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85 results for “species persistence”
data set to bioRxiv preprint 'Persistent cross-species SARS-CoV-2 variant infectivity predicted via comparative molecular dynamics simulation
<p>This is supporting data and software code for the following preprint in bioRxiv</p> <p><strong>Persistent cross-species SARS-CoV-2 variant infectivity predicted via comparative molecular dynamics simulation</strong></p> <p>https://www.biorxiv.org/content/10.1101/2022.04.18.488629v1</p>
Data from: Is a community state reachable, and why?, and Coexistence and collapse: an experimental investigation of the persistent communities of a protist species pool
<p>Deterministic models have difficulties to take into account stochasticity during community assembly. As a tool to circumvent this problem, we present a qualitative discreteevent model, where consequences of interspecific interactions are described as rules. This model provides a map of all possible future dynamics for a given system, which allows to exhaustively describe the possible pathways during an assembly process. Such a description does not rely on species traits details and is insensitive to stochastic effects. This allows to show that subsets of species are sometimes impossible to reach starting from larger sets of species, and therefore to question the reachability of community states during the system’s dynamics. Applying the model to an experimental dataset studying the collapse of protist communities, we obtain a very good theory-experiment agreement. We finally discuss what the notion of reachability can bring to community assembly.</p>
Species persistence and mean rank abundance in global Nutrient Network plots from 2007-2019
This dataset uses data from the NutNet dataset to examine how temporal and spatial rarity are related, how temporal and spatial rarity predict species loss in ambient and experimentally perturbed plots. We use data from all sites that had NPK and/or fencing treatments with a minimum of five years of cover data when data was downloaded on August 2, 2019; 49 sites in all were used. Perturbations were NPK treatments (nitrogen, phosphorus, potassium and micronutrients) and fencing (vertebrate herbivore exclusion). Temporal rarity was assessed as the percentage of years a species was found in a plot (calculated in R script) and spatial rarity was assessed as the mean rank percentile of a species across all years in a plot (included in data table). We found that persistence (i.e. temporal rarity) was a better predictor than local abundance (i.e. spatial rarity) of whether a species would be absent in a neighboring plot, despite the rarity axes being correlated. Additionally, perturbations reduced persistence most strongly in highly persistent species and low abundance species, further suggesting these are unique dimensions of rarity.
Data and code corresponding to the article "Interaction network structure explains species temporal persistence in empirical plant-pollinator communities"
<p>This upload contains the Datasets and code to generate the results of the article "Interaction network structure explains species temporal persistence in empirical plant-pollinator communities".</p><p>The database comprises two files containing the abundances of plants and pollinators, and one containing the interaction networks among plants and pollinators. </p><p>The code folder contains the code to generate the results, and to generate the figures of the manuscript. </p>
Systematic and persistent bias against introduced species
<p>Data used for Pereyra et al 2023 "Systematic and persistent bias against introduced species"</p> <p>The file data_Pereyra_et_al_2023.csv has the dataet, while the file attributes.csv has column descriptions. </p>
Fig. 3 in Persistent low avian malaria in a tropical species despite high community prevalence
Fig. 3. Maximum likelihood phylogenetic inference of (A) Haemoproteus and (B) Plasmodium from the Australasian region. Sequences were included if they were at least 479 nucleotides in length and were found to be unique from a pairwise distance analysis (see methods). Bootstrap support values are shown if greater than 50. Dots indicate the 14 lineages that were detected in this study and their colour denotes the bird species they occurred within [Purple = PCFW (M. c. coronatus), Red = RBFW (M. melanocephalus), Yellow = BSR (P. cerviniventris), Grey = WGH (L. unicolor)]. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Persistent low avian malaria in a tropical species despite high community prevalence
Fig. 2. (A) Malarial parasite prevalence across years in four bird species, buff-sided robin (BSR, n = 66), purple-crowned fairy-wren (PCFW, n = 731), red-backed fairy-wren (RBFW, n = 78), white-gaped honeyeater (WGH, n = 25). Fisher's exact P-values test for annual differences in infection within each bird species. (B) Longitudinal sampling of infected PCFW adults (individuals presented were sampled more than twice and were identified as infected with Haemoproteus or Plasmodium). Dotted lines indicate uncertainty in years when no sample was available. Each individual was infected with a single lineage. (C) Percentage of individual PCFW infected within each age category. (D) Local phylogenetic relationship between parasite lineages, colours refer to host species as for (A). Maximum likelihood tree was inferred using GTR + G + I with 1000 bootstrap replicates; novel lineages are indicated by *. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Persistent low avian malaria in a tropical species despite high community prevalence
Fig. 1. Map of Australia and the Kimberly region. Sampling was conducted at the Australian Wildlife Conservancy's Mornington Wildlife Sanctuary (17̊31′S, 126̊6'E). Star indicates the location of the field site where samples were collected.
Forestation at the right time with the right species can generate persistent carbon benefits in China
<p>This collection contains the datasets used in our study ‘<strong>Forestation at the right time with the right species can generate persistent carbon benefits in China</strong>’.</p> <p><em><strong>Part A: Data</strong></em></p> <p>Most of the data presented here are after pre-processing, such as transforming the projection, extracting variables, clipping to the study region (70<sup>o</sup>E-140<sup>o</sup>E,15<sup>o</sup>N-55<sup>o</sup>N), and resampling to 1-km.</p> <p>The original source of these data sets (usually global, at different resolutions) is given in 'data_original.txt' as well as in the 'Data availability' of the main text.</p> <p>1. potential_china_forest_1km.rar: contains the potential forest distributions for China at 1-km resolution from multiple source (Random Forest, WRI and ORCHIDEE). Note: the forest distribution is in the form of logical variables in the .mat file, where a value of 1 or true means that the grid point is potentially forestable, and a value of 0 or false means this grid is not suitable for forest.</p> <p>2. ori_carbon_all_grid_1km.mat: Living biomass carbon densities in 2010 for China at 1-km (unit: Mg C ha-1). Both aboveground and belowground biomass carbon are included. The original biomass map is from Spawn et al. 2020.</p> <p>3. Forest_inventory_data_5th_9th.xlsx: 1) The forest area reported in 5th to 9th national forest inventory 2) The forest area of different age classes derived form the 9th national forest inventory.</p> <p>4. data_original.txt: the original source of these data sets</p> <p><strong>Part B: MATLAB Code</strong></p> <p>This file (Matlab_code.rar) contains the code, functions and parameters for our analysis of the data, mainly MATLAB files (.m or mat)</p> <p><strong>Part C: Demo/Example data and code</strong></p> <p>This file (Demo.rar) contains the demo of our code running, which includes the demo code along with code comments, input data for the demo, and the expected output results.</p> <p><strong>Part D: Docs</strong></p> <p>Reference and guidelines (Docs.rar).</p> <p>If you have any questions or suggestions, please contact xuhaotony@pku.edu.cn</p>
Data from: A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish
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Data from: Soil microbiomes underlie population persistence of an endangered plant species
Microbiomes can dramatically alter individual plant performance, yet how these effects influence higher order processes is not well resolved. In particular, little is known about how microbiome effects on individual plants alter plant population dynamics, a question critical to imperiled species conservation. Here, we integrate bioassays, multidecadal demographic data, and integral projection modeling to determine how the presence of the natural soil microbiome underlies plant population dynamics. Simulations indicated that the presence of soil microbiomes boosted population growth rates (λ) of the endangered Hypericum cumulicola by 13% on average, the difference between population growth versus decline in 76% of patches. The greatest benefit (47% increase in λ) occurred in low nutrient, high elevation habitats, suggesting that the soil microbiome may help expand H. cumulicola's distribution to include these stressful habitats. Our results demonstrate that soil microbiomes can significantly affect plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning. plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning.
Data from: Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species
<p>The evolution of postzygotic isolation is thought to be a key step in maintaining species boundaries upon secondary contact, yet the dynamics and persistence of hybrid incompatibilities in naturally hybridizing species are not well understood. Here, we explore these issues using genetic mapping in three independent populations of recombinant inbred lines between naturally hybridizing monkeyflowers <em>Mimulus guttatus</em> and <em>M. nasutus</em> from the sympatric Catherine Creek population. We discover that the three <em>M. guttatus</em> founders differ dramatically in admixture history, with nearly a quarter of one founder's genome introgressed from <em>M. nasutus</em>. Comparative genetic mapping in the three RIL populations reveals three new putative inversions, each one segregating among the <em>M. guttatus</em> founders, two due to admixture. We find strong, genome-wide transmission ratio distortion in all RILs, but patterns are highly variable among the three populations. At least some of this distortion appears to be explained by epistatic selection favoring parental genotypes, but tests of inter-chromosomal linkage disequilibrium also reveal multiple candidate Dobzhansky-Muller incompatibilities. We also map several genetic loci for hybrid pollen viability, including two interacting pairs that coincide with peaks of distortion. Remarkably, even with this limited sample of three <em>M. guttatus</em> lines, we discover abundant segregating variation for hybrid incompatibilities with <em>M. nasutus,</em> suggesting this population harbors diverse contributors to postzygotic isolation. Moreover, even with substantial admixture, hybrid incompatibilities between <em>Mimulus</em> species persist, suggesting postzygotic isolation might be a potent force in maintaining species barriers in this system. </p>
Data and analysis code of "Forestation at the right time with the right species can generate persistent carbon benefits in China"
<p>This collection contains the datasets used in our study ‘<strong><em>Forestation at the right time with the right species can generate persistent carbon benefits in China</em></strong>’.</p> <p> </p> <p><strong><em>Part A: Data</em></strong></p> <p>Most of the data presented here are after pre-processing, such as transforming the projection, extracting variables, clipping to the study region (70<sup>o</sup>E-140<sup>o</sup>E,15<sup>o</sup>N-55<sup>o</sup>N), and resampling to 1-km.</p> <p>The original source of these data sets (usually global, at different resolutions) is given in 'data_original.txt' as well as in the 'Data availability' of the main text.</p> <p>1. Climate_china_1km.7z: This compressed file contains the annual precipitation and temperature from Peng et al. 2019 at 1km.</p> <p>2. Soil_china_1km.7z: This compressed file contains the soil properties derived from Soilgrid250m for China at 1-km resolution.</p> <p>3. Topography_china_1km.7z: This compressed file contains the topographic properties derived from Global Multi-resolution Terrain Elevation Data 2010 for China at 1-km resolution.</p> <p>4. MaxEnt_process.7z: This compressed file contains all the input data and model results of the MaxEnt model: 1) environment layers in ’.asc’, 2) rarefied occurrence points for the 15 forest types, 3) MaxEnt results in ’.tif’ (average of the 10-folds results)</p> <p>5. Potential_china_forest_1km.7z: contains the potential forest distributions for China at 1-km resolution from multiple source (Random Forest, WRI and ORCHIDEE). Note: the forest distribution is in the form of logical variables in the .mat file, where a value of 1 or true means that the grid point is potentially forestable, and a value of 0 or false means this grid is not suitable for forest.</p> <p>6. Existing_china_forest_1km.7z: contains the existing forest distributions for China at 1-km resolution from multiple source (FI2013-2017, Hansen, MODIS, ESA-CCI, CNLUCC, GLC-FCS30 and GlobeLand30). Note: the existing forest distribution is in the form of logical variables in the .mat file, where a value of 1 or true means there is forest distribution, and a value of 0 or false means there is currently no forest distribution.</p> <p>7. Crop_urban_china_1km.7z: similar to the Existing_china_forest_1km.zip, but stores the distribution of cropland and urban.</p> <p>8. Masks_area_china_1km.7z: area mask and the shp files of the national and provincial boundaries of China.</p> <p>9. CMIP6_outputs.7z: contains historical (1970-2014) and future (2015-2100) climate and CO2 fertilization factor simulated by Earth System Models participating in CMIP6.</p> <p>10. Ori_carbon_all_grid_1km.mat: Living biomass carbon densities in 2010 for China at 1-km (unit: Mg C ha<sup>-1</sup>). Both aboveground and belowground biomass carbon values are included. The original biomass map is from Spawn et al. 2020.</p> <p>11. Forest_inventory_data_5th_9th.xlsx: 1) The forest area reported in 5th to 9th national forest inventory 2) The forest area of different age classes derived from the 9th national forest inventory.</p> <p>12. Forest_age_CN2019.7z: the forest stand age map for China updated to 2019.</p> <p>13. data_original.txt: the original source of these data sets</p> <p><strong>Part B: MATLAB Code</strong></p> <p>This file (Matlab_code.7z) contains the code, functions and parameters for our analysis of the data, mainly MATLAB files (.m or mat)</p> <p><strong>Part C: Demo/Example data and code</strong></p> <p>This file (Demo.7z) contains the demo of our code running, which includes the demo code along with code comments, input data for the demo, and the expected output results.</p> <p><strong>Part D: Docs</strong></p> <p>Reference and guidelines (Docs.7z).</p> <p>If you have any questions or suggestions, please contact xuhaotony@pku.edu.cn</p>
Data for "Negative density dependence promotes persistence of a globally rare yet locally abundant plant species (Oenoethera coloradensis)"
<p>This dataset was used to perform the analyses in the manuscript "Negative density dependence promotes persistence of a globally rare yet locally abundant plant species (Oenoethera coloradensis)"</p>
Data from: Persistent species relationships characterize migrating bird communities across stopover sites and seasons
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Data from: Soil microbiomes underlie population persistence of an endangered plant species
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Data from: The combined effects of multiple invasive species on persistence of imperiled Pahrump Poolfish
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Data from: Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species
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Can niche plasticity mediate species persistence under ocean acidification?
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FIGURES 1–2 in A new fossil species of Bolitophagini (Coleoptera: Tenebrionidae) from Baltic amber suggests the genus Eledonoprius Reitter is persistent in the Western Palaearctic since the Tertiary
FIGURES 1–2. Eledonoprius incoronatus sp. nov., holotype: 1 – habitus, dorsal view; 2 – habitus, lateral view. Scale bars represent 0.5 mm.
ScienceDex guides
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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.