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364 results for “Community: dynamics”
Data from: Rate of permafrost thaw and associated plant community dynamics in peatlands of northwestern Canada
<p>This dataset was collected to document the changing plant community, and associated environmental factors, as warming climate conditions accelerate permafrost thaw in northern peatland environments. Due to the insulative properties of dry, surface peat layers, discontinuous permafrost is preferentially found in peatlands, termed peat plateaux, where the volumetric expansion of ice-rich permafrost has resulted in a raised, dry ground surface dominated by lichens and, often, stunted black spruce forests. As ground temperatures warm, and the ice-rich permafrost thaws, the ground surface sinks to, or below, the water table, and these peat plateau environments change dramatically from black spruce and lichen-dominated peat plateaux to treeless moss- and sedge-dominated collapse scar environments. Data are from a set of 17 sites distributed along a latitudinal gradient in the Mackenzie Valley of Northwestern Canada. At each site, a transect of five to nine contiguous 1x1m quadrats was sampled, spanning the transition from peat plateau to collapse scar environments and, thus, capturing the zone of active permafrost thaw within peat plateaux as they transition to collapse scars. Fourteen of these sites were sampled at two time periods: 2007 and 2008 (T1: time 1), and 2017 and 2018 (T2: time 2) enabling an assessment of 10-year changes (9 years for one site). This dataset includes quadrat-level measurements of plant community composition (percent cover by species), frost depth, water table depth, peat depth, soil moisture, and canopy cover. Site level measurements consist of maximum peat depth, along with pH and electrical conductivity of collapse scar water samples, as well as the annual rate of lateral permafrost thaw. We also include basic site location parameters, as well as several climatic parameters, interpolated for each site using BioSIM software.</p>
Assembly, persistence, and disassembly dynamics of Quaternary Caribbean frugivore communities
<p>How communities assemble and restructure is of critical importance to ecological theory, evolutionary theory, and conservation, but long-term perspectives on the patterns and processes of community assembly are rarely integrated into traditional community ecology, and the utility of communities as an ecological concept has been repeatedly questioned in part due to a lack of temporal perspective. Through a synthesis of paleontological and neontological data, I reconstruct Caribbean frugivore communities over the Quaternary (2.58 mya – present). Numerous Caribbean frugivore lineages arise during periods coincident with the global origins of plant-frugivore mutualisms. The persistence of many of these lineages into the Quaternary is indicative of long-term community stability, but an analysis of Quaternary extinctions reveals a non-random loss of large-bodied mammalian and reptilian frugivores. Anthropogenic impacts, including human niche construction, underlie the recent reorganization of frugivore communities, setting the stage for continued declines and evolutionary responses in plants that have lost mutualistic partners. These impacts also support ongoing and future introductions of invader complexes: introduced plants and frugivores that further exacerbate native biodiversity loss by interacting more strongly with one another than with native plants or frugivores. This work illustrates the importance of paleontological data and perspectives in conceptualizing ecological communities, which are dynamic and important entities.</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>
Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
1.Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. 2.Here we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype specific transmission pathways in a social carnivore. 3.We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father and/or mother offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks, or co-infection best structured the FIVPle network. 4.While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype specific. 5.Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.
Dataset - Dynamic persistence of intracellular bacterial communities of uropathogenic Escherichia coli in a human bladder-chip model of urinary tract infections
<p>Dataset for manuscript posted at biorxiv: https://doi.org/10.1101/2021.01.03.42483 and in revision for eLife. Data corresponding to each main figure and its associated figure supplements are in seperate .zip folders.</p>
Understanding arid‐region waterbird community dynamics during lake dry‐downs
<p>These data were collected to explore changes in the bird community associated with Lake Ngami, Botswana, through successive drydown periods. Our analysis shows significant shifts, driven partially by changes in water level, in the species composition of the bird community over the period of study. The data set contains standardised half-hour point counts for the bird community of Lake Ngami, Botswana; and R code used for community-level analyses of the resulting time series. Counts were undertaken every 4 months from October 2007-July 2009.</p> <p>We used the data to test three theoretical predictions: simplification of the bird community over time due to a reduction in habitat area and concurrent niche loss; large fluctuations in densities of mobile, opportunistic species; and high variance in predator and prey abundance. Despite temporal variance in species accumulation, we observed no obvious simplification of the bird community over time. There were distinct but consistent groupings of abundance and composition across transitional stages in lake water levels. The data do show some rapid shifts in functional composition, such as loss of deepwater foragers; winners and losers also occurred within foraging guilds.</p>
Multispecies modelling reveals potential for habitat restoration to re-establish boreal vertebrate community dynamics
<p>1. The restoration of habitats degraded by industrial disturbance is essential for achieving conservation objectives in disturbed landscapes. In boreal ecosystems, disturbances from seismic exploration lines and other linear features have adversely affected biodiversity, most notably leading to declines in threatened woodland caribou. Large-scale restoration of disturbed habitats is needed, yet empirical assessments of restoration effectiveness on wildlife communities remain rare.</p> <p>2. We used 73 camera trap deployments from 2015-2019 and joint species distribution models to investigate how habitat use by the larger vertebrate community (>0.2 kg) responded to variation in key seismic line characteristics (line-of-sight, width, density and mounding) following restoration treatments in a landscape disturbed by oil and gas development in northeastern Alberta.</p> <p>3. The proportion of variation explained by line characteristics was low in comparison to habitat type and season, suggesting short-term responses to restoration treatments were relatively weak. However, we predicted that lines with characteristics consistent with restored conditions would support altered community composition, with reduced use by wolf and coyote, thereby indicating that line restoration will result in reduced contact rates between caribou and these key predators.</p> <p>4. Our analysis provides a framework to assess and predict wildlife community responses to emerging restoration efforts. With the growing importance of habitat restoration for caribou and other vertebrate species, we recommend longer-term monitoring combined with landscape-scale comparisons of different restoration approaches to more fully understand and direct these critical conservation investments. Only by combining rigorous multispecies monitoring with large-scale restoration will we effectively conserve biodiversity within rapidly changing environments.</p>
Data from: Diversification dynamics in Caribbean rain frogs (Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation
<p><span>Adaptive radiation</span><span> is proposed to play a key role in generating differences in species richness among lineages and geographic regions. Due to the importance of ecological divergence in adaptive radiation, species richness is predicted to be influenced by equilibrium diversity dynamics, although the concept continues to generate much debate. An additional important question is whether radiating clades have intrinsic biological characteristics that make them particularly prone to diversify. We tackle these questions by analyzing <em>i</em>) the temporal patterns of diversification of Caribbean <em>Eleutherodactylus</em> frogs, and <em>ii</em>) assembly of the complete native anuran community of the Caribbean archipelago (197 species), testing for the presence of equilibrium dynamics and whether diversification patterns of <em>Eleutherodactylus</em> differ from those of the rest of the Caribbean anurans. Diversification rates follow the predicted pattern of rapid diversification early in the radiation, which gradually decreases towards the present. <em>Eleutherodactylus</em> diversification is significantly faster than that of the Caribbean anuran community, and although equilibrium dynamics influence richness of all Caribbean anurans, <em>Eleutherodactylus</em> shows higher carrying capacity. Our results indicate that ecological opportunity <em>per se</em> is not sufficient for adaptive radiation and that diverse lineages present intrinsic characteristics that enable them to make the most of available opportunity.</span></p>
Revealing the drivers of parasite community assembly: using avian haemosporidians to model global dynamics of parasite species turnover
<p>Why do some regions share more or fewer species than others? Community assembly relies on the ability of individuals to disperse, colonize, and thrive in new regions. Therefore, many distinct factors, such as geographic distance and environmental features, can determine the odds of a species colonizing a new environment. For parasites, host community composition (i.e., resources) also plays a key role in their ability to colonize a new environment as they rely on their hosts to complete their life cycle. Thus, variation in host community composition and environmental conditions should determine parasite turnover among regions. Here, we explored the global drivers of parasite turnover using avian malaria and malaria-like (haemosporidian) parasites. We compiled global databases on avian haemosporidian lineages distributions, environmental conditions, avian species distributions and functional traits and ran generalized dissimilarity models to uncover the main drivers of parasite turnover. We demonstrated that haemosporidian parasite turnover is mainly driven by geographic distance followed by host functional traits, environmental conditions, and host distributions. The main host functional traits associated with high parasite turnover were the predominance of resident (i.e., non-migratory) species and strong territoriality while the most important climatic drivers of haemosporidian turnover were mean temperature and temperature seasonality. Overall, we establish the importance of geographic distance as a key predictor of ecological dissimilarity and show that host resources influence parasite turnover more strongly than environmental conditions. We also evidenced that parasite turnover is most pronounced among tropical and less interconnected regions (i.e., regions with mostly territorial and non-migratory hosts). Our findings provide a robust foundation for the prediction of avian pathogen spread and the emergence of infectious diseases.</p>
Supplementary Tables and Datasets for publication: Spatial and finely tuned temporal metagenomics of river compartments reveals viral community dynamics in an urban stream
<p>This is a data dump of the tables, genomes, and .faa files that were too large to submit as part of the publication titled: Spatial and finely tuned temporal metagenomics of river compartments reveals viral community dynamics in an urban stream</p> <p> </p> <p>Files here include:</p> <p>-Fasta file containing 1230 vMAGs.</p> <p>-Zip file containing individual fasta files for 125 MAGs</p> <p>-Annotations output for DRAM and DRAM-v for all MAGs and vMAGs</p> <p>-.faa proteins file for the full Freshwater / Wastewater / TARA Oceans dataset that was used for vContact2 biogeography analyses</p>
Sims et al. A Tale of Two Pools: The Dynamic Influence of Subsurface Geological Processes on the Assembly and Diversification of Thermophilic Microbial Communities in Hydrothermal Systems - Supplementary Datasets
<p>These datasets comprise the supplementary datasets found in Sims et al. A Tale of Two Pools: The Dynamic Influence of Subsurface Geological Processes on the Assembly and Diversification of Thermophilic Microbial Communities in Hydrothermal Systems, <strong><em>Geochimica et Cosmiochimica Act </em></strong></p>
Spatio-temporal dynamics of insect communities in constructed and natural tidal marshes with distinct landscape positions
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Data from: Distance-dependent seedling mortality and long-term spacing dynamics in a neotropical forest community
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Assembly, persistence, and disassembly dynamics of Quaternary Caribbean frugivore communities
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Data from: Hydrological dynamics, wetland morphology and vegetation structure determine riparian arthropod communities in constructed wetlands
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Data from: Spatiotemporal dynamics of the ant community in a dry forest differ by vertical strata but not by successional stage
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Data from: Diversification dynamics in Caribbean rain frogs (Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation
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Data from: Seasonal dynamics in terrestrial insect communities after the impact of the Brumadinho Tailings Dam Disaster
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Data from: Moss community dynamics and canopy-mediated environmental influences during primary succession in a glacier retreat zone
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A dynamic ancestral graph model and GPU-based simulation of a community based on metagenomic sampling
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.