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68 results for “species abundance distributions”
Bayesian species distribution models integrate presence-only and presence-absence data to predict deer distribution and relative abundance
<p>Using geospatial data of wildlife presence to predict a species distribution across a geographic area is among the most common tools in management and conservation. The collection of high-quality presence-absence data through structured surveys is, however, expensive, and managers usually have access to larger amounts of low-quality presence-only data collected by citizen scientists, opportunistic observations, and culling returns for game species. Integrated Species Distribution Models (ISDMs) have been developed to make the most of the data available by combining the higher-quality, but usually scarcer and more spatially restricted presence-absence data, with the lower quality, unstructured, but usually more extensive presence-only datasets. Joint-likelihood ISDMs can be run in a Bayesian context using INLA (Integrated Nested Laplace Approximation) methods that allow the addition of a spatially structured random effect to account for data spatial autocorrelation. Here, we apply this innovative approach to fit ISDMs to empirical data, using presence-absence and presence-only data for the three prevalent deer species in Ireland: red, fallow and sika deer. We collated all deer data available for the past 15 years and fitted models predicting distribution and relative abundance at a 25 km<sup>2</sup> resolution across the island. Models' predictions were associated to spatial estimates of uncertainty, allowing us to assess the quality of the model and the effect that data scarcity has on the certainty of predictions. Furthermore, we checked the performance of the three species-specific models using two datasets, independent deer hunting returns and deer densities based on faecal pellet counts. Our work clearly demonstrates the applicability of spatially-explicit ISDMs to empirical data in a Bayesian context, providing a blueprint for managers to exploit unexplored and seemingly unusable data that can, when modelled with the proper tools, serve to inform management and conservation policies.</p>
Unveiling global species abundance distributions - Callaghan et al. 2023 - Nature Ecology and Evolution
<p>This repository represents some data and code to reproduce the main figures from Callaghan et al. 2023. Unveiling the global species abundance distributions of Eukaryotes. Nature Ecology and Evolution.</p>
How environmental factors affect the abundance and distribution of two congeneric species of Amazonian frogs
<p>In this study, we test the hypothesis that, at a fine scale, environmental variables influence differently sister species that live in sympatry and are phylogenetically closely related. We sampled two Amazonian anuran species, <em>Phyzelaphryne</em> <em>miriamae</em> and <em>Phyzelaphryne</em> sp., in 11 permanent sampling modules distributed across ~600 km in the Purus-Madeira Interfluve between 2013 and 2014. Using mixed generalized linear models, we found that the species have distinct environmental associations, which may facilitate their coexistence in sympatry. <em>Phyzelaphryne</em> <em>miriamae</em> was more frequent in environments with low precipitation and low water tables, suggesting this species is better adapted to live in drier places. In contrast, <em>Phyzelaphryne</em> sp. appeared to be a generalist regarding to habitat and resource use. These patterns are in accordance with the hypothesis that environmental variables influence sister species differently on a fine scale. <em>Phyzelaphryne</em> <em>miriamae</em> is larger than <em>Phyzelaphryne</em> sp., which may make it more resistant to dehydration, allowing it to explore drier environments. In conclusion, our results are in concordance with the hypothesis that the evolution of characteristics resulting from selection may have reduced competition for resources between closely related species, thus facilitating coexistence in sympatry.</p>
FragSAD: A database of diversity and species abundance distributions from habitat fragments
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Bayesian species distribution models integrate presence-only and presence-absence data to predict deer distribution and relative abundance
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Species Abundance Distributions (SADs) for local tree communities in 1-ha forest plots on 20 tropical islands in the Indo-Pacific region
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Hierarchical multi-grain models improve descriptions of species’ environmental associations, distribution, and abundance
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Data from: Odonate species occupancy frequency distribution and abundance – occupancy relationship patterns in temporal and permanent water bodies in a subtropical area
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Data from: Incorporating abundance information and guiding variable selection for climate-based ensemble forecasting of species' distributional shifts
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Data from: The biogeographical patterns of species richness and abundance distribution in stream diatoms are driven by climate and water chemistry
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How environmental factors affect the abundance and distribution of two congeneric species of Amazonian frogs
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Data from Jenkinson et al. 2020: Biogeographical variation in the distribution, abundance, and interactions among key species on rocky reefs of the northeast Pacific
<p>See Metadata tab for full description of transect survey data.</p>
Data from: The importance of factors controlling species abundance and distribution varies in native and non-native species.
How variation in factors controlling species abundance and distribution between native and non-native ranges compares to that within ranges remains poorly understood. We used a globally distributed ruderal, Centaurea solstitialis (Centaurea), to explore the possibility that the importance of those factors exhibits great variation between and within ranges. To test our hypothesis, we established seed addition experiments with soil disturbance (turnover and control) and biocide (fungicides, insecticide, and control) treatments in two regions within native (the Caucasus and south-western Turkey) and non-native (the western United States – US – and central Argentina) distributions. Also, we estimated the rate of vegetation recovery after disturbance (resilience) and related it to Centaurea density in experimental plots. Disturbance strongly increased Centaurea density in all regions. Density was similar between the native Caucasus and non-native Argentina and much greater in those regions than in the native Turkey and non-native US in biocide-free plots. Fungicides had positive effects on density in the US and negative ones in the Caucasus and Argentina, resulting in no differences between those three regions and greater density in the US than Turkey. Insecticide applications promoted Centaurea density in Turkey and Argentina, but inter-regional comparisons of density in treated plots were comparable to those in biocide-free plots. Overall, plants were smaller and less fecund in Turkey than the other regions, except the US. The greatest fungal attack was documented in Turkey, and herbivory was stronger there and in Argentina than in the Caucasus and US. The resilience of the local community explained a large proportion of variation in Centaurea density. These results support our hypothesis, and reveal that the speed at which competition is re-gained after disturbance may influence global variation in Centaurea abundance. Because many ruderals exhibit native and non-native distributions, our results are likely to be generalized to other systems.
Using species distribution modeling to generate relative abundance information in unstable territories: conservation of Felidae in Mexico
<p>Raw data used in the abovementioned manuscript</p>
Distribution. Lowland forests of W Brazil, E Peru, and N Bolivia, S of the Amazon River. Because of abundance of individuals in the C. castanea complex, hampering precise species identification in the field and in collections, a detailed assessment ofits distribution is still needed. in Phyllostomidae
Distribution. Lowland forests of W Brazil, E Peru, and N Bolivia, S of the Amazon River. Because of abundance of individuals in the C. castanea complex, hampering precise species identification in the field and in collections, a detailed assessment ofits distribution is still needed.
Figures 10–13 in Six freshwater microturbellarian species (Platyhelminthes) in permanent wetlands of the Coastal Plain of southern Brazil: new records, abundance, and distribution
Figures 10–13. Photographs of specimens in vivo after squeeze preparation (10, 12) and diagrammatic reconstructions (11, 13) in dorsal view of species of Dalytyphloplanida recorded for the Coastal Plain of southern Brazil. 10, 11. Baicalellia evelinae. 12, 13. Gieysztoria chiqchi. Details of the penis stylet are shown in 11B and 13B.
Figures 8, 9 in Six freshwater microturbellarian species (Platyhelminthes) in permanent wetlands of the Coastal Plain of southern Brazil: new records, abundance, and distribution
Figures 8, 9. Photograph of specimen in vivo after squeeze preparation (8) and diagrammatic reconstruction (9) in dorsal view of Stenostomum hemisphericum recorded for the Coastal Plain of southern Brazil.
Figures 2–7 in Six freshwater microturbellarian species (Platyhelminthes) in permanent wetlands of the Coastal Plain of southern Brazil: new records, abundance, and distribution
Figures 2–7. Photographs of specimens in vivo after squeeze preparation (2, 4, 6) and diagrammatic reconstructions in dorsal view (3, 5, 7) of species of Catenula recorded in the Coastal Plain of southern Brazil. 2, 3. Catenula evelinae. 4, 5. C. leuca. 6, 7. C. turgida. Scale bars = 100 µm.
Figure 1 in Six freshwater microturbellarian species (Platyhelminthes) in permanent wetlands of the Coastal Plain of southern Brazil: new records, abundance, and distribution
Figure 1. Study areas in the Coastal Plain of the southern Brazilian state of Rio Grande do Sul (white area): Terra de Areia (1 = 29°29'05" S, 049°52'21" W), Osório (2 = 29°53'20" S, 050°08'09" W, and 3 = 29°52'02" S, 050°05'16" W), Tramandaí (4 = 30°05'09" S, 050°10'24" W), and Capivari do Sul (5 = 30°10'22" S, 050°23'10" W).
Data and code for "Tree species abundance changes at the edges of their climatic distribution: an interplay between climate change, plant traits, and forest management"
<p>## Secondary data and code to accompany the research entitled "Tree species abundance changes at the edges of their climatic distribution: an interplay between climate change, plant traits, and forest management" by Padullés Cubino et al. (2024).</p> <p># There are four folders with (1) "raw data", (2) "processed data", (3) "results", and (4) "scripts".</p> <p># The raw and processed data folders contain the CSV and XLSX files with all the data used for analysis and produced from them</p> <p># The "results" folder contains the figures and table presented in the manuscript.</p> <p># The "scripts" folder contains four scripts for the analyses described in the manuscript:</p> <p> 01_preparation_ClimEdge.R -> data cleaning and processing</p> <p> 02_script_Fig1.R -> code to produce Fig1</p> <p> 03_script_Fig2.R -> code to produce Fig2</p> <p> 04_script_Table1_Fig3.R -> code to produce Table 1 and Fig3</p> <p># If anything is unclear, please contact the corresponding author for clarification (padullesj@gmail.com).</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.