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171 results for “environmental association”
Environmental DNA reveals fine-scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft and hard-bottom habitats
<p>Accurate knowledge on spatiotemporal distributions of marine species and their association with surrounding habitats is crucial to inform adaptive management actions responding to coastal degradation across the globe. Here, we investigate the potential use of environmental DNA (eDNA) to detect species-habitat associations in a patchy coastal area of the Baltic Sea. We directly compare species-specific qPCR analysis of eDNA with baited remote underwater video systems (BRUVS), two non-invasive methods widely used to monitor marine habitats. Four focal species (cod Gadus morhua, flounder Platichthys flesus, plaice Pleuronectes platessa and goldsinny wrasse Ctenolabrus rupestris) were selected based on contrasting habitat associations (reef- vs. sand-associated species), as well as differential levels of mobility and residency, to investigate whether these factors affected the detection of species-habitat associations from eDNA. To this end, a species-specific qPCR assay for goldsinny wrasse is developed and made available herein. In addition, potential correlations between eDNA signals and abundance counts (MaxN) from videos were assessed. Results from Bayesian multi-level models revealed strong evidence for a sand association for sedentary flounder (98% posterior probability) and a reef association for highly resident wrasse (99% posterior probability) using eDNA, in agreement with BRUVS. However, contrary to BRUVS, eDNA sampling did not detect habitat associations for cod or plaice. We found a positive correlation between eDNA detection and MaxN for wrasse (posterior probability 95%), but not for the remaining species and explanatory power of all relationships was generally limited. Our results indicate that eDNA sampling can detect species-habitat associations on a fine spatial scale, yet this ability likely depends on the mobility and residency of the target organism, with associations for sedentary or resident species most likely to be detected. Combined sampling with conventional non-invasive methods is advised to improve detection of habitat associations for mobile and transient species, or for species with low eDNA concentrations. </p>
Data of two neotropical Colaptes woodpeckers' nests fate and environmental features associated with them
<p><span>Understanding factors affecting nest survival of woodpeckers in threatened landscapes is a key tool for land managers, particularly when conservation depends on public policies. However, information of Neotropical woodpeckers breeding in southern temperate forests is noticeably sparse despite the worrying conservation status of these ecosystems and woodpeckers' key role as cavity providers. Our objective was to assess the relationship between tree cavity features, vegetation structure, and landscape configuration on the nest survival of the Green-barred Woodpecker (<em>Colaptes</em> <em>melanochloros</em>) and the Campo Flicker (<em>C</em>. <em>campestris</em>). We monitored nests of these woodpeckers during three breeding seasons from 2015–2018 in a woodland of east-central Argentina threatened by selective tree logging and soil material extraction. We recorded features that presumably influence nest survival at a micro-scale (cavity, cavity-tree features, and foliage cover around the cavity) and a macro-scale (forest cover and shape index within a 500 m circle around the nest). We did not find support for a relationship between daily nest survival rates (DSR) and cavity features, vegetation structure, or landscape configuration. However, </span><span>new cavities were more successful than reused ones for the Green-barred Woodpecker. We also found a surprisingly high rate (~33% of nest failures) of nest abandonment for both species. Abandonment may be a factor regulating this population and causes of abandonment warrants further investigation. Given the importance of new cavities to the success of Green-barred Woodpeckers, our results indicate the preservation of medium-size trees (20 cm < DBH < 50 cm) with wood softened by degradation processes (preferred by the species to excavate cavities) would facilitate persistence of both of this woodpecker and the cavity-nesting community. Effective audit of soil material extraction and controlled selective timber logging practices (including preservation of mature trees) in compliance with existing regulations could contribute to this type of habitat maintenance.</span></p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (16S rRNA gene sequencing data)
<p>Microbiome data accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals". Data is available for alpha- and beta- diversity, as well as for individual taxa both in binary and quantitative phenotypic representation. Data is available for 827 individuals that gave consent for their data to be shared outside of the Milieu intérieur consortium. </p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (Metadata)
<p>Associated demographic, lifestyle, environmental and biochemical metadata accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals". Data is available for 827 individuals that gave consent for their data to be shared outside of the Milieu intérieur consortium. </p>
Text-fig. 2 Associate Professor RNDr. Václav Ziegler CSc. in Faculty of Education of Charles University at Prague during Trends in didactics of biology, conference on the 20th anniversary of the restoration activities of the Department of Biology and Environmental Studies at the Faculty of Education of Charles University in Prague 2. October 2014. (photo: author 2014) in Václav Ziegler Septagenarian
Text-fig. 2 Associate Professor RNDr. Václav Ziegler CSc. in Faculty of Education of Charles University at Prague during Trends in didactics of biology, conference on the 20th anniversary of the restoration activities of the Department of Biology and Environmental Studies at the Faculty of Education of Charles University in Prague 2. October 2014. (photo: author 2014)
Wood Buffalo Environmental Association (WBEA) Historical Monitoring Data used in "Passive Tracer Modelling at Super-Resolution with WRF-ARW to Assess Mass-Balance Schemes"
<p>Wood Buffalo Environmental Association (WBEA) Historical Monitoring Data from two monitoring stations Bertha Ganter – Fort McKay and Barge Landing for 20 August 2013 to 2 September 2013. This data was used in "Passive Tracer Modelling at Super-Resolution with WRF-ARW to Assess Mass-Balance Schemes" (Fathi et al., 2022 - egusphere-2022-1125) for model output and observational data comparisons. The same data can be accessed and downloaded from "<a href="https://wbea.org/historical-monitoring-data/">https://wbea.org/historical-monitoring-data/</a>".</p>
Environmental context and herbivore traits mediate the strength of associational effects in a meta-analysis of crop diversity
<p>1. Crop diversification offers a promising solution to meet expanding global food demands while maintaining ecosystem services. Diversification strategies that employ mixed planting to reduce pest damage (e.g., intercropping), termed "associational effects" (AE) in the ecological literature, can decrease (associational resistance) or increase (associational susceptibility) herbivore abundance on a focal plant. While application of AE to agroecosystems typically reduces pest abundance, the range of outcomes varies widely.</p> <p>2. We conducted a meta-analysis using 272 estimates of insect herbivore abundance on crops neighbored by a conspecific or heterospecific from 44 studies undertaken on six continents. We focus on four agricultural crops well-represented from sites across the globe to test hypotheses related to understanding how herbivore traits (diet breadth, feeding guild, origin), plant traits (crop type, phylogenetic distance to neighbor), and environmental context (climate, experimental design) contribute to variation in the outcomes of associational effects.</p> <p>3. Overall, bicultures provided a strong reduction of insect abundance on the focal crop. Climate and interactions between herbivore traits, particularly diet breadth and origin, and plant traits or environmental context mediated the strength of associational effects.</p> <p>4. Bicultures provided the strongest reductions in insect abundance at low latitudes and this effect decreased at higher latitudes, but only for insects with certain traits. Abundance of generalist herbivores and globally distributed pests tended to be most strongly negatively affected by bicultures, under certain contexts, whereas specialist herbivores and native pests were less affected by neighbors.</p> <p>5. Synthesis and application. This meta-analysis highlights that variability in AE is determined in part by the interactive effects of herbivore traits and environmental context and provides guidance for incorporating beneficial ecological interactions into integrated pest management strategies.</p>
Files associated with Christopher Holder and Anand Gnanadesikan, How well do Earth System Models capture apparent relationships between phytoplankton biomass and environmental variables? [Version 1]
<p><strong>1. process_cmip_rf.m</strong> is a matlab script that reads a single file, generates a random forest using the parameters in the associated paper and computes permutation importance and sensitivities. Note- in order to get process_cmip_rf.m to work as written you must have the Statistics and Machine Learning toolbox installed on Matlab and download the table_modis.asc file below. </p> <p>Files 2-16 are tabular filew containing all datapoints used in Random Forest analysis for the NCAR CESM2 model. Columns are</p> <p> 1. Index of point, enabling a mapping back to the model grid if the resolution is known.</p> <p> 2. Longitude</p> <p> 3. Latitude</p> <p> 4. Month</p> <p> 5. Iron in mol/m<sup>3</sup>.</p> <p> 6. Mixed layer in m.</p> <p> 7. Ammonia in mol/m<sup>3</sup></p> <p> 8. Nitrate in mol/m<sup>3</sup>.</p> <p> 9. Phytoplankton carbon in mol/m<sup>3</sup>.</p> <p> 10. Phosphate in mol/m<sup>3</sup>.</p> <p> 11. Shortwave radiation (net solar radiation at ocean surface in W/m<sup>2</sup>).</p> <p> 12. Silicate in mol/m<sup>3</sup>.</p> <p> 13. Salinity in PSU</p> <p> 14. Temperature in C.</p> <p> 15. Upwelling velocity in m/s.</p> <p>If variable is not included in the dataset, the column will be filled with zeros.</p> <p><strong>2.table_cesm2.asc:</strong> Data created from Danabasoglu, G., 2019, NCAR CESM model output prepared for CMIP6 CMIP esm-pi-control <a href="http://doi.org/10.22033/ESGF/CMIP6.7579">http://doi.org/10.22033/ESGF/CMIP6.7579</a>. Grid is 360x180x12</p> <p><strong>3.table_cems2_fv2.asc:</strong> Data created from Danabasoglu, G., 2019, NCAR CESM-FV2 model output prepared for CMIP6 CMIP pi-control <a href="http://doi.org/10.22033/ESGF/CMIP6.11301">http://doi.org/10.22033/ESGF/CMIP6.11301</a>. Grid is 360x180x12</p> <p><strong>4. table_cesm2_waccm.asc: </strong>Data created from Danabasoglu, G., 2019, NCAR CESM2-WACCM model output prepared for CMIP6 CMIP piControl <a href="http://doi.org/10.22033/ESGF/CMIP6.10094">http://doi.org/10.22033/ESGF/CMIP6.10094</a>. Grid is 360x180x12</p> <p><strong>5. table_cesm2_waccm_fv2.asc</strong>: Data created from Danabasoglu, G., 2019, NCAR CESM-WACCM-FV2 model output prepared for CMIP CMIP piControl, <a href="http://doi.org/10.22033/ESGF/CMIP6.11302">http://doi.org/10.22033/ESGF/CMIP6.11302</a>. Grid is 360x180x12</p> <p><strong>6. table_gfdl_cm4.asc</strong>: Data created from Guo, Huan; John, Jasmin G; Blanton, Chris et al,2018, NOAA-GFDL GFDL-CM4 model output piControl, <a href="http://doi.org/10.22033/ESGF/CMIP6.8666">http://doi.org/10.22033/ESGF/CMIP6.8666</a>. Grid is 360x180x12</p> <p><strong>7.table_gfdl_esm4.asc</strong> Data created from Krasting, John P.; John, Jasmin G; Blanton, Chris et al., 2018, NOAA-GFDL GFDL-ESM4 model output prepared for CMIP6 CMIP piControl, <a href="http://doi.org/10.22033/ESGF/CMIP6.8669">http://doi.org/10.22033/ESGF/CMIP6.8669</a>. Grid 360x180x12</p> <p><strong>8. table_ipsl_cm5a2_inca.asc:</strong> Data created from Boucher, Olivier; Denvil, Sébastien; Levavasseur, Guillaume et al.: 2021, IPSL IPSL-CM5A2-INCA model output prepared for CMIP6 CMIP piControl <a href="http://doi.org/10.22033/ESGF/CMIP6.13683">http://doi.org/10.22033/ESGF/CMIP6.13683</a>. Grid is 182x149x12</p> <p><strong>9.</strong> <strong>table_ipsl_cm6a_lr.asc:</strong> Data created from Boucher, Olivier; Denvil, Sébastien; Levavasseur, Guillaume et al., 2018:, IPSL IPSL-CM6A-LR model output prepared for CMIP6 CMIP piControl, <a href="http://doi.org/10.22033/ESGF/CMIP6.5251">http://doi.org/10.22033/ESGF/CMIP6.5251</a>. Grid is 362x332x12.</p> <p><strong>10</strong>. <strong>table_mpi_esm1-2-ham.asc:</strong> Neubauer, David; Ferrachat, Sylvaine; Siegenthaler-Le Drian, Colombe et al., 2019: HAMMOZ-Consortium MPI-ESM1.2-HAM model output prepared for CMIP6 CMIP piControl, <a href="http://doi.org/10.22033/ESGF/CMIP6.5037">http://doi.org/10.22033/ESGF/CMIP6.5037</a>. Grid is 256x220x12.</p> <p><strong>11</strong>. <strong>table_mpi_esm1-2-hr.asc:</strong> Data created from Jungclaus, Johann; Bittner, Matthias; Wieners, Karl-Hermann et al., 2019: MPI-M MPI-ESM1.2-HR model output prepared for CMIP6 CMIP piControl <a href="http://doi.org/10.22033/ESGF/CMIP6.6674">http://doi.org/10.22033/ESGF/CMIP6.6674</a>. Grid is 802x404x12.</p> <p><strong>12</strong>. <strong>table_mpi_esm1-2-lr.asc:</strong> Data created from Wieners, Karl-Hermann; Giorgetta, Marco; Jungclaus, Johann et al. 2019:MPI-M MPI-ESM1.2-LR model output prepared for CMIP6 CMIP piControl</p> <p> <a href="http://doi.org/10.22033/ESGF/CMIP6.6675">http://doi.org/10.22033/ESGF/CMIP6.6675</a>. Grid is 256x220x12.</p> <p><strong>13. </strong><strong>table_noresm2-lm.asc: </strong>Seland, Øyvind; Bentsen, Mats; Oliviè, Dirk Jan Leo et al.,2019 NCC NorESM2-LM model output prepared for CMIP6 CMIP piControl, <a href="http://doi.org/10.22033/ESGF/CMIP6.8217">http://doi.org/10.22033/ESGF/CMIP6.8217</a>. Grid is 360x385x12</p> <p><strong>14.</strong><strong> table_noresm2-mm.asc</strong>: Data created from Bentsen, Mats; Oliviè, Dirk Jan Leo; Seland, Øyvind et al.,2019 <strong>:</strong> NCC NorESM2-MM model output prepared for CMIP6 CMIP piControl, <a href="http://doi.org/10.22033/ESGF/CMIP6.8221">http://doi.org/10.22033/ESGF/CMIP6.8221</a>. Grid is 360x385x12.</p> <p>15-16. <strong>table_kostadinov.asc, </strong><strong>table_modis.asc</strong> Data is a merger of observational products and model output Observational climatologies for temperature, salinity, mixed layer depth, silicate, phosphate, and nitrate were downloaded from the World Ocean Atlas (WOA) 2018 (Garcia et al., 2019; Locarnini et al., 2019; Zweng et al., 2019). MODIS-POC was downloaded from oceancolor.nasa.gov. Kostadinov POC is taken from <a href="https://doi.pangaea.de/10.1594/PANGAEA.859005">https://doi.org/10.1594/PANGAEA.859005</a> Grid is 360x180x12.</p>
Associated Dataset for Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes
<p>The dataset contains the final methylation call set (n=14,627,533), variant calling file for population genomics analyses, analysis codes/scripts, and other associated files related to the research (Constitutive and variable patterns of genome-wide DNA methylation in populations from spatial-environmental range extremes of the bumble bee <em>Bombus vosnesenskii)</em>. Raw WGBS reads generated in this study have been deposited and are currently available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under NCBI BioProject PRJNA956115.</p>
Distribution System Environmental and Sequencing Datasets for Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking Water Associated Pathogens in a Full-Scale Drinking Water Distribution System
<p>The dataset of environmental parameters and sequence fastqs used to create figures and do analysis in the paper <strong>Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking Water Associated Pathogens in a Full-Scale Drinking Water Distribution System </strong>submitted to Environmental Science & Technology</p>
Environmental DNA reveals fine-scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft and hard-bottom habitats
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Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities
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Data of two neotropical Colaptes woodpeckers' nests fate and environmental features associated with them
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Data from: Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri
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Raw amplitude measurements for arctic bird vocalizations from Utqiagvik, Alaska, with associated environmental data and modelling code
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Environmental context and herbivore traits mediate the strength of associational effects in a meta-analysis of crop diversity
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Data from: Environmental variation associated with topography explains butterfly diversity along a tropical elevation gradient
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Environmental, molecular, and life history data associated with ecological and evolutionary nematode responses to soil phosphorus availability, McMurdo Dry Valleys, Antarctica
Elemental stoichiometry is a useful theoretical framework for understanding the sources and controls on nutrient availability that can structure the composition, diversity, and life history of biotic communities. One such relationship, as postulated by the growth rate hypothesis (GRH), is that organismal development rate is positively linked to cellular phosphorus (P). To test the GRH as part of the McMurdo Dry Valleys Long Term Ecological Research (LTER) program, we examined the effects of phosphorus (P) availability both in situ and in vitro, on the evolution of growth and development of free-living soil nematodes (primarily Plectus murrayi) that occur in the McMurdo Dry Valleys of Antarctica. During the 2008-2009 austral summer, we collected soils from two glacial till sequences, the Ross Sea till and Taylor II till, occurring in the Lake Fryxell and Lake Bonney basins, respectively, of Taylor Valley. Through a variety of subsequent analyses, we generated the environmental, molecular, and life history trait data contained herein. In addition, this package contains body size and biomass data for nematodes isolated from soil samples collected during the 1999-2000 and 2004-2005 austral summers.
Data from: Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes
Morphological plasticity is a genotype-by-environment interaction that enables organisms to increase fitness across varying environments. Symbioses with diverse microbiota may aid in acclimating to this variation, but whether the associated bacteria community is phenotype-specific remains unstudied. Here we induce morphological plasticity in three species of sea urchins and measure changes in the associated bacterial community. While each host species had unique microbial communities, the expression of morphological plasticity resulted in the convergence for a phenotype-specific microbiome that was, in part, driven by differentially associating with α- and γ-proteobacteria. Furthermore, these results suggest that phenotype-specific signatures were the product of the environment, and are correlated with ingestive and digestive structures. By manipulating diet quantity over time, we also support that differentially associating with microbiota along a phenotypic continuum is bidirectional. Taken together, our data support the idea of a phenotype-specific microbial community and that phenotypic plasticity extends beyond a genotype-by-environment interaction.
Tick microbiomes in neotropical forest fragments are best explained by tick-associated and environmental factors rather than host blood source
<p>The composition of tick microbiomes varies both within and among tick species. Whether this variation is intrinsic (related to tick characteristics), or extrinsic (related to vertebrate host and habitat) is poorly understood but important, as microbiota can influence the reproductive success and vector competence of ticks. We aimed to uncover what intrinsic and extrinsic factors best explain the microbial composition and taxon richness of 11 species of Neotropical ticks, collected from eight species of small mammals in 18 forest fragments across central Panama. Microbial richness varied among tick species, life stages, and collection sites, but was not related to host blood source. Microbiome composition was best explained by tick life stage, with bacterial assemblages of larvae being a subset of those of nymphs. Collection site explained most of the bacterial taxa with differential abundance across intrinsic and extrinsic factors. <i>Francisella </i>and <i>Rickettsia </i>were highly prevalent, but their proportional abundance differed greatly among tick species and we found both positive and negative co-occurrence between members of these two genera. Other tick endosymbionts (e.g. <i>Coxiella</i>, <i>Rickettsiella</i>) were associated with specific tick species. In addition, we detected <i>Anaplasma</i> and <i>Bartonella </i>in several tick species. Our results indicate that the microbial composition and richness of Neotropical ticks are principally related to intrinsic factors (tick species, life stage) and collection site. Taken together, our analysis informs how tick microbiomes are structured and can help anchor our understanding of tick microbiomes from tropical environments more broadly.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.