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799 results for “abundance data”
Plant abundance data from the 2016 Chimney Tops 2 Fire in Gatlinburg, TN
We surveyed understory plant communities during the second growing season (2018) after the 2016 fire at sites in WUI near Gatlinburg (hereafter “exurban”) and in GSMNP (hereafter "natural"). We chose sites based on dominant forest vegetation type (available for GSMNP) and elevation to minimize the potential confounding effects of these variables. We used stratified random sampling in ESRI ArcMap to select 18 sites, nine in natural locations and nine in exurban locations; within the location type we randomly selected sites to represent fire severity categories, three no burn, three low/medium burn, and three high burn. In the field, we randomly selected two 1x1 m permanent plots to survey and identify each individual plant in the understory to at least genus level, and to count the number of individuals for each taxon. We generated taxa lists and count of individuals per taxa by aggregating plot level records by month. Individuals that could not be identified to at least genus level due to immature characteristics or herbivore damage were assigned observational taxonomic unit numbers (OTUs).
Range size and local abundance data for angiosperm communities across an elevation gradient, Rocky Mountain Biological Lab, 2021-2022
This dataset contains abundance and range size data for angiosperm communities at three sites in Washington Gulch near the Rocky Mountain Biological Laboratory (RMBL, Gothic, Colorado, USA) for 2021 and 2022. RMBL is located in the East River valley of the West Elk mountains, approximately 10 kilometers from Crested Butte, Colorado. Study sites were located at 2815 m (38°53'50"N, 106°58'43"W), 3165 m (38°57'38"N, 107°01'53"W) and 3380 m (38°58'10"N, 107°01'53"W) in elevation, and contained five 1.2 m x 1.2 m plots each. We identified all vascular plants to species level. Each plot was sampled once per year near the peak of the growing season (approximately mid-July, depending on the year and elevation). In each plot, we counted all individuals of every species. To quantify abundance, we averaged local abundance across all five plots at each site and the two data collection years, and then ranked species by averaged abundance within each site (highest to lowest). We calculated range size as Extent of Occurrence (EOO) and Area of Occupancy (AOO). We calculated AOO and EOO with GBIF data using the ‘red’ package. We then ranked species by AOO within each site (largest to smallest).
Selected trait data for the most abundant phytoplankton, zooplankton, benthic invertebrates, and fishes of the Upper San Francisco Estuary
This data set includes selected trait data from published literature and online databases for the most common phytoplankton, zooplankton, benthic invertebrate, and fish taxa at long term monitoring stations in the Upper San Francisco Estuary, which includes the Sacramento-San Joaquin River Delta, Suisun Bay, and Grizzly Bay.
Combined data on plant species abundance and composition from LTER and other grasslands in the United States, 1943 - 2010
Understanding how biotic mechanisms confer stability in variable environments is a fundamental quest in ecology, and one that is becoming increasingly urgent with global change. Several mechanisms, notably a portfolio effect associated with species richness, compensatory dynamics generated by negative species covariance and selection for stable dominant species populations can increase the stability of the overall community. While the importance of these mechanisms is debated, few studies have contrasted their importance in an environmental context. We compiled nine long-term datasets of grassland species composition to evaluate the strength of biotic mechanisms of community stability and assess how these mechanisms change across precipitation gradients. Data were collected in replicate plots over time at nine different sites throughout the US (replicates within a site range from 5-100, plot sizes from 0.1 m² to 17 m²; minimum 9 years, maximum 30 years). Species abundance was measured as either percent cover, biomass, or allometrically-derived biomass. At all sites the measurement techniques and management regimes remained constant over the collection period, and the data collection methods were not relativized. For example, sites in which species composition were measured as percent cover do not require their estimates to sum to 100. For sites with long-term experimental treatments, only the control plots were included. These data have been presented in: Lauren M. Hallett, Joanna S. Hsu, Elsa E. Cleland, Scott L. Collins, Timothy L. Dickson, Emily C. Farrer, Laureano A. Gherardi, Katherine L. Gross, Richard J. Hobbs, Laura Turnbull, Katharine N. Suding. 2014. Biotic mechanisms of community stability shift along a precipitation gradient. Ecology 95:1693–1700. http://dx.doi.org/10.1890/13-0895.1
Alaskan Peatland Experiment: Community structure and productivity data for 2007-2010 II - Species Abundance
This dataset contains abundance for vascular and non vascular plants at the Alaska Peatland Experiment in 2007 and 2009. Two peatland types are included, a bog site and a fen site. Within the fen site a water table manipulation has been ongiong since 2005, with control, lowered and raised water table treatment plots. Measurements collected in 2007 included quadrats passively warmed using open top chamebr (OTC), although these quadrats were not measured in 2009. Data at the bog was measured in 2009, and plots include an area established within the lowland black spruce permafrost plateau (permafrost), and two plots established within collapse scars embedded within the plateau. One collapse scar formed ~ 45 years ago (old collapse) and the other formed ~ 25 years ago based upon aerial photography provided by the BCEF LTER. The data provided in this data set can be sorted by year, site and plot, in addition to warming treatment.
Long-term fish abundance data for Wisconsin Lakes Department of Natural Resources and North Temperate Lakes LTER 1944 - 2012 (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/346/6, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/356/3. The abstract below was extracted from the Level 0 data package and is included for context: This dataset describes long-term (1944-2012) variations in the relative abundance of fish populations representing nine species in Wisconsin lakes. Data were collected by Wisconsin Department of Natural Resource fisheries biologists as part of routine lake fisheries assessments. Individual survey methodologies varied over space and time and are described in more detail by Rypel, A. et al., 2016. Seventy-Year Retrospective on Size-Structure Changes in the Recreational Fisheries of Wisconsin. Fisheries, 41, pp.230-243. Available at: http://afs.tandfonline.com/doi/abs/10.1080/03632415.2016.1160894
Model outputs for occurrence and hunting data‐based models of wild boar distribution and abundance, July 2019 update
<p>These maps are wild boar habitat suitability outputs based on newly available data of wild boar, and models for predicting wild boar relative abundance using hunting yields.</p> <p><strong>Objectives</strong>:</p> <p>- Validation of previously produced hunting yield maps and new ones<br> - Downscaling to 10x10 km grid<br> - Downscaling to 2x2 km grid</p> <p><strong>Model settings and predictors: </strong> <br> - Model from ENETWILD report August 2019<br> - Assuming cells as municipality in 10x10 km grid downscaling<br> - Assuming cells as hunting grounds in 2x2 km grid downscaling </p> <p><strong>Conclusions guiding future methodological steps</strong><br> - To update wild boar hunting yield data for some specific regions;<br> - To increase hunting yield data resolution;<br> - To explore model independent parametrization for each bioregion.</p> <p><strong>Files:</strong></p> <p>August_2019_HY_nut00_10x10 >> Model outputs based on hunting yield GLM analyses<br> August_2019_occurrences_bioclim >> Model outputs based on Bioclim analyses<br> August_2019_occurrences_glm >> Model outputs based on Generalised linear model<br> August_2019_occurrences_ksvm >> Model outputs based on Support vector Machine analyses<br> August_2019_occurrences_maxent >> Model outputs based on Maxent analyses<br> August_2019_occurrences_randomForest>> Model outputs based on Random Forest analyses</p> <p>---------------------------------------------------------------------------------------------------------------------------------------------------------</p> <p>These maps are models obtained in intermediate phases of the ENETWILD project based on available information. <br> There are frequent updates in order to improve the results. For methodological approach and details check the paper: </p> <p>ENETWILD‐consortium, P. Acevedo, S .Croft, G C Smith, J. A. Blanco-Aguiar, J. Fernandez-Lopez, M. Scandura, M. Apollonio, E.Ferroglio, Oliver Keuling, M. Sange, S. Zanet, F. Brivio, T. Podgórski, K.Petrović, G. Body, A. Cohen, R. Soriguer, J. Vicente (2019). ENETwild modelling of wild boar distribution and abundance: update of occurrence and hunting data‐based models. EFSA Supporting Publications, 16(8), 1674E.<br> <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fefsa.onlinelibrary.wiley.com%2Fdoi%2Fabs%2F10.2903%2Fsp.efsa.2019.EN-1674&data=02%7C01%7C%7Ca8ad922eefde42f5cb5208d7c5054851%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637194498792136402&sdata=fqdiYEOqYIlHaDbp5a7kVdGQ6FWuFEydJNhSWOghH%2FQ%3D&reserved=0">https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/sp.efsa.2019.EN-1674</a></p> <p>.</p> <p>Permission for reuse occurrence outputs records is granted under the terms of a CC-BY-NC license.<br> Permission for reuse hunting yield outputs is granted under the terms indicated by EFSA.</p>
Data from: An effective method for ecosystem-scale manipulation of bird abundance and species richness
Manipulation experiments are a cornerstone of ecological research, but can be logistically challenging to execute – particularly when they are intended to isolate the ecological role of large, vagile species, like birds. Despite indirect evidence that birds are influential in many ecosystems, large-scale, multi-year bird manipulation experiments are rare. When these studies are conducted, they are typically realized with caged or netted exclosures, an approach that can be expensive, risky for wildlife, and difficult to maintain. In cases where caged exclosures are not appropriate, alternate approaches are needed to allow rigorous empirical studies on the ecological role of birds. Here, we present and validate a method for experimentally increasing the abundance and richness of birds at the scale of entire aquatic ecosystems. Unlike bird exclusion, this approach is experimentally tractable, appealing to land managers, and possible to deploy over large spatial scales. We tested the efficacy of our approach for increasing bird abundance and species richness at 16 central California ponds. Based on bird visitation data obtained by summer camera trapping, our approach significantly increased bird species richness and abundance at manipulated ponds compared to control ponds. Attractant treatments mitigated the negative effects of a major drought on bird species richness, and generated a near-doubling of bird abundance in the presence of attractants. Treatments had no effect on most mammal species, with the exception of ground squirrels, which increased in abundance in the presence of attractants. These results suggest that attractants are effective in increasing bird abundance and richness. We encourage researchers to consider this approach for experimentally isolating the ecological role of birds in aquatic and open terrestrial ecosystems, especially in cases where cost or logistical constraints preclude the use of caged or netted exclosures.
Data from: Estimation of regional annual abundance and evidence for increasing numbers of white sharks off central California
<p>Raw data consisting of individual identification photographs of white sharks (Carcharodon carcharias) and data table with corresponding metadata. These data support PhD thesis of Paul E. Kanive entitled "VITAL RATES, ANNUAL ABUNDANCE, AND MOVEMENT OF WHITE SHARKS IN THE NORTHEASTERN PACIFIC" and peer-reviewed manuscript "Estimation of regional annual abundance and evidence for increasing numbers of white sharks off central California."</p>
Vortex input files -- Ashe et al., "Minding the data-gap trap: predicting the dynamics of abundant dolphin species under uncertainty"
<p>Vortex input file used for analyses presented in:<br> "Minding the data-gap trap: predicting the dynamics of abundant dolphin species under uncertainty", <br> by Erin Ashe, Rob Williams, Christopher Clark, Christine Erbe, Leah Gerber, Ailsa Hall, Philip Hammond, Robert C. Lacy, Randall Reeves, & Nicole Vollmer<br> </p>
Sequence data for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers"
<p>Sequence data (Illumina MiSeq runs) for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers". File names indicate unique run identifiers. In the manuscript, shorter names are used:</p> <ul> <li>NC12: 140602_M00528_0019_000000000-A88YD</li> <li>NC17: 140918_M00528_0047_000000000-A8GHU</li> <li>NC22b: 141105_M00528_0062_000000000-AAPC2</li> <li>NCki: 140207_M00528_0069_000000000-A5TY9</li> </ul> <p> </p>
Supporting data for "Mammalian species abundance across a gradient of tropical land-use intensity: A hierarchical multi-species modelling approach"
<p>Combined camera trap and live trap dataset underlying the analyses in a Biological Conservation paper (https://doi.org/10.1016/j.biocon.2017.05.007), provided in .csv format. This spatially- and temporally-replicated dataset is suitable for occupancy modelling.</p> <p>The first 3 columns in the dataset are:</p> <p>1) Trap location name – old-growth forest, logged forest and oil palm plantation locations have the prefixes "Old", "Log" and "Palm", respectively</p> <p>2) Sampling occasion number – camera trap and live trap occasions have the prefixes “Lvtrap” and “Ctrap”, respectively, and are defined in the paper</p> <p>3) Calendar year in which sampling took place (most locations were sampled in > 1 calendar years)</p> <p>Following these 3 columns, there are 66 columns for each of the mammal species detected during the study (species common names are used). The values for each species represent the number of independent captures, as defined in the paper. This can be reduced to detection/non-detection data (zeroes and ones), if needed, for occupancy modelling.</p>
Data and code: Microgeographic variation in demography and thermal regimes stabilize regional abundance of a widespread freshwater fish
<p>Predicting the persistence of species under climate change is an increasingly important objective in ecological research and management. However, biotic and abiotic heterogeneity can drive asynchrony in population responses at small spatial scales, complicating species-level assessments. For widely distributed species consisting of many fragmented populations, such as brook trout (<em>Salvelinus fontinalis</em>), understanding drivers of asynchrony in population dynamics can improve predictions of range-wide climate impacts. We analyzed demographic time-series from mark-recapture surveys of eleven natural brook trout populations in eastern Canada over 13 years to examine the extent, drivers, and consequences of fine-scale population variation. The focal populations were genetically differentiated, occupied a small area (~25 km<sup>2</sup>) with few human impacts, and experienced similar climate conditions. Recruitment was highly asynchronous, weakly related to climate variables, and showed population-specific relationships with other demographic processes, generating diverse population dynamics. In contrast, individual growth was mostly synchronized among populations and driven by a shared positive relationship with stream temperature. Outputs from population-specific models were unrelated to four of five hypothesized drivers (recruitment, growth, reproductive success, phylogenetic distance), but variation in groundwater inputs strongly influenced stream temperature regimes and stock-recruitment relationships. Finally, population asynchrony generated a portfolio effect that stabilized regional species abundance. Our results demonstrate that population demographic and habitat diversity at microgeographic scales can play a significant role in moderating species responses to climate change. Moreover, we suggest that the absence of human activities within study streams preserved natural habitat variation and contributed to asynchrony in brook trout abundance, while the small study area eased monitoring and increased the likelihood of detecting asynchrony. Therefore, anthropogenic habitat degradation, landscape context, and spatial scale must be considered when developing management strategies to monitor and maintain populations that are diverse, stable, and resilient to climate change.</p>
Unpublished data: Quantifying CO2 Emissions and Carbon Sequestration from Digestate-Amended Soil Using Natural 13C Abundance as a Tracer
<p>Unprocessed data of CO2 evolution measured daily on cavity ring-down spectroscopy analyser (G2201-i CRDS isotopic CO2/CH4 analyser, Picarro, Santa Clara, CA, USA).</p>
Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance
<p>Plants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes on a shared host plant. We tested the role of a plant-beneficial soil bacterium (<em>Acidovorax radicis</em>) in altering eco-evolutionary interactions between different aphid genotypes (Sitobion avenae; genotypes Sickte and Fescue) feeding on barley (<em>Hordeum vulgare</em>). We measured fecundity, longevity and population growth of two aphid genotypes reared separately or together (population mixture) on three different barley varieties that were inoculated with or without <em>A. radicis</em>. Results showed that across all plant varieties <em>A. radicis</em> increased plant growth and suppressed aphid populations via reduced longevity and fecundity. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Using Lotka-Volterra modelling, we demonstrated that while <em>A. radicis</em> inoculation decreased growth rates for both aphid genotypes it increased the competitiveness of one genotype against the other. In general, in the presence of <em>A. radicis</em>, the Fescue aphid genotype became more inhibitory of Sickte aphids, while Sickte aphids facilitated the growth of Fescue aphids. Our work demonstrates that plant rhizosphere microbiomes exert community-level influences by mediating eco-evolutionary interactions between herbivores and host plants. By altering competitive interaction outcomes among aphids and thus impacting processes such as rapid evolution, soil microbes contribute to the short- and long-term structure and functioning of terrestrial habitats.</p>
Data for: Specialist carabids in mixed montane forests are positively associated with biodiversity-oriented forestry and abundance of roe deer
<p>The ongoing transition within forest management towards more biodiversity-oriented practices, such as close-to-nature forestry and retention forestry, may benefit forest fauna such as forest-specialized ground beetles (Coleoptera: Carabidae). However, it remains unclear how forest carabids are jointly affected by these practices in Central European montane forests, which host particularly sensitive, range-restricted carabid species, and where biodiversity-oriented forestry is widely applied. Moreover, roe deer (<em>Capreolus capreolus</em>), the most common large herbivore in these forests, is intensively managed to reduce browsing pressure, but it is yet unknown how this may affect carabids, alongside the effect of silviculture. On 66 1-ha plots in the Black Forest region of Germany, we sampled carabids with pitfall traps, measured roe deer abundances using camera trapping, and measured several structural variables directly related to close-to-nature and retention practices, as well as variables describing microclimate and landscape-level forest cover. We found that the carabid assemblage was dominated by forest specialists, with little influence from fragmentation of the surrounding forest. Higher broadleaf share (and canopy cover for montane specialists) was correlated with higher carabid activity-density. Increasing stand maturity (and lying deadwood volume for montane specialists), was correlated with higher species richness. Plots with higher roe deer abundances showed higher carabid richness and activity-density. Assemblage composition changed along the altitudinal gradient, and both richness and activity-density increased with elevation. Thus, carabid communities, including montane specialists and several species of conservation interest, stand to benefit from close-to-nature and retention practices, if applied throughout the altitude range of montane forests. Forest carabids may additionally profit from maintaining higher roe deer abundances, but further research is needed to understand this causal link, as well as to weigh the costs and benefits of deer culling for forest biodiversity.</p>
Supporting material for von Fromm et al (2024) Global synthesis of SOC abundance and persistence profile data
<p>This file contains the supporting material for von Fromm et al (2024) Controls and relationships of soil organic carbon abundance and persistence vary across pedo-climatic regions published in Global Change Biology (https://doi.org/10.1111/gcb.17320). </p> <p>The data comes originally from the International Soil Radiocarbon Database (ISRaD; <a href="https://soilradiocarbon.org/">https://soilradiocarbon.org/</a>). We filtered the data and applied a mass-preserving spline function. For more details see the corresponding manuscript and the github repository (https://github.com/SophievF/Global_SOC_Abundance_Persistence).</p>
Data from: Geographic distribution of terpenoid chemotypes in Tanacetum vulgare mediates tansy aphid occurrence but not abundance
<p>Intraspecific variation of specialized metabolites in plants, such as terpenoids, are used to determine chemotypes. Tansy (<em>Tanacetum vulgare</em> L.) exhibits diverse terpenoid profiles that affect insect communities. However, it is not fully known whether patterns of their chemical composition and associated insects vary beyond the community scale. Here, we investigated the geographic distribution of mono- and sesquiterpenoid chemotypes in tansy leaves and their relationships with specific insect communities across Germany. We sampled tansy leaves from ten plants with and five plants without aphids in each of 26 sites along a north-south and west-east transect in Germany. Hexane-extracted metabolites from leaf tissues were analyzed by gas chromatography-mass spectrometry (GC-MS). Plant morphological traits, aphid occurrence and abundance, and occurrence of ants were recorded locally. The effect of plant chemotype, plant morphological parameters, and abiotic site parameters such as soil types, temperature and precipitation on insect occurrences were analyzed. Plants clustered into four monoterpenoid and four sesquiterpenoid chemotype classes. Monoterpene classes differed in their latitudinal distribution, whereas sesquiterpenes were more evenly distributed across the transect. Aphid and ant occurrence was influenced by monoterpenoids. Plants of monoterpenoid class 1 were colonized by aphids and ants significantly more often than expected by chance, whereas in other classes there were no significant differences. Aphid abundance was affected by soil type, and average annual temperature positively correlated with the occurrence of ants. We found significant geographic patterns in the distribution of tansy chemodiversity and show that monoterpenoids affect aphid and ant occurrence, while the soil type can influence aphid abundance. We show that geographic variation in plant chemistry influences insect community assembly on tansy plants.</p>
Data from: Unexpected stability in faunal population abundances following an estuary-wide collapse of oysters
<p>Data describing the number and lengths of fish and macroinvertebrates sampled from long-term fisheries independent sampling in Florida’s coastal waters. Original data were collected by the Florida Fish and Wildlife Conservation Commission (FWC) Fish and Wildlife Research Institute (FWRI).</p>
SeaFlow data v1: High-resolution abundance, size and biomass of small phytoplankton measured by flow-cytometry
<p>SeaFlow is an underway flow cytometer designed to continuously monitor the optical properties of the smallest phytoplankton from a ship's flow-through seawater system. It collects high-resolution data, generating the equivalent of 1 sample every 3 minutes or every 1 km (for a ship moving at 10 knots).</p> <p>The dataset provides measurements of cell abundance, cell size (equivalent spherical diameter) and carbon biomass for small phytoplankton populations: the cyanobacteria Prochlorococcus, Synechococcus, Crocosphaera, and small eukaryotic phytoplankton (<5 μm ESD). Data processing followed the methods outlined in <a href="https://doi.org/10.1038/s41597-019-0292-2">Ribalet et al. (2019)</a>. For more information, visit the <a href="https://seaflow.netlify.app/">SeaFlow website</a>.</p> <p><strong>New in version 1.6 </strong>The updated dataset includes flow cytometric measurements from 89 cruises, spanning nearly 14,000 hours of observations across 130,000 km of the surface oceans.</p>
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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.