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234 results for “community analysis”
Data for a meta-analysis of the effect of kelp forests on fish communities around the world from observational and experimental studies spanning 1983-2020
Data for Pérez-Matus, A., Micheli, F., Konar, B., Shears, N., Low, N., Okamoto, D., Wernberg, T., Krumhansl, K., Ling, S., Kinsgford, M., Navarrete-Fernandez, T., Ruz, C., and Byrnes, J. 2024. Kelp forests as nursery and foundational habitat for reef fish. Ecology. For the definitive analysis, see the paper. Code is at https://github.com/jebyrnes/fish_kelp_meta. This data set concerns the effects of kelp on fish community composition. Data was mined as part of the National Center for Ecological Analysis and Synthesis (NCEAS) working group on "Global impacts of climate change on kelp forest ecosystems." It consists of digitized information from studies searched (see methods) examining fish community composition with and without kelp. To summarize the study, conservation of marine biodiversity requires an understanding of the habitats needed to support and replenish species of interest. It also requires knowledge about the abundance and diversity of multi-species assemblages. Variation in the distribution and composition of kelp forests, one of the most productive marine coastal habitats globally, can have major influences on reef fishes – a group of ecologically and socio-economically important species. In the face of widespread and escalating loss of kelp forests, quantification of these effects is urgently needed to assess and project cascading impacts on biodiversity. Here, we evaluate relationships between kelp forests and associated reef fish populations using a global meta-analysis of experimental kelp removals and comparative surveys of kelp and adjacent non-kelp habitats. These analyses show that kelp forests increase the abundance of reef fishes, though the significance of this effect varied depending on the structural complexity of kelp forests. In experimental studies, kelp forests have a significant positive effect on fish species richness, revealing that kelp act as true foundation species by supporting the diversity of associated multi-species assemblag
Data for a global meta-analysis of passive experimental warming effects on plant traits and community properties
This database contains the data used in a global meta-analysis of warming effects on plants. L0 data are available upon request; they include the raw data from 126 warming experiments. The L1 data are the result of merged L0 data and are cleaned for typos and are standardized names. L1 data contain plant trait and community property measurements in both warmed and ambient conditions. L2 data contain the effect sizes of warming for each study. These data came from 126 warming experiments across the globe.
Plant-mediated root methane emissions and oxidation in a thermokarst bog complex in the Bonanza Creek LTER Experimental Forest V - Raw Microbial Community Analysis Data 2015
Vascular plants are important in the wetland methane cycle but their effect on production, oxidation, and transport has high uncertainty, limiting our ability to predict emissions. Vegetation operated on top of baseline methane emissions, which varied with proximity to the thawing permafrost margin. Emissions from vegetated plots increased over the season, resulting in cumulative seasonal methane emissions that were 4.1-5.2 g m-2 season-1 greater than unvegetated plots. Mass balance calculations signify these greater emissions were due to increased methane production (3.0-3.5 g m-2 season-1) and decreased methane oxidation (1.1-1.6 g m-2 season-1). Minimal oxidation occurred along the plant-transport pathway and oxidation was suppressed outside the plant pathway. Our data indicate suppression of methane oxidation was stimulated by root exudates fueling competition among microbes for electron acceptors. Root exudates are known to fuel methane production and our work provides evidence they also decrease methane oxidation. This dataset contains 2015 results from monthly DNA analyses taken on cores from natural conditions in a bog complex in the Bonanza Creek LTER.
Data from: Bringing multivariate support to multiscale codependence analysis: assessing the drivers of community structure across spatial scales
1. Multiscale codependence analysis (MCA) quantifies the joint spatial distribution of a pair of variables in order to provide a spatially-explicit assessment of their relationships to one another. For the sake of simplicity, the original definition of MCA only considered a single response variable (e.g. a single species). However, that definition would limit the application of MCA when many response variables are studied jointly, for example when one wants to study the effect of the environment on the spatial organisation of a multi-species community in an explicit manner. 2. In the present paper, we generalize MCA to multiple response variables. We conducted a simulation study to assess the statistical properties (i.e. type I error rate and statistical power) of multivariate MCA (mMCA) and found that it had honest type I error rate and sufficient statistical power for practical purposes, even with modest sample sizes. We also exemplified mMCA by applying it to two ecological data sets. 3. The simulation study confirmed the adequacy of mMCA from a statistical standpoint: it has honest type I error rates and sufficient power to be useful in practice. Using mMCA, we were able to detect variation in fish community structure along the Doubs River (in France), which was associated with large spatial structures in the variation of physical and chemical variables related to water quality. Also, mMCA usefully described the spatial variation of an Oribatid mite community structure associated with a gradient of water content superimposed on various smaller-scale spatial features associated with vegetation cover in the peat blanket surrounding Lac Geai (in Québec, Canada). 4. In addition to demonstrating the soundness of mMCA in theory and practice, we further discuss the strengths and assumptions of mMCA and describe other potential scenarios where it would be helpful to biologists interested in assessing influence of environmental conditions on community structure in a spatially-explicit way.
Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders
1. Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival. 2. We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web building and the other actively hunting, which co-occur in wet forest on East Maui. We hypothesize that trophic niches differ significantly both 1) among species within a clade, indicating food resource partitioning, and 2) between the two clades, corresponding with their differences in foraging strategy. 3. To assess niches of the spider species, we measure a) web architecture, the structure of the hunting tool, and b) site choice, the physical placement of the web in the habitat. We then test whether differences in these parameters translate into meaningful differences in trophic niche by measuring c) stable isotope signatures of carbon and nitrogen in the spiders' tissues, and d) gut content of spiders based on metabarcoding data. 4. We find significant interspecific differences in web architecture and site choice. Importantly, these differences are reflected in stable isotope signatures among the five web-building species, as well as significant isotopic differences between web-builders and active hunters. Gut content data also show interspecific and inter-clade differences. Pairwise overlaps of web architecture between species are positively correlated with overlaps of isotopic signature. 5. Our results reveal trophic niche partitioning among species within each clade, as well as between the web-building and actively hunting clades. Based on the correlation between web architecture and stable isotopes, it appears that the isotopic signatures of spiders' tissues are influenced by architectural differences among their webs. Our findings indicate an important link between web structure, microhabitat preference and diet in the Hawaiian Tetragnatha.
Data from: A new digital method of data collection for spatial point pattern analysis in grassland communities
<p>A major objective of plant ecology research is to determine the underlying processes responsible for the observed spatial distribution patterns of plant species. Plants can be approximated as points in space for this purpose, and thus, spatial point pattern analysis has become increasingly popular in ecological research. The basic piece of data for point pattern analysis is a point location of an ecological object in some study region. Therefore, point pattern analysis can only be performed if data can be collected. However, due to the lack of a convenient sampling method, a few previous studies have used point pattern analysis to examine the spatial patterns of grassland species. This is unfortunate because being able to explore point patterns in grassland systems has widespread implications for population dynamics, community-level patterns and ecological processes. In this study, we develop a new method to measure individual coordinates of species in grassland communities. This method records plant growing positions via digital picture samples that have been sub-blocked within a geographical information system (GIS). Here, we tested out the new method by measuring the individual coordinates of <i>Stipa</i><i> grandis</i> in grazed and ungrazed <i>S. grandis</i> communities in a temperate steppe ecosystem in China. Furthermore, we analyzed the pattern of <i>S. grandis</i> by using the pair correlation function <i>g</i>(<i>r</i>) with both a homogeneous Poisson process and a heterogeneous Poisson process. Our results showed that individuals of <i>S. grandis</i> were overdispersed according to the homogeneous Poisson process at 0-0.16 m in the ungrazed community, while they were clustered at 0.19 m according to the homogeneous and heterogeneous Poisson processes in the grazed community. These results suggest that competitive interactions dominated the ungrazed community, while facilitative interactions dominated the grazed community. In sum, we successfully executed a new sampling method, using digital photography and a Geographical Information System, to collect experimental data on the spatial point patterns for the populations in this grassland community.</p>
River dams and the stability of bird communities: A hierarchical Bayesian analysis in a tropical hydroelectric power plant
<ol> <li>The effects of anthropogenic disturbance upon the stability of wildlife communities depend on the heterogeneity and connectivity of habitat remnants on multiple scales. The number of hydroelectric dams in biodiversity hotspots (Africa, South America and Asia) is growing rapidly. To establish their environmental impact, it is essential to understand the dynamics of wildlife communities before and following the establishment of dams.</li> <li>We evaluated the impacts of the filling of the Serra do Facão hydroelectric reservoir in the São Marcos river, central Brazil, upon the bird community. Using data from 1,145 surveys across 20 sampling sites over eight years, two years before and six years after the filling of the reservoir, we assessed the resistance, i.e., maintenance close to an equilibrium state during the disturbance, and resilience, i.e., ability to return to the original state following the disturbance, of the bird community. We used spatiotemporal hierarchical Bayesian models to assess the effects of reservoir filling on five community parameters: abundance, richness, phylogenetic diversity, functional diversity and species composition.</li> <li>In the period subsequent to reservoir filling, there was (i) a marked reduction in bird abundance, richness, phylogenetic diversity and functional diversity, and (ii) a reduction in the proportion of forest species, coupled with an increase in the proportion of savanna species. Except for bird abundance, none of the other community attributes returned to their original levels, even after six years. Our findings indicate that Cerrado bird communities have both low resistance and low resilience to habitat loss associated with the establishment of hydroelectric reservoirs.</li> <li> <i>Synthesis and applications.</i> The environmental costs of hydroelectric dams are still underestimated or neglected in Brazil. A new paradigm in the assessment of their environmental impacts is warranted, incorporating (i) models of spatiotemporal variations based on long-term monitoring with surveys initiated before disturbances and (ii) measures of functional and phylogenetic diversity, such that society can understand the costs and benefits of the establishment of new hydroelectric dams and make informed decisions. Biodiversity loss could be minimized by ensuring the preservation and connectivity of alluvial habitats, capable of maintaining the supply of resources and the functional and phylogenetic attributes of bird communities associated with such habitats.</li> </ol>
Finding functionality: Rasch analysis of the Functionality Appreciation Scale in community-dwelling adults in the US
<div class="abstract-content selected"> <div class="abstract-content selected"> <p><strong class="sub-title">Introduction: </strong>The Functionality Appreciation Scale (FAS) measures an individual's appreciation for the functions their body can perform, regardless of the individual's physical limitations. Prior studies reported on internal consistency, test-retest reliability, convergent validity, and exploratory or confirmatory factor analyses, but Rasch analysis has not yet been performed to evaluate the structural validity of the FAS.</p> <p><strong class="sub-title">Methods: </strong>We recruited community-dwelling adults at the Minnesota State Fair and through contact lists of participants identifying interest in research done in the Brain Body Mind Lab (University of Minnesota). Community-dwelling adults with spinal cord injury (SCI) completed the FAS over Zoom. We analyzed the FAS using Rasch Measurement Theory, which produced the following outputs: item, and person fit, targeting, unidimensionality, person separation reliability (PSR), local item dependence (LID), principal component analysis of residuals (PCAR), and differential item functioning (DIF).</p> <p><strong class="sub-title">Results: </strong>We recruited 567 participants (average age 52.15 ± 17.5 years, 63.84% women), among which 14 adults with SCI. After rescoring 3 items and deleting 1 item, the FAS had good person and item fit (except item 4). The PCAR and subsequent paired <em>t</em>-tests (3.53%) confirmed the unidimensionality of the scale. There was no DIF and only one item pair had LID (item 5-6). PSR was 0.75, reflecting a capacity to differentiate groups of people with high or low functionality appreciation levels. However, there was a significant ceiling effect (28.04%) and the person mean location was 3.06 ± 2.07 logits, indicating the FAS is too easy for community-dwelling adults in the US.</p> <p><strong class="sub-title">Discussion: </strong>The 6-item Rasch-based FAS demonstrated unidimensionality, good item fit (except item 4) and person fit, but the FAS will require more difficult items to be added to improve the targeting of the scale, and better reliability.</p> </div> </div>
Data on soil variables (with plot IDs) and grassland species traits used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. Journal of Vegetation Science, 35, e13259. Available from: https://doi.org/10.1111/jvs.13259
<p>File <a href="../api/records/10983049/draft/files/Plot_IDs_990ua.txt/content" target="_blank" rel="noopener noreferrer">Plot_IDs_990ua.txt</a> contains the IDs of the 1-m2 plots used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. The plot data are stored in the sPlot database (PPBio South Brazilian Grassland Database).</p> <p>File <a href="../api/records/10983049/draft/files/E_990ua_21SoilVar.txt/content" target="_blank" rel="noopener noreferrer">E_990ua_21SoilVar.txt</a> contains data on soil variables evaluated in the 250 m transects, but here expanded to the 990 1-m2 plots (each transect was sampled using 10 1-m2 pots).</p> <p>File <a href="../api/records/10983049/draft/files/B_769spp_4t.txt/content" target="_blank" rel="noopener noreferrer">B_769spp_4t.txt</a> is the species trait database collected in the framework of several research projects in the Quantitative Ecology Lab (EcoQua) and Grassland Vegetation Studies Lab (LevCamp) of Universidade Federal do Rio Grande do Sul (UFRGS). Data gaps were filled by compiled from the TRY database and data imputation.</p> <p> </p> <p> </p>
A meta-analysis of the effects of habitat aridity, evolutionary history of grazing, and grazing intensity on bee and butterfly communities worldwide
<p>A variety of habitat-associated factors moderate effects of grazing on insect biodiversity. Here, we examine how aridity, evolutionary history of grazing, and grazing intensity individually and interactively mediate the effect of livestock grazing on pollinator diversity (native bees and butterflies).</p> <p>Using a meta-analysis of 59 studies published in the primary literature we characterized the response of pollinator communities to grazing across several continents.</p> <p>In very humid habitats high grazing intensities generally had negative impacts on pollinator abundance and richness, but these effects were not found in semi-arid habitats, where livestock grazing intensity did not interact with aridity to impact pollinator abundance or richness. However, within semi-arid habitats livestock grazing was associated with reduced pollinator richness in areas with short evolutionary histories grazing.</p> <p>Pollinator life history mediated effects of livestock grazing on pollinator communities: livestock grazing had negative impacts on richness of social bees and butterflies but not solitary bees, though abundances of all three pollinator categories were consistently reduced under livestock grazing.</p> <p>Our synthesis suggests that effects of cattle on pollinators may be driven by impacts on nesting habitats (e.g., soil compaction), rather than consumption or alteration of forb cover. Our collective findings have importance for coordinating grazing management and pollinator conservation efforts and help to distinguish how grazing practices could impact pollinator biodiversity across ecoclimatic regions.</p>
Code for data analysis - intra-community variability of leaf-out in temperate tree canopies
<p>The code and data were used for producing the results of "Phenology across scales: an intercontinental analysis of leaf-out dates in temperate deciduous tree communities", by Delpierre et al.</p>
Lemonade Creek, Yellowstone National Park, USA - Microbial Community Analysis - Metabolomics Data
<p>Polar metabolomics data (targeted and untargeted) used for analysis of microbial community function over a diurnal cycle in Lemonade Creek, Yellowstone National Park, USA.</p> <p> </p> <p><code>GNPS_positive-2.xlsx</code> Comparison of GNPS data used for main metabolite analysis with targeted metabolite features. Done to support the accuracy of the GNPS results for metabolites identified outside the targeted set.</p> <p> </p> <p><code>NEG_506963_FinalEMA-HILIC_Identifications.xlsx</code> Negative ionization targeted metabolite identification quality and confidence results (prepared by the Joint Genome Institute, USA).</p> <p><code>NEG_msms_mirror_plots.tar.gz</code> Negative ionization targeted metabolite mirror plots.</p> <p><code>NEG_peak_height.tab</code> Negative ionization targeted metabolite peak height file (main results file used for abundance analysis).</p> <p><code>POS_506963_FinalEMA-HILIC_Identifications.xlsx</code> Positive ionization targeted metabolite identification quality and confidence results (prepared by the Joint Genome Institute, USA).</p> <p><code>POS_msms_mirror_plots.tar.gz</code> Positive ionization targeted metabolite mirror plots.</p> <p><code>POS_peak_height.tab</code> Positive ionization targeted metabolite peak height file (main results file used for abundance analysis).</p> <p> </p> <p><code>NEG_peak_height.csv</code> Negative ionization untargeted metabolite peak height file (main results file used for abundance analysis).</p> <p><code>POS_peak_height.csv</code> Positive ionization untargeted metabolite peak height file (main results file used for abundance analysis).</p>
Figure 1 in Physicochemical, microbiological and parasitological analysis of water for human consumption in a quilombola community in Alagoas
Figure 1. Map of the quilombola community of Santa Luzia do Norte – AL. Source – Google Maps, 2019.
Example dataset for 18S rRNA microbial community analysis
<p>Original, trimmed (sequencing primers removed) and trimmed+subsampled reads for the Study Group lesson on Microbial Ecology.</p>
Figure 2 in Community analysis of soil-inhabiting nematodes in natural vegetations of Singalila National Park, West Bengal (India)
Figure 2. Taxonomic diversity (abundance and genera) of nematode orders in Singalila National Park.
Lemonade Creek, Yellowstone National Park, USA - Microbial Community Analysis - Cyanidiophyceae genome data for HGT analysis
<p>This dataset consists of 12 metagenome samples that were collected from one of three environments in Yellowstone National Park:</p> <ul> <li>4 samples (numbered 1, 2, 3, 4) are from the "CreekBiofilm" environment.</li> <li>4 samples (1, 2, 3, 4) are from the "Endolithic" environment.</li> <li>4 samples (1, 2, 3, 4) are from the "Soil" environment.</li> </ul> <p>We have found that there are two species of cyanidiophyceae present in these samples: one *Galdieria sulphuraria* (the `*Gsulp*` files) and one *Cyanidioschyzon merolae* (the `*Cmer*` files). For each of these species I extracted their contigs from the metagenome assembly if they had >=10% of their lengths covered by hits with >90% ID to the respective reference genome (i.e., contigs with >10% coverage of hits with >90% ID to a given reference genome). The majority of contigs have >90% hit coverage however, to prevent removal of contigs with novel sequences (arising via HGT or other processes), I used a lenient threshold of 10%. The naming of the files indicate which sample the contigs are from and which of the two cyanidiophyceae species they are putatively from. NOTE: that there are very few predicted proteins in the `YNP_CreekBiofilm_*_Gsulp*` files. This is because this environment is completely dominated by the other algal species and so we recovered very few contigs from this species from these environments.</p>
Dataset for the paper "Network-Based Differential Abundance Analysis: Bridging Community Interactions and Host-Microbiome Dynamics."
<p>The files with extension rds are files that contain simulated data and the tsv files contain original data along with their meta data.</p>
Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
<p>Raw data set for npj Bioflims and Microbiome article: “Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis”</p>
Supporting isotopic data for: Amino acid isotope analysis reveals variation in gut microbial contribution to host protein metabolism in a wild small mammal community
<p>Herbivory is a dominant feeding strategy among animals, yet herbivores are often protein limited. The gut microbiome is hypothesized to help maintain host protein balance by provisioning essential macromolecules, but this has never been tested in wild consumers. Using amino acid carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) isotope analysis, we estimated the proportional contributions of essential amino acids (AA<sub>ESS</sub>) synthesized by gut microbes to five co-occurring desert rodents representing herbivorous, omnivorous, and insectivorous functional groups. We found that herbivorous rodents occupying lower trophic positions (<em>Dipodomys </em>spp.) routed a substantial proportion (~40–50%) of their AA<sub>ESS</sub> from gut microbes, while higher trophic level omnivores (<em>Peromyscus </em>spp.) and insectivores (<em>Onychomys arenicola</em>) obtained most of their AA<sub>ESS</sub> (~58%) from plant-based energy channels but still received ~20% of their AA<sub>ESS</sub> from gut microbes. These findings empirically demonstrate that gut microbes play a key functional role in host protein metabolism in wild animals. </p>
Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.