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799 results for “abundance data”
Data from: Abundance, origin and phylogeny of plants do not predict community-level patterns of pathogen diversity and infection
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Data from: Species richness, endemism, and abundance patterns: tests of two fractal models in a serpentine grassland
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Data from: Dominant bee species and floral abundance drive parasite temporal dynamics in plant-pollinator communities
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Data for: Sequencing and variant detection of eight abundant plant-infecting tobamoviruses across Southern California wastewater
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At-sea seabird censuses. Data on the species encountered (including marine mammals), their abundance, distribution and behavior. Data collected aboard cruises off the coast of the Western Antarctic Penninsula, 1993 - 2018.
The objectives of the LTER seabird component during the 92-93 season cruises were similar. These objectives included 1) determining the pelagic abundance and distribution of Adelie Penguins, 2) examining how the physical and biological characteristics of the marine environment influence these parameters and, 3) using these data to identify foraging areas that may be important to Adelie populations being studied as part of land-based work at Palmer Station. Secondary objectives included documenting the abundance and distribution of other seabirds and marine mammals within the LTER study area. The focus of the January cruise was the nearshore foraging habitat,which required sampling at smaller scales. All seabird censuses were thus conducted within approximately 100 kms of Palmer Station while traversing a sampling grid with stations at 10km intervals. The first two days (18-20 January) of this cruise were spent covering the selected grid as rapidly as possible resulting in 45 transects spaced at 45-60 minute intervals. There were no stops at the 10km stations during this Fast Grid phase. Upon completion of the Fast Grid, a force 12 gale suspended data collection for 24 hours. From January 22-25 the grid direction was reversed and the grid repeated. During this Slow Grid phase, 2-M net tows were done at 10km intervals and BOPS and 1-M and 2-M net tows every 20 km. All seabird censuses during the cruise were done using the procedures outlined in the previous paragraph.
At-sea seabird censuses. Data on the species encountered (including marine mammals), their abundance, distribution and behavior. Data collected aboard cruises off the coast of the Western Antarctic Penninsula, 1993, 1999 and 2001.
The objectives of the LTER seabird component during the 92-93 season cruises were similar. These objectives included 1) determining the pelagic abundance and distribution of Adelie Penguins, 2) examining how the physical and biological characteristics of the marine environment influence these parameters and, 3) using these data to identify foraging areas that may be important to Adelie populations being studied as part of land-based work at Palmer Station. Secondary objectives included documenting the abundance and distribution of other seabirds and marine mammals within the LTER study area. The focus of the January cruise was the nearshore foraging habitat,which required sampling at smaller scales. All seabird censuses were thus conducted within approximately 100 kms of Palmer Station while traversing a sampling grid with stations at 10km intervals. The first two days (18-20 January) of this cruise were spent covering the selected grid as rapidly as possible resulting in 45 transects spaced at 45-60 minute intervals. There were no stops at the 10km stations during this Fast Grid phase. Upon completion of the Fast Grid, a force 12 gale suspended data collection for 24 hours. From January 22-25 the grid direction was reversed and the grid repeated. During this Slow Grid phase, 2-M net tows were done at 10km intervals and BOPS and 1-M and 2-M net tows every 20 km. All seabird censusesduring the cruise were done using the procedures outlined in theprevious paragraph.
At-sea seabird censuses. Data on the species encountered (including marine mammals), their abundance, distribution and behavior. Data collected aboard cruises off the coast of the Western Antarctic Penninsula, 1993 - 2018.
The objectives of the LTER seabird component during the 92-93 season cruises were similar. These objectives included 1) determining the pelagic abundance and distribution of Adelie Penguins, 2) examining how the physical and biological characteristics of the marine environment influence these parameters and, 3) using these data to identify foraging areas that may be important to Adelie populations being studied as part of land-based work at Palmer Station. Secondary objectives included documenting the abundance and distribution of other seabirds and marine mammals within the LTER study area. The focus of the January cruise was the nearshore foraging habitat, which required sampling at smaller scales. All seabird censuses were thus conducted within approximately 100 kms of Palmer Station while traversing a sampling grid with stations at 10km intervals. The first two days (18-20 January) of this cruise were spent covering the selected grid as rapidly as possible resulting in 45 transects spaced at 45-60 minute intervals. There were no stops at the 10km stations during this Fast Grid phase. Upon completion of the Fast Grid, a force 12 gale suspended data collection for 24 hours. From January 22-25 the grid direction was reversed and the grid repeated. During this Slow Grid phase, 2-M net tows were done at 10km intervals and BOPS and 1-M and 2-M net tows every 20 km. All seabird censuses during the cruise were done using the procedures outlined in the previous paragraph. Seventy-two 30-minute transects and 15 station censuses were completed during the January cruise. Athough seabirds were widely distributed throughout the study area, the highest densities and greatest biomass occurred consistently within 2-5 km of Anvers Island and several major island groups to the south and west near the Antarctic Peninsula. Adelie Penguins were the dominant component of this seabird assemblage in terms of both abundance and biomass. South Polar Skuas ranked second and Black-browed Al
At-sea seabird censuses. Data on the species encountered (including marine mammals), their abundance, distribution and behavior. Data collected aboard cruises off the coast of the Western Antarctic Penninsula, 1993, 1999 and 2001.
The objectives of the LTER seabird component during the 92-93 season cruises were similar. These objectives included 1) determining the pelagic abundance and distribution of Adelie Penguins, 2) examining how the physical and biological characteristics of the marine environment influence these parameters and, 3) using these data to identify foraging areas that may be important to Adelie populations being studied as part of land-based work at Palmer Station. Secondary objectives included documenting the abundance and distribution of other seabirds and marine mammals within the LTER study area. The focus of the January cruise was the nearshore foraging habitat,which required sampling at smaller scales. All seabird censuses were thus conducted within approximately 100 kms of Palmer Station while traversing a sampling grid with stations at 10km intervals. The first two days (18-20 January) of this cruise were spent covering the selected grid as rapidly as possible resulting in 45 transects spaced at 45-60 minute intervals. There were no stops at the 10km stations during this Fast Grid phase. Upon completion of the Fast Grid, a force 12 gale suspended data collection for 24 hours. From January 22-25 the grid direction was reversed and the grid repeated. During this Slow Grid phase, 2-M net tows were done at 10km intervals and BOPS and 1-M and 2-M net tows every 20 km. All seabird censusesduring the cruise were done using the procedures outlined in theprevious paragraph.
Supplementary material 1 from: Schenk J, Geisen S, Kleinboelting N, Traunspurger W (2019) Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth. Metabarcoding and Metagenomics 3: e46704. https://doi.org/10.3897/mbmg.3.46704
: Data type: species data
Supplementary material 1 from: Schenk J, Geisen S, Kleinboelting N, Traunspurger W (2019) Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth. Metabarcoding and Metagenomics 3: e46704. https://doi.org/10.3897/mbmg.3.46704
: Data type: species data
Datasets: New technologies in the mix: Assessing N-mixture models for abundance estimation using automated detection data from drone surveys
<p>These data set contains data from 11 surveys of radio-collared using remotely piloted aircraft systems (RPAS), thermal <br> imaging and automated detection.The MODELDEV .csv contains data points used to develop the modified Horvitz Thompson estimator models in the paper "New technologies in the mix: Assessing N-mixture models for abundance estimation using automated detection data from drone surveys" which is accepted into publication in the journal Ecology and Evolution as of 11/06/2020. The TESTING .csv contains data points used for model testing in in the same publication. </p>
Training data for "Apply modeling on population or community data to see effect of year, habitat or site on species abundance"
<p>Datasets for the "Apply modeling on population or community data to see effect of year, habitat or site on species abundance" Galaxy for ecology tutorial</p>
Data from: The difference between generalist and specialist: the effects of wide fluctuations in main food abundance on numbers and reproduction of two co-existing predators
<p>Specialist individuals within animal populations have shown to be more efficient foragers and/or to have higher reproductive success than generalist individuals, but interspecific reproductive consequences of the degree of diet specialisation in vertebrate predators have remained unstudied. Eurasian pygmy owls (hereafter POs) have less vole-specialised diets than Tengmalm's owls (TOs), both of which mainly subsist on temporally fluctuating food resources (voles). To test whether the specialist TO is more limited by the main prey abundance than the generalist PO, we studied breeding densities and reproductive traits of co-existing POs and TOs in central-western Finland during 2002-2019. Breeding densities of POs increased with augmenting densities of voles in the previous autumn, whereas breeding densities of TOs increased with higher vole densities in both the previous autumn and the current spring. In years of vole scarcity, PO females started egg-laying earlier than TOs, whereas in years of vole abundance TO females laid eggs substantially earlier than PO females. The yearly mean clutch size and number of fledglings produced of both POs and TOs increased with abundance of voles in the current spring. POs laid large clutches and produced large broods in years of both high and low vole abundance, whereas TOs were able to do so only in years of high vole abundance. POs were able to raise on average 73% of the eggs to fledglings whereas TOs only 44%. The generalist foraging strategy of POs including flexible switching from main prey to alternative prey (small birds) appeared to be more productive than the strictly vole-specialized foraging strategy of TOs. In contrast to earlier studies at the individual-level, specialist predators at the species level (in this case TOs) appear to be less effective than generalists (POs), but diet specialisation was particularly costly under conditions when scarcity of main foods limited offspring production.</p>
Data from: Artificial agri-environment scheme ponds do not replicate natural environments despite higher aquatic and terrestrial invertebrate richness and abundance
<p class="MsoNoSpacing">1. Farmland ponds are a highly threatened freshwater habitat which has undergone dramatic losses during the last 200 years due to land drainage schemes and agricultural intensification. Agri-environment schemes (AES) incentivise farmers to adopt farming methods to benefit biodiversity, yet there are a paucity of data evaluating the success of artificially created AES ponds as analogues of natural ponds in an attempt to recreate lost environments.</p> <p class="MsoNoSpacing">2. We examined variation in environmental parameters and aquatic and terrestrial invertebrate communities between 38 natural ponds and 91 artificial ponds that were created in south-west Ireland (<i>n</i>=129).</p> <p class="MsoNoSpacing">3. Artificial ponds in agricultural grassland did not replicate natural ponds in adjacent semi-natural habitats differing significantly in size, pH, conductivity, productivity (indicated by submerged and emergent plant cover including algae) and surrounding vegetation structure i.e. sward height. These differences significantly influenced aquatic and terrestrial invertebrate community structure with a suite of indicator taxa in both natural and artificial ponds.</p> <p class="MsoNoSpacing">4. The conservation value of artificial ponds in agricultural grasslands should not be underestimated as they had 43% higher aquatic species richness and 33% higher aquatic species abundance than natural ponds in adjacent semi-natural habitats.</p> <p class="MsoNoSpacing"><i>5. Synthesis and applications</i>. We demonstrate that artificial agri-environment scheme ponds created in agricultural grasslands, whilst not direct analogues of natural ponds in adjacent semi-natural habitats, do fulfil a role in preserving high local biodiversity albeit representing a different community of species. Creation of ponds in farmland as well as in adjacent natural habitats could provide a wider range of environmental conditions and richer associated macroinvertebrate communities, increasing landscape connectivity and further enhancing regional biodiversity.</p>
Data from: Altitude shapes the environmental drivers of large-scale variation in abundance of a widespread mammal species
<p>Habitat quality and heterogeneity directly influence the distribution and abundance of organisms at different spatial scales. Determining the main environmental factors driving the variation in species abundance is crucial to understand the underlying ecological processes and this is especially important for widely distributed species living in contrasting environments. However, the responses to environmental variation are usually described at relatively small spatial scales. Here, we studied the variation in abundance of a widely distributed mustelid, the European badger (<i>Meles meles</i>), across France.<b> </b>We used (1) direct detections of 9,439 dead and living badgers, from 2006 to 2009, to estimate badger relative abundance in 703 small agricultural regions of metropolitan France and (2) a Bayesian modelling approach to identify the main environmental determinants influencing badger abundance.<b> </b>Despite a continuous distribution of badger in France, we found large variation in badger abundance between regions, explained by environmental factors. Among a set of 13 environmental variables, we demonstrated that badger abundance in lowlands (< 400 m a.s.l.) was mostly driven by biotic factors such as potential food resources (earthworm abundance and fruits crops) and forest fragmentation. Conversely, in mountainous areas, abiotic factors (i.e. soil texture and climate) drove the variation in badger relative abundance.<b> </b>These results underline the importance of mapping the abundance of wildlife species based on environmental suitability, and highlight the complexity of drivers influencing species abundance at such large spatial scales. Altitude shaped the environmental drivers (biotic <i>vs.</i> abiotic) that most influenced relative abundance of a widespread species. In the case of badger, such abundance maps are crucial to identify critical areas for species management as this mustelid is a main wild vector of bovine tuberculosis in several countries.</p>
Data from: Evaluating predictive performance of statistical models explaining wild bee abundance in a mass-flowering crop
<p>Wild bee populations are threatened by current agricultural practices in many parts of the world, which may put pollination services and crop yields at risk. Loss of pollination services can potentially be predicted by models that link bee abundances with landscape-scale land-use, but there is little knowledge on the degree to which these statistical models are transferable across time and space. This study assesses the transferability of models for wild bee abundance in a mass-flowering crop across space (from one region to another) and across time (from one year to another). The models used existing data on bumblebee and solitary bee abundance in winter oilseed rape fields, together with high-resolution land-use crop-cover and semi-natural habitats data, from studies conducted in five different regions located in four countries (Sweden, Germany, Netherlands, and the UK), in three different years (2011, 2012, 2013). We developed a hierarchical model combining all studies and evaluated the transferability using cross-validation. We found that both the landscape-scale cover of mass-flowering crops and permanent semi-natural habitats, including grasslands and forests, are important drivers of wild bee abundance in all regions. However, while the negative effect of increasing mass-flowering crops on the density of the pollinators is consistent between studies, the direction of the effect of semi-natural habitat is variable between studies. The transferability of these statistical models is limited, especially across regions, but also across time. Our study demonstrates the limits of using statistical models in conjunction with widely available land-use crop-cover classes for extrapolating pollinator density across years and regions, likely in part because input variables such as cover of semi-natural habitats poorly capture variability in pollinator resources between regions and years.</p>
Data from: Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions
Environmental DNA (eDNA) promises to ease non-invasive quantification of fish biomass or abundance, but its integration within conservation and fisheries management is currently limited by a lack of understanding of the influence of eDNA collection method and environmental conditions on eDNA concentrations in water samples. Water temperature is known to influence the metabolism of fish and consequently could strongly affect eDNA release rate. As water temperature varies in temperate regions (both seasonally and geographically), the unknown effect of water temperature on eDNA concentrations poses practical limitations on quantifying fish populations using eDNA from water samples. This study aims to clarify how water temperature and the eDNA capture method alter the relationships between eDNA concentration and fish abundance/biomass. Water samples (1 L) were collected from 30 aquaria including triplicate of 0, 5, 10, 15 and 20 Brook Charr specimens at two different temperatures. Water samples were filtered with five different types of filters. The eDNA concentration obtained by quantitative PCR (qPCR) varied significantly with fish abundance and biomass and type of filters (Mixed-design ANOVA, P < 0.001). Results also show that fish released more eDNA in warm water than cold water and that eDNA concentration better reflects fish abundance/biomass at high temperature. From a technical standpoint, higher levels of eDNA were captured with glass fiber (GF) than mixed cellulose ester (MCE) filters and support the importance of adequate filters to quantify fish abundance based on the eDNA method. This study supports the importance of including water temperature in fish abundance/biomass prediction models based on eDNA.
Data from: Abundance-dependent effects of neighborhood dissimilarity and growth rank reversal in a Neotropical forest
Why tropical forests harbor an exceptional number of species with striking differences in abundances remains an open question. We propose a theoretical framework to address this question in which rare species may have different extirpation risks depending on species ranks in tree growth and sensitivities to neighborhood interactions. To evaluate the framework, we studied tree growth and its responses to neighborhood dissimilarity (ND) in traits and phylogeny for 146 species in a Neotropical forest. We found that tree growth was positively related to ND, and common species were more strongly affected by ND than rare species, which may help delay dominance of common species. Rare species grew more slowly at the community-wide average ND than common species. But rare species grew faster when common species tended to dominate locally, which may help reduce extirpation risk of rare species. Our study highlights that tree growth rank among species depends on their responses to neighborhood interactions, which can be important in fostering diversity maintenance in tropical forests.
Data from: The influence of geomorphic processes on plant distribution and abundance as reflected in plant tolerance curves
Ecologists describe plant distribution using direct gradient analysis, by which a tolerance curve of species abundance is described along an environmental gradient (any environmental variable that affects plant distribution). Soil moisture is generally the gradient in low relief areas that explains the most variation. Traditional direct gradient analyses have used terrain structure (i.e. transects up or down hillslopes) as a correlate to soil moisture. Here we use a numerical tectonic and geomorphic process-based landscape development model to create two landscapes with different geomorphic characteristics (i) to demonstrate the influence of geomorphic processes on soil moisture patterns and plant distribution and (ii) to evaluate the effectiveness of transects in describing moisture gradients and tolerance curves on landscapes dominated by creep or overland flow. We use a topographic index to approximate the distribution of soil moisture as it is determined by the shape of these different landscapes. Transects are placed on hillslopes in each model landscape and used to construct tolerance curves. Results show that transect methods that use the distance from the channel to the ridgeline as an approximation of soil moisture create variable tolerance curves for the same plant both within a single landscape and between different landscapes. The reason for these differences is that transects do not take into account the 3-dimensional landscape form that explains water movement. Landscapes have regions of convexity and flow path divergence and regions of concavity and flow path convergence which, along with hillslope length, determine contributing area. In addition, hillslope curvature results in varying capacities to retain water. However, when the topographic index is used instead of hillslope transect position, tolerance curves from the same and different landscapes reflect the differences the topographic structure has on soil moisture. We thus show that traditional methods of direct gradient analysis are not always adequate as they do not tend to consider that soil moisture depends on hillslope length, curvature, and slope. Furthermore, we show that within and between landscapes there are differences in spatial distributions of soil moisture that are reflections of the geomorphic processes that created them.
Data from: A hierarchical distance sampling model to estimate abundance and covariate associations of species and communities
Distance sampling is a common survey method in wildlife studies, because it allows accounting for imperfect detection. The framework has been extended to hierarchical distance sampling (HDS), which accommodates the modelling of abundance as a function of covariates, but rare and elusive species may not yield enough observations to fit such a model. We integrate HDS into a community modelling framework that accommodates multi-species spatially replicated distance sampling data. The model allows species-specific parameters, but these come from a common underlying distribution. This form of information sharing enables estimation of parameters for species with sparse data sets that would otherwise be discarded from analysis. We evaluate the performance of the model under varying community sizes with different species-specific abundances through a simulation study. We further fit the model to a seabird data set obtained from shipboard distance sampling surveys off the East Coast of the USA. Comparing communities comprised of 5, 15 or 30 species, bias of all community-level parameters and some species-level parameters decreased with increasing community size, while precision increased. Most species-level parameters were less biased for more abundant species. For larger communities, the community model increased precision in abundance estimates of rarely observed species when compared to single-species models. For the seabird application, we found a strong negative association of community and species abundance with distance to shore. Water temperature and prey density had weak effects on seabird abundance. Patterns in overall abundance were consistent with known seabird ecology. The community distance sampling model can be expanded to account for imperfect availability, imperfect species identification or other missing individual covariates. The model allowed us to make inference about ecology of species communities, including rarely observed species, which is particularly important in conservation and management. The approach holds great potential to improve inference on species communities that can be surveyed with distance sampling.
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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.