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.

RevDate: 2018-07-10
CmpDate: 2018-07-10

Meng L, Huang J, J Dong (2018)

Assessment of rural ecosystem health and type classification in Jiangsu province, China.

The Science of the total environment, 615:1218-1228.

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.

RevDate: 2018-06-06

Peters K, Worrich A, Weinhold A, et al (2018)

Current Challenges in Plant Eco-Metabolomics.

International journal of molecular sciences, 19(5): pii:ijms19051385.

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.

RevDate: 2018-05-02

Toni M, Manciocco A, Angiulli E, et al (2018)

Review: Assessing fish welfare in research and aquaculture, with a focus on European directives.

Animal : an international journal of animal bioscience pii:S1751731118000940 [Epub ahead of print].

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.

RevDate: 2018-06-19
CmpDate: 2018-06-18

Hannigan GD, Duhaime MB, Koutra D, et al (2018)

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.

PLoS computational biology, 14(4):e1006099 pii:PCOMPBIOL-D-17-01664.

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.

RevDate: 2018-05-09

Ching T, Himmelstein DS, Beaulieu-Jones BK, et al (2018)

Opportunities and obstacles for deep learning in biology and medicine.

Journal of the Royal Society, Interface, 15(141):.

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.

RevDate: 2018-06-26
CmpDate: 2018-06-26

Emery M, Willis MMS, Hao Y, et al (2018)

Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.

PLoS genetics, 14(3):e1007267 pii:PGENETICS-D-17-02075.

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.

RevDate: 2018-05-21

Psonis N, Antoniou A, Karameta E, et al (2018)

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.

Molecular phylogenetics and evolution, 125:100-115.

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.

RevDate: 2018-04-16

Anderegg LDL, Berner LT, Badgley G, et al (2018)

Within-species patterns challenge our understanding of the leaf economics spectrum.

Ecology letters, 21(5):734-744.

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.

RevDate: 2018-07-05
CmpDate: 2018-07-05

Jablonski KE, Boone RB, PJ Meiman (2018)

An agent-based model of cattle grazing toxic Geyer's larkspur.

PloS one, 13(3):e0194450 pii:PONE-D-17-41169.

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.

RevDate: 2018-06-08
CmpDate: 2018-06-08

Heider K, Lopez JMR, J Scheffran (2018)

The potential of volunteered geographic information to investigate peri-urbanization in the conservation zone of Mexico City.

Environmental monitoring and assessment, 190(4):219 pii:10.1007/s10661-018-6597-3.

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.

RevDate: 2018-04-04

Liu XY, Koba K, Koyama LA, et al (2018)

Nitrate is an important nitrogen source for Arctic tundra plants.

Proceedings of the National Academy of Sciences of the United States of America, 115(13):3398-3403.

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.

RevDate: 2018-07-02
CmpDate: 2018-07-02

Lee EC, Arab A, Goldlust SM, et al (2018)

Deploying digital health data to optimize influenza surveillance at national and local scales.

PLoS computational biology, 14(3):e1006020 pii:PCOMPBIOL-D-17-01896.

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.

RevDate: 2018-04-16
CmpDate: 2018-04-16

Willey B, Waiswa P, Kajjo D, et al (2018)

Linking data sources for measurement of effective coverage in maternal and newborn health: what do we learn from individual- vs ecological-linking methods?.

Journal of global health, 8(1):010601.

Background: Improving maternal and newborn health requires improvements in the quality of facility-based care. This is challenging to measure: routine data may be unreliable; respondents in population surveys may be unable to accurately report on quality indicators; and facility assessments lack population level denominators. We explored methods for linking access to skilled birth attendance (SBA) from household surveys to data on provision of care from facility surveys with the aim of estimating population level effective coverage reflecting access to quality care.

Methods: We used data from Mayuge District, Uganda. Data from household surveys on access to SBA were linked to health facility assessment census data on readiness to provide basic emergency obstetric and newborn care (BEmONC) in the same district. One individual- and two ecological-linking methods were applied. All methods used household survey reports on where care at birth was accessed. The individual-linking method linked this to data about facility readiness from the specific facility where each woman delivered. The first ecological-linking approach used a district-wide mean estimate of facility readiness. The second used an estimate of facility readiness adjusted by level of health facility accessed. Absolute differences between estimates derived from the different linking methods were calculated, and agreement examined using Lin's concordance correlation coefficient.

Results: A total of 1177 women resident in Mayuge reported a birth during 2012-13. Of these, 664 took place in facilities within Mayuge, and were eligible for linking to the census of the district's 38 facilities. 55% were assisted by a SBA in a facility. Using the individual-linking method, effective coverage of births that took place with an SBA in a facility ready to provide BEmONC was just 10% (95% confidence interval CI 3-17). The absolute difference between the individual- and ecological-level linking method adjusting for facility level was one percentage point (11%), and tests suggested good agreement. The ecological method using the district-wide estimate demonstrated poor agreement.

Conclusions: The proportion of women accessing appropriately equipped facilities for care at birth is far lower than the coverage of facility delivery. To realise the life-saving potential of health services, countries need evidence to inform actions that address gaps in the provision of quality care. Linking household and facility-based information provides a simple but innovative method for estimating quality of care at the population level. These encouraging findings suggest that linking data sets can result in meaningful evidence even when the exact location of care seeking is not known.

RevDate: 2018-04-11
CmpDate: 2018-04-11

Hervé MR, Nicolè F, KA Lê Cao (2018)

Multivariate Analysis of Multiple Datasets: a Practical Guide for Chemical Ecology.

Journal of chemical ecology, 44(3):215-234.

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.

RevDate: 2018-05-22
CmpDate: 2018-05-22

Ma Z, Guo D, Xu X, et al (2018)

Evolutionary history resolves global organization of root functional traits.

Nature, 555(7694):94-97.

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.

RevDate: 2018-03-27

Stefanidis K, Panagopoulos Y, M Mimikou (2018)

Response of a multi-stressed Mediterranean river to future climate and socio-economic scenarios.

The Science of the total environment, 627:756-769.

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.

RevDate: 2018-07-20
CmpDate: 2018-07-20

Dietze MC, Fox A, Beck-Johnson LM, et al (2018)

Iterative near-term ecological forecasting: Needs, opportunities, and challenges.

Proceedings of the National Academy of Sciences of the United States of America, 115(7):1424-1432.

Two foundational questions about sustainability are "How are ecosystems and the services they provide going to change in the future?" and "How do human decisions affect these trajectories?" 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.

RevDate: 2018-04-23
CmpDate: 2018-04-23

Tucker MA, Böhning-Gaese K, Fagan WF, et al (2018)

Moving in the Anthropocene: Global reductions in terrestrial mammalian movements.

Science (New York, N.Y.), 359(6374):466-469.

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.

RevDate: 2018-01-24

Filippova N, T Bulyonkova (2017)

The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia).

Biodiversity data journal pii:Biodiversity Data Journal.

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.

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.

RevDate: 2018-02-21
CmpDate: 2018-02-21

Marshall HH, Griffiths DJ, Mwanguhya F, et al (2018)

Data collection and storage in long-term ecological and evolutionary studies: The Mongoose 2000 system.

PloS one, 13(1):e0190740 pii:PONE-D-16-48212.

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.

RevDate: 2017-12-19

Walter JM, Coutinho FH, Dutilh BE, et al (2017)

Ecogenomics and Taxonomy of Cyanobacteria Phylum.

Frontiers in microbiology, 8:2132.

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.

RevDate: 2018-07-10
CmpDate: 2018-07-10

Dornburg A, Townsend JP, Z Wang (2017)

Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data.

Advances in genetics, 100:1-47.

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.

RevDate: 2017-12-26
CmpDate: 2017-12-26

Mainali KP, Bewick S, Thielen P, et al (2017)

Statistical analysis of co-occurrence patterns in microbial presence-absence datasets.

PloS one, 12(11):e0187132 pii:PONE-D-17-28139.

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.

RevDate: 2018-03-03
CmpDate: 2017-12-12

Schwager E, Mallick H, Ventz S, et al (2017)

A Bayesian method for detecting pairwise associations in compositional data.

PLoS computational biology, 13(11):e1005852 pii:PCOMPBIOL-D-17-00827.

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.

RevDate: 2017-12-19

Crouzeilles R, Ferreira MS, Chazdon RL, et al (2017)

Ecological restoration success is higher for natural regeneration than for active restoration in tropical forests.

Science advances, 3(11):e1701345 pii:1701345.

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.

RevDate: 2018-01-04
CmpDate: 2018-01-04

Goleiji E, Hosseini SM, Khorasani N, et al (2017)

Forest fire risk assessment-an integrated approach based on multicriteria evaluation.

Environmental monitoring and assessment, 189(12):612 pii:10.1007/s10661-017-6225-7.

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.

RevDate: 2018-06-18
CmpDate: 2018-06-18

Corander J, Fraser C, Gutmann MU, et al (2017)

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Nature ecology & evolution, 1(12):1950-1960.

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.

RevDate: 2017-12-19
CmpDate: 2017-10-23

Wang D, Li L, Wu G, et al (2017)

De novo transcriptome sequencing of Isaria cateniannulata and comparative analysis of gene expression in response to heat and cold stresses.

PloS one, 12(10):e0186040 pii:PONE-D-17-21462.

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.

RevDate: 2018-02-23
CmpDate: 2018-02-23

Tedesco PA, Beauchard O, Bigorne R, et al (2017)

A global database on freshwater fish species occurrence in drainage basins.

Scientific data, 4:170141 pii:sdata2017141.

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.

RevDate: 2018-05-29
CmpDate: 2018-05-29

Soltész Z, Erdélyi K, Bakonyi T, et al (2017)

West Nile virus host-vector-pathogen interactions in a colonial raptor.

Parasites & vectors, 10(1):449 pii:10.1186/s13071-017-2394-z.

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.

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.

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.

RevDate: 2017-10-31
CmpDate: 2017-10-19

Bauer M, Graf IR, Ngampruetikorn V, et al (2017)

Exploiting ecology in drug pulse sequences in favour of population reduction.

PLoS computational biology, 13(9):e1005747 pii:PCOMPBIOL-D-17-00696.

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.

RevDate: 2018-06-04
CmpDate: 2018-06-04

Cardoso D, Särkinen T, Alexander S, et al (2017)

Amazon plant diversity revealed by a taxonomically verified species list.

Proceedings of the National Academy of Sciences of the United States of America, 114(40):10695-10700.

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.

RevDate: 2018-01-23

Fisher RA, Koven CD, Anderegg WRL, et al (2018)

Vegetation demographics in Earth System Models: A review of progress and priorities.

Global change biology, 24(1):35-54.

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.

RevDate: 2018-05-23
CmpDate: 2018-05-23

Jiang SY, Sun HB, Qin JH, et al (2016)

[Functional production regionalization for Fritillariae Cirrhosae Bulbus based on growth and quality suitability assessment].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3194-3201.

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.

RevDate: 2018-05-23
CmpDate: 2018-05-23

Liu X, Yang YF, Song HP, et al (2016)

[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].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3186-3193.

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.

RevDate: 2018-05-23
CmpDate: 2018-05-23

Miao Q, Yuan YJ, Luo GM, et al (2016)

[Study on ecological suitability of Gardenia jasminoides based on ArcGIS and Maxent model].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3181-3185.

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.

RevDate: 2018-05-23
CmpDate: 2018-05-23

Lu YY, Yang YM, Ma XH, et al (2016)

[Ecology suitability study of Chinese materia medica Gentianae Macrophyllae Radix].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3176-3180.

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.

RevDate: 2018-05-23
CmpDate: 2018-05-23

Shi ZW, Ma CJ, Kang CZ, et al (2016)

[Ecological suitability regionalization for Gastrodia elata in Zhaotong based on Maxent and ArcGIS].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3155-3163.

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.

RevDate: 2018-05-23
CmpDate: 2018-05-23

Wang HQ, Wang Q, Ma L, et al (2016)

[Production regionalization study of Lycii Fructus].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3127-3131.

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.

RevDate: 2017-10-10
CmpDate: 2017-10-10

Joshi J, Couzin ID, Levin SA, et al (2017)

Mobility can promote the evolution of cooperation via emergent self-assortment dynamics.

PLoS computational biology, 13(9):e1005732 pii:PCOMPBIOL-D-16-01975.

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.

RevDate: 2017-10-16
CmpDate: 2017-10-16

Müller M, Seifert S, Lübbe T, et al (2017)

De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech.

PloS one, 12(9):e0184167 pii:PONE-D-17-14250.

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.

RevDate: 2018-03-05
CmpDate: 2018-03-05

Oliveira BF, São-Pedro VA, Santos-Barrera G, et al (2017)

AmphiBIO, a global database for amphibian ecological traits.

Scientific data, 4:170123 pii:sdata2017123.

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.

RevDate: 2017-10-18
CmpDate: 2017-10-18

Chen H, Peng S, Dai L, et al (2017)

Oral microbial community assembly under the influence of periodontitis.

PloS one, 12(8):e0182259 pii:PONE-D-16-50165.

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 & 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" (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.

RevDate: 2017-08-07

Reiczigel J, L Rozsa (2017)

Do small samples underestimate mean abundance? It depends on what type of bias we consider.

Folia parasitologica, 64:.

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.

RevDate: 2018-01-16

Kissling WD, Ahumada JA, Bowser A, et al (2018)

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale.

Biological reviews of the Cambridge Philosophical Society, 93(1):600-625.

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.

RevDate: 2018-02-02
CmpDate: 2018-02-02

Votier SC, Fayet AL, Bearhop S, et al (2017)

Effects of age and reproductive status on individual foraging site fidelity in a long-lived marine predator.

Proceedings. Biological sciences, 284(1859):.

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.

RevDate: 2018-04-03

Orsini L, Brown JB, Shams Solari O, et al (2018)

Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.

Molecular ecology, 27(4):886-897.

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.

RevDate: 2017-11-16
CmpDate: 2017-08-29

Igea J, Miller EF, Papadopulos AST, et al (2017)

Seed size and its rate of evolution correlate with species diversification across angiosperms.

PLoS biology, 15(7):e2002792 pii:pbio.2002792.

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.

RevDate: 2018-06-20
CmpDate: 2018-06-19

Zhang AL, Sun XY, Yin Q, et al (2017)

Functional characterization of the promoter of carbonyl reductase 1 gene in porcine endometrial cells.

Journal of Zhejiang University. Science. B, 18(7):626-634.

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.

RevDate: 2018-04-09
CmpDate: 2018-03-19

Mennis J, Mason M, Ambrus A, et al (2017)

The spatial accuracy of geographic ecological momentary assessment (GEMA): Error and bias due to subject and environmental characteristics.

Drug and alcohol dependence, 178:188-193.

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.

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.

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.

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.

RevDate: 2018-04-16
CmpDate: 2018-04-16

Gámez M, López I, Rodríguez C, et al (2017)

Ecological monitoring in a discrete-time prey-predator model.

Journal of theoretical biology, 429:52-60.

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.

RevDate: 2017-06-27

Vizzini S, Martínez-Crego B, Andolina C, et al (2017)

Ocean acidification as a driver of community simplification via the collapse of higher-order and rise of lower-order consumers.

Scientific reports, 7(1):4018 pii:10.1038/s41598-017-03802-w.

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.

RevDate: 2017-06-08

Hampton SE, Jones MB, Wasser LA, et al (2017)

Skills and Knowledge for Data-Intensive Environmental Research.

Bioscience, 67(6):546-557.

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.

RevDate: 2018-04-17
CmpDate: 2018-04-17

Mormul RP, Mormul TDS, Santos GMB, et al (2017)

Looking for attitudes related to amphibian species decline: how are peer-reviewed publications of education activities compared to ecological research?.

Anais da Academia Brasileira de Ciencias, 89(1 Suppl 0):491-496.

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.

RevDate: 2018-04-02
CmpDate: 2018-04-02

Padilla O, Rosas P, Moreno W, et al (2017)

Modeling of the ecological niches of the anopheles spp in Ecuador by the use of geo-informatic tools.

Spatial and spatio-temporal epidemiology, 21:1-11.

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.

RevDate: 2018-07-06

Wilsenach J, Landi P, C Hui (2017)

Evolutionary fields can explain patterns of high-dimensional complexity in ecology.

Physical review. E, 95(4-1):042401.

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.

RevDate: 2018-05-23
CmpDate: 2018-05-23

Alroy J (2017)

Effects of habitat disturbance on tropical forest biodiversity.

Proceedings of the National Academy of Sciences of the United States of America, 114(23):6056-6061.

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.

RevDate: 2018-04-30
CmpDate: 2017-10-30

Cicconardi F, Marcatili P, Arthofer W, et al (2017)

Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation.

Molecular phylogenetics and evolution, 112:230-243.

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.

RevDate: 2018-01-25
CmpDate: 2017-12-11

Cavaliere M, Feng S, Soyer OS, et al (2017)

Cooperation in microbial communities and their biotechnological applications.

Environmental microbiology, 19(8):2949-2963.

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.

RevDate: 2018-01-16

Parsons MH, Apfelbach R, Banks PB, et al (2018)

Biologically meaningful scents: a framework for understanding predator-prey research across disciplines.

Biological reviews of the Cambridge Philosophical Society, 93(1):98-114.

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.

RevDate: 2018-01-25
CmpDate: 2017-08-16

Fox MA, Brewer LE, L Martin (2017)

An Overview of Literature Topics Related to Current Concepts, Methods, Tools, and Applications for Cumulative Risk Assessment (2007-2016).

International journal of environmental research and public health, 14(4): pii:ijerph14040389.

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.

RevDate: 2017-09-06
CmpDate: 2017-09-05

Pocock MJ, Tweddle JC, Savage J, et al (2017)

The diversity and evolution of ecological and environmental citizen science.

PloS one, 12(4):e0172579 pii:PONE-D-16-29886.

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.

RevDate: 2018-07-02
CmpDate: 2017-08-28

Berney C, Ciuprina A, Bender S, et al (2017)

UniEuk: Time to Speak a Common Language in Protistology!.

The Journal of eukaryotic microbiology, 64(3):407-411.

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.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.


Order from Amazon

This is a must read book for anyone with an interest in invasion biology. The full title of the book lays out the author's premise — The New Wild: Why Invasive Species Will Be Nature's Salvation. Not only is species movement not bad for ecosystems, it is the way that ecosystems respond to perturbation — it is the way ecosystems heal. Even if you are one of those who is absolutely convinced that invasive species are actually "a blight, pollution, an epidemic, or a cancer on nature", you should read this book to clarify your own thinking. True scientific understanding never comes from just interacting with those with whom you already agree. R. Robbins

Electronic Scholarly Publishing
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Woodinville, WA 98077

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )