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328 results for “Ecology: community”
Microbial Community Composition in lakes - Ecological characteristics of the sample at North Temperate Lakes LTER 2002 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by ecological characteristics of the sample allows the user to retrieve sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The data can be filtered by lake name, sample date, lake information (region, type, size, depth), and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The output includes links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample
warmXtrophic: plant community responses to the individual and interactive effects of climate warming and herbivory across multiple years at Kellogg Biological Station Long-Term Ecological Research Sites (KBS LTER), Michigan, USA, and University of Michigan Biological Station (UMBS), Michigan, USA.
Climate change has both direct and indirect effects on ecological communities. Whereas most climate change ecology experiments manipulate abiotic drivers to measure direct effects of climate on species or communities, fewer quantify the indirect effects through biotic interactions, especially over multiple sites and years. In this factorial experiment we manipulate temperature through open-top chambers, and the level of insect herbivory through insecticide. At two early successional field sites separated by 3 degrees of latitude and 3°C of mean annual temperature (University of Michigan Biological Station, Pellston, MI and Kellogg Biological Station, Hickory Corners, MI), 6 replicate 1-m2 plots per treatment were installed in May 2015. 12 plots per site are at ambient temperature, 12 are warmed with year-round non-UV filtering polycarbonate and wood frame construction OTCs for tall-stature plants (Welshofer et al. 2018 MEE). Insecticide reduces insect herbivory in half the plots (Welshofer et al. 2018 Oecologia). Over the course of the experiment, OTCs warmed the plant communities by 1.9°C-3.0°C on average over the growing season. Each year, through 2021, plant traits and community responses were measured at the species level: plant phenology (green-up, flowering, flowering duration, seed set); plant percent cover (aerial % cover of the 1m2 plot); plant traits (specific leaf area, C and N content), herbivory damage to leaves, and plant species biomass (only in 2021). Further methodological details are found within each response variable metadata. This experiment is ongoing and further data package updates are planned. L0 data is available upon request. R scripts can be found here: https://github.com/SpaCE-Lab-MSU/warmXtrophic. The biotic and abiotic community context and relative strengths of direct vs. indirect effects may yield ecological surprises under climate change unless addressed together. Large-scale experiments like this one can improve our ability to unde
Environmental and ecological controls of coral community metabolism on Palmyra Atoll
These data sets describe Palmyra Atoll coral reef Environmental and ecological controls of coral community metabolism. Data was collected between August—October 2012. Data in this package was published under: Koweek, D., R. Dunbar, J. Rogers, G. Williams, N. Price, D. Mucciarone, and L. Teneva, Environmental and ecological controls of coral community metabolism on Palmyra Atoll Coral Reefs. There are six data files associated with Koweek et al. This data was originally published at NOAA’s National Center for Environmental Information. See Data Provenance section for more details.
MCR LTER: Coral Reef: Priority effects in coral-macroalgae interactions can drive alternate community paths in the absence of top-down control, data for Adam 2022 Ecology
These data were generated in support of the manuscript: Adam TC, Holbrook SJ, Burkepile DE, Speare KE, Brooks AJ, Ladd MC, Shantz AA, Thurber RLV, and Schmitt RJ, Ecology The outcomes of species interactions can vary greatly in time and space with the outcomes of some interactions determined by priority effects. On coral reefs, benthic algae rapidly colonize the disturbed substrate. In the absence of top-down control from herbivorous fishes, these algae can inhibit the recruitment of reef-building corals, leading to a persistent phase shift to a macroalgae-dominated state. Yet, corals may also inhibit colonization by macroalgae, and thus the effects of herbivores on algal communities may be strongest following disturbances that reduce coral cover. Here, we report results from experiments conducted on the fore reef of Moorea, French Polynesia, where we: 1) tested the ability of macroalgae to invade coral-dominated and coral-depauperate communities under different levels of herbivory, 2) explored the ability of juvenile corals (Pocillopora spp.) to suppress macroalgae, and 3) quantified the direct and indirect effects of fish herbivores and corallivores on juvenile corals. We found that macroalgae proliferated when herbivory was low but only in recently disturbed communities where coral cover was also low. When coral cover was < 10%, macroalgae increased 20-fold within one year under reduced herbivory conditions relative to high herbivory controls. Yet, when coral cover was high (50%), macroalgae were suppressed irrespective of the level of herbivory despite ample space for algal colonization. Once established in communities with low herbivory and low coral cover, macroalgae suppressed recruitment of coral larvae, reducing the capacity for coral replenishment. However, when we experimentally established small juvenile corals (2 cm diameter) following a disturbance, juvenile corals inhibited macroalgae from invading local neighborhoods, even in the absence of herbivore
Data and script: Community size can affect the signals of ecological drift and niche selection on biodiversity
<p>Updated version of the code. Data files are the same. This is the final version of the code, associated with a manuscript published in Ecology (doi: 10.1002/ecy.3014). A preprint is also available: https://www.biorxiv.org/content/10.1101/515098v1.abstract</p> <p>This is a unique dataset on insect communities sampled identically in a total of 200 streams in climatically highly different regions (100 in Brazil and 100 in Finland). The sampling design included 5 streams (communities) per watershed and provided us replicates of metacommunities (watersheds). Data also include information on in-stream variables (such as current velocity (m/s), depth (cm), stream width (cm), % of sand (0.25-2 mm), gravel (2-16 mm), pebble (16-64 mm), cobble (64-256 mm), and boulder (256-1024 mm), % of canopy cover by riparian vegetation, pH, conductivity, total nitrogen, and total phosphorus) and catchment level variables (such as average slope, % of native forest cover, pasture, agriculture, planted forests, urban areas, mining, water bodies, bare soil, secondary forest cover, and mixed land uses).</p> <p>In addition to the dataset, here we also provide and R code used to investigate the relationship between beta diversity and community size. This code calculates 4 types of beta-diversity metric for each of 100 watersheds (5 streams) in Brazil and Finland. Beta diversity: Sorensen and Bray-Curtis dissimilarity between all pairs. Beta deviation from null models: Raup-Crick (vegan version) and Bray-Curtis beta-deviation (based on the scripts by Chris Catano and Jonathan Myers). These beta diversity metrics are modelled against community size, environmental heterogeneity and spatial extent.</p> <p> </p>
Structure and composition and carbon Stocks of woody plant community in assisted and unassisted ecological succession in a Tamaulipan thornscrub, Mexico
<p>In November of 2017, the structure and composition of woody plant communities were investigated through a floristic composition and diversity evaluation on three areas: a control area, an assisted ecological succession area and an unassisted ecological succession area.</p>
Ecological barriers mediate spatiotemporal shifts of bird communities at a continental scale
<p>### Ecological barriers mediate spatiotemporal shifts of bird communities ###</p> <p>Marjakangas, Bosco et al. 2022</p> <p>Methods explained in the publication (open access)</p> <p>--> readme file explains how to use the data and code</p>
Temporal heterogeneity increases with spatial heterogeneity in ecological communities
Heterogeneity is increasingly recognized as a foundational characteristic of ecological systems. Indeed, spatial heterogeneity is commonly used in alternative state theory as an early indicator of regime shifts. To evaluate if spatial heterogeneity of communities is a predictor of temporal heterogeneity, we used mixed effects models to synthesize 68 community datasets spanning freshwater and terrestrial systems where measures of species abundance were replicated over space and time. Overall, we found a significant positive relationship between spatial and temporal heterogeneity across all ecosystems. In addition, lifespan and successional stage were related to temporal heterogeneity. Therefore we found evidence that spatial heterogeneity is a potential tool to predict temporal heterogeneity in ecological communities. This data package consists of six files. First we used a (1) R script to derive community dynamic metrics from source files to calculate (2) spatial and temporal heterogeneity over time as well as other measures of the community. We used this derived dataset to run analyses (3) with a R script to study the relationship between spatial and temporal heterogeneity communities. These analyses resulted in three figures, (4) the overall relationship between spatial and temporal heterogeneity, (5) output of mixed models investigating how experimental and biological factors affect this relationship, and (6) figures exploring how lifespan of the study organism affects the relationship between spatial and temporal datasets.
Figure 4 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 4. Copepod species composition (centre) and copepodid stage structures of the dominant species (left: Oyashio region, right: Okhotsk Sea). All data are integrated means of a 0– 500 m water column based on the IONESS samples in the Oyashio region (St. 19) and Okhotsk Sea (St. OK24) from October to November 1996. Error bars for the copepodid stage indicate standard deviations of each daily duplicate.
Figure 3 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 3. Vertical distribution of zooplankton biovolume in the Oyashio region (upper panels) and Okhotsk Sea (lower panels) from September to December in 1996–1998. Note that the biovolume axes are not the same between panels. Tc: thermocline.
SSP: An R package to estimate sampling effort in studies of ecological communities
<p>SSP (simulation-based sampling protocol) is an R package that uses simulations of ecological data and dissimilarity-based multivariate standard error (MultSE) as an estimator of precision to evaluate the adequacy of different sampling efforts for studies that will test hypothesis using permutational multivariate analysis of variance. The procedure consists in simulating several extensive data matrixes that mimic some of the relevant ecological features of the community of interest using a pilot data set. For each simulated data, several sampling efforts are repeatedly executed and MultSE calculated. The mean value, 0.025 and 0.975 quantiles of MultSE for each sampling effort across all simulated data are then estimated and standardized regarding the lowest sampling effort. The optimal sampling effort is identified as that in which the increase in sampling effort does not improve the highest MultSE beyond a threshold value (e.g. 2.5 %). The performance of SSP was validated using real data. In all three cases, the simulated data mimicked the real data and allowed to evaluate the relationship MultSE – n beyond the sampling size of the pilot studies. SSP can be used to estimate sample size in a wide variety of situations, ranging from simple (e.g. single site) to more complex (e.g. several sites for different habitats) experimental designs. The latter constitutes an important advantage in the context of multi-scale studies in ecology. An online version of SSP is available for users without an R background.</p>
Data for manuscript: Ecological lags govern the pace and outcome of plant community responses to 21st century climate change
<p>These data were used in the analyses reported in Block et al. "Ecological lags govern the pace and outcome of plant community responses to 21st century climate change".</p>
R code and data for: How much is enough? Minimum sample sizes in community ecology
<p>minimum_sample_sizes_code.R includes the complete set of instructions used to carry out the analyses in the related manuscript, plus save the computed data files and generate the text figures. data_files.tar.gz includes all of the files generated by the R code.</p>
FIGURE 4 in What are the best modern analogs for ancient South American mammal communities? Evidence from ecological diversity analysis (EDA)
FIGURE 4. Linear regression of MAP on correspondence axis 1 (CA1) score; estimated MAP for each of fossil locality based on CA1 score is indicated. Abbreviations: LV, La Venta; QH, Quebrada Honda; RU, Rümikon; SC, Santa Cruz; TG, Tinguiririca.
FIGURE 6. Classification Tree results and predictions for the five fossil localities. A in What are the best modern analogs for ancient South American mammal communities? Evidence from ecological diversity analysis (EDA)
FIGURE 6. Classification Tree results and predictions for the five fossil localities. A) Results and predictions for CT1, vegetative cover. B) Results and predictions for CT2, biogeographic realm. Abbreviations: LV, La Venta; QH, Quebrada Honda; RU, Rümikon; SC, Santa Cruz; TG, Tinguiririca.
FIGURE 3 in What are the best modern analogs for ancient South American mammal communities? Evidence from ecological diversity analysis (EDA)
FIGURE 3. Axes three and four of the correspondence analysis. A) Positions of the fossil localities and 179 modern ecoregions; B) Positions of the 22 variables. Note that the scale is not the same in the two graphs.
FIGURE 2 in What are the best modern analogs for ancient South American mammal communities? Evidence from ecological diversity analysis (EDA)
FIGURE 2. Axes one and two of the correspondence analysis. A) Positions of the fossil localities and 179 modern ecoregions; B) Positions of the 22 variables. Note that the scale is not the same in the two graphs.
FIGURE 1 in What are the best modern analogs for ancient South American mammal communities? Evidence from ecological diversity analysis (EDA)
FIGURE 1. Locations of the 179 modern ecoregions (colored areas) and the five fossil localities (stars) used in this study. Ecoregions are overlain on a grayscale global mean annual precipitation (MAP) map derived from Fick and Hijmans (2017), with lighter regions indicating areas of higher MAP and darker regions indicating areas of lower MAP. Abbreviations: LV, La Venta, Colombia; QH, Quebrada Honda, Bolivia; RU, Rümikon, Switzerland; SC, Santa Cruz, Argentina; TG, Tinguiririca, Chile.
FIGURE 7 in What are the best modern analogs for ancient South American mammal communities? Evidence from ecological diversity analysis (EDA)
FIGURE 7. Classification Tree results for CT3, biome. Abbreviations: LV, La Venta; QH, Quebrada Honda; RU, Rümikon; SC, Santa Cruz; TG, Tinguiririca.
FIGURE 5 in What are the best modern analogs for ancient South American mammal communities? Evidence from ecological diversity analysis (EDA)
FIGURE 5. Composite hierarchical cluster analysis with the positions of the five fossil localities (dagger symbols) indicated. Solid black lines indicate the results when all five fossil localities are included in the analysis; dashed black lines indicate the results when each fossil locality is analyzed individually. The position of Rümikon did not vary in the two analysis. Abbreviations: LV, La Venta; QH, Quebrada Honda; RU, Rümikon; SC, Santa Cruz; TG, Tinguiririca.
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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)
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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.