Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,956
datasets available to search
ShareScore release 0.9.0
Dataset results
1,956 results for “test data”
Data from: Testing classical species properties with contemporary data: how 'bad species' in the brassy ringlets (Erebia tyndarus complex, Lepidoptera) turned good
All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods i) rely on simplified demographic models that may fail to capture some attributes of biological species, ii) do not make explicit use of the geographic information contained in the data, and iii) are often computationally intensive. In this paper we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We 1) obtained RAD sequencing data from a carefully designed sample, 2) applied two genotype clustering algorithms to identify genetic clusters and 3) performed within-clusters and between-clusters analyses of isolation by distance (IBD) as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes Factor Delimitation (BFD*) coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analysed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information.
Data from: Is sex advantageous in adverse environments? A test of the abandon-ship hypothesis
Understanding the evolution and maintenance of sexual reproduction remains a long-standing challenge in evolutionary biology. Stress often induces sexual reproduction in facultatively sexual species (those species capable of both sexual and asexual reproduction). The abandon-ship hypothesis predicts higher allocation to sex under stress to allow low-fitness individuals to recombine their genotype, potentially increasing offspring fitness. However, effective tests of the abandon-ship hypothesis, particularly in multicellular organisms, are lacking. Here we test the abandon-ship hypothesis, using cyanogenic and acyanogenic defense phenotypes of the short-lived perennial herb Trifolium repens. Cyanogenesis provides an effective defense against herbivores and is under relatively simple genetic control (plants dominant for cyanogenesis at two alleles express the defended phenotype). Thus, maladapted individuals can acquire adaptive defense alleles for their offspring in a single episode of sexual reproduction. Plants were grown under high- and low-herbivory treatments (plants were exposed to herbivorous snails) and a control treatment (no herbivory). Herbivores reduced growth and fitness in all treated plants, but herbivory induced higher sexual allocation only in maladapted (acyanogenic) individuals. Overall, our results support the abandon-ship hypothesis.
Data from: Testing the limits of pheromone stigmergy in spatially constrained robotic swarms
Area coverage and collective exploration are key challenges for swarm robotics. Previous research in this field has drawn inspiration from ant colonies, with real, or more commonly virtual, pheromones deposited into a shared environment to coordinate behaviour through stigmergy. Repellent pheromones can facilitate rapid dispersal of robotic agents, yet this has been demonstrated only for relatively small swarm sizes (N<30). Here, we report findings from swarms of real robots (Kilobots) an order of magnitude larger (N>300), and from realistic simulation experiments up to N=400. We identify limitations to stigmergy in a spatially constrained environment – a free but bounded two-dimensional workspace – using repellent binary pheromone. At larger N a simple, stigmergic avoidance algorithm becomes first no better, then inferior to, the area coverage of non-interacting random walkers. Thus, with ever-increasing swarm sizes, the assumption of robustness and scalability for such approaches may need to be re-examined. Instead, subcellular biology, and diffusive processes, may prove a better source of inspiration at large N in spatially constrained or high agent density environments.
Data from: Size doesn't matter, sex does: a test for boldness in sister species of Brachyrhaphis fishes
The effect of divergent natural selection on the evolution of behavioral traits has long been a focus of behavioral ecologists. Predation, due to its ubiquity in nature and strength as a selective agent, has been considered an important environmental driver of behavior. Predation is often confounded with other environmental factors that could also play a role in behavioral evolution. For example, environments that contain predators are often more ecologically complex and "risky" (i.e., exposed and dangerous). Previous work shows that individuals from risky environments are often more bold, active, and explorative than those from low-risk environments. To date, most comparative studies of environmentally driven behavioral divergence are limited to comparisons among populations within species that occur in divergent selective environments but neglect comparisons between species following speciation. This limits our understanding of how behavior evolves post-speciation. The Central American live-bearing fish genus Brachyrhaphis provides an ideal system for examining the relationship between selective environments and behavior, within and between species. Here, we test for differences in boldness between sister species B. roseni and B. terrabensis that occur in streams with and without piscivorous predators, respectively. We found that species do differ in boldness, with species that occur with predators being bolder than those that do not. Within each species, we found that sexes differed in boldness, with males being bolder than females. We also tested for a relationship between size (a surrogate for metabolic rate) and boldness, but found no size effects. Therefore, sex, not size, affects boldness. These results are consistent with the hypothesis that complex and risky environments favor individuals with more bold behavioral traits, but they are not consistent with the hypothesis that size (and therefore metabolic rate) drives divergence in boldness. Finally, our results provide evidence that behavioral trait divergence continues even after speciation is complete.
Data from: Testing the benefits of conservation set-asides for improved habitat connectivity in tropical agricultural landscapes
1. Habitat connectivity is important for tropical biodiversity conservation. Expansion of commodity crops, such as oil palm, fragments natural habitat areas, and strategies are needed to improve habitat connectivity in agricultural landscapes. The Roundtable on Sustainable Palm Oil (RSPO) voluntary certification system requires that growers identify and conserve forest patches identified as High Conservation Value Areas (HCVAs) before oil palm plantations can be certified as sustainable. We assessed the potential benefits of these conservation set-asides for forest connectivity. 2. We mapped HCVAs and quantified their forest cover in 2015. To assess their contribution to forest connectivity, we modelled range expansion of forest-dependent populations with five dispersal abilities spanning those representative of poor dispersers (e.g., flightless insects) to more mobile species (e.g., large birds or bats) across 70 plantation landscapes in Borneo. 3. Because only 21% of HCVA area was forested in 2015, these conservation set-asides currently provide few connectivity benefits. Compared to a scenario where HCVAs contain no forest (i.e., a no-RSPO scenario), current HCVAs improved connectivity by ~3% across all dispersal abilities. However, if HCVAs were fully reforested, then overall landscape connectivity could improve by ~16%. Reforestation of HCVAs had the greatest benefit for poor to intermediate dispersers (0.5-3 km per generation), generating landscapes that were up to 2.7 times better connected than landscapes without HCVAs. By contrast, connectivity benefits of HCVAs were low for highly mobile populations under current and reforestation scenarios, because range expansion of these populations was generally successful regardless of the amount of forest cover. 4.Synthesis and applications. The RSPO requires that HCVAs be set aside to conserve biodiversity, but HCVAs currently provide few connectivity benefits because they contain relatively little forest. However, reforested HCVAs have the potential to improve landscape connectivity for some forest species (e.g., winged insects), and we recommend active management by plantation companies to improve forest quality of degraded HCVAs (e.g., by enrichment planting). Future revisions to the RSPO's Principles and Criteria (P&C) should also ensure that large (i.e., with a core area >2 km2) HCVAs are reconnected to continuous tracts of forest to maximise their connectivity benefits.
Data from: Testing the depth-differentiation hypothesis in a deepwater octocoral
The depth-differentiation hypothesis proposes that the bathyal region is a source of genetic diversity and an area where there is a high rate of species formation. Genetic differentiation should thus occur over relatively small vertical distances, particularly along the upper continental slope (200–1000 m) where oceanography varies greatly over small differences in depth. To test whether genetic differentiation within deepwater octocorals is greater over vertical rather than geographical distances, Callogorgia delta was targeted. This species commonly occurs throughout the northern Gulf of Mexico at depths ranging from 400 to 900 m. We found significant genetic differentiation (FST = 0.042) across seven sites spanning 400 km of distance and 400 m of depth. A pattern of isolation by depth emerged, but geographical distance between sites may further limit gene flow. Water mass boundaries may serve to isolate populations across depth; however, adaptive divergence with depth is also a possible scenario. Microsatellite markers also revealed significant genetic differentiation (FST = 0.434) between C. delta and a closely related species, Callogorgia americana, demonstrating the utility of microsatellites in species delimitation of octocorals. Results provided support for the depth-differentiation hypothesis, strengthening the notion that factors covarying with depth serve as isolation mechanisms in deep-sea populations.
Data from: Screening test for neutralizing antibodies against yellow fever virus, based on a flavivirus pseudotype
Given the possibility of yellow fever virus reintroduction in epidemiologically receptive geographic areas, the risk of vaccine supply disruption is a serious issue. New strategies to reduce the doses of injected vaccines should be evaluated very carefully in terms of immunogenicity. The plaque reduction test for the determination of neutralizing antibodies (PRNT) is particularly time-consuming and requires the use of a confinement laboratory. We have developed a new test based on the use of a non-infectious pseudovirus (WN/YF17D). The presence of a reporter gene allows sensitive determination of neutralizing antibodies by flow cytometry. This WN/YF17D test was as sensitive as PRNT for the follow-up of yellow fever vaccinees. Both tests lacked specificity with sera from patients hospitalized for acute Dengue virus infection. Conversely, both assays were strictly negative in adults never exposed to flavivirus infection or vaccination, and in patients sampled some time after acute Dengue infection. This WN/YF17D test will be particularly useful for large epidemiological studies and for screening for neutralizing antibodies against yellow fever virus.
Data from: Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae)
Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate non-monophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian Computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.
Data from: Testing an hypothesis of hybrid zone movement for toads in France
Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.
Flight Test data_v1.0._OD_WP3_D3.4.1
<p>Flight Test data_v1.0._OD_WP3_D3.4.1 Preliminary Report</p>
Data from: Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing
Migration traits are presumed to be complex and to involve interaction among multiple genes, thus we employed both univariate analyses and multivariate Random Forest (RF) machine learning algorithm to conduct association mapping of 15,239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer- and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration-timing (p < 0.000005) that explained 46% of trait variation. Alignment to the annotated S. salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an estrogen target gene) on chromosome Ssa03. Additionally, multivariate analyses with RF identified that these 3 SNPs plus 15 additional SNPs explained up to 60% of trait variation. These candidate SNPs may provide the ability to predict adult migration-timing of steelhead to facilitate conservation management of this species and this study demonstrates the benefit of multivariate analyses for association studies.
Data for: A test of Sensory Drive in plant-pollinator interactions: habitat heterogeneity shapes pollinator preference for a floral visual signal
<p>DATA:</p> <p>FinnKoski_PollData_Final: Pollinator visitation data to floral arrays analyzed</p> <p>Spectra used for vismodels.zip: reflectance spectra of flowers and floral backgrounds, irradiance spectra</p> <p>ColorContrastData: visual contrast data analyzed</p> <p>CODE: </p> <p>vismod_code.R : code used for visual system modeling and calculation of contrast</p> <p>SAS_modelcode.R: SAS code used to analyze pollinator visitation data and color contrast data</p>
Data from: Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron
<p>Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plants barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from <i>Rhododendron </i>species and compared discrimination success with standard plant barcodes<i>. </i>We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+<i>matK</i>+<i>rbcL</i>+<i>trnH-psbA. </i>In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3-4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.</p>
Daily United States COVID-19 Testing and Outcomes Data By State, March 7, 2020 to March 7, 2021
<p>The COVID Tracking Project was a volunteer organization launched from The Atlantic and dedicated to collecting and publishing the data required to understand the COVID-19 outbreak in the United States. Our dataset was in use by national and local news organizations across the United States and by research projects and agencies worldwide.</p> <p>Every day, we collected data on COVID-19 testing and patient outcomes from all 50 states, 5 territories, and the District of Columbia by visiting official public health websites for those jurisdictions and entering reported values in a spreadsheet. The files in this dataset represent the entirety of our COVID-19 testing and outcomes data collection from March 7, 2020 to March 7, 2021. This dataset includes official values reported by each state on each day of antigen, antibody, and PCR test result totals; the total number of probable and confirmed cases of COVID-19; the number of people currently hospitalized, in intensive care, and on a ventilator; the total number of confirmed and probable COVID-19 deaths; and more.</p>
TCGA-HNSC NIFTI Test Data
<p>This data is part of the TCGA-HNSC dataset provided by The Cancer Imaging Archive (TCIA) and is<br> released under the Creative Commons Attribution 3.0 Unported License.</p> <p>Citations & Data Usage Policy <br> Users of this data must abide by the TCIA Data Usage Policy and the Creative Commons Attribution <br> 3.0 Unported License under which it has been published. Attribution should include references to <br> the following citations:</p> <p>TCGA Attribution<br> "The results <published or shown> here are in whole or part based upon data generated by the TCGA <br> Research Network: http://cancergenome.nih.gov/."</p> <p>Data Citation<br> Zuley, M. L., Jarosz, R., Kirk, S., Lee, Y., Colen, R., Garcia, K., … Aredes, N. D. (2016). <br> Radiology Data from The Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma [TCGA-HNSC] <br> collection. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2016.LXKQ47MS</p> <p>TCIA Citation<br> Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, <br> Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a <br> Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, <br> pp 1045-1057.</p>
Optimal Spectral Sampling Forward Model Test Data
<p>Binary and ASCII files for tests of the OSS forward model application.</p>
Data from: Metabolism drives demography in an experimental field test
<p>Metabolism should drive demography by determining the rates of both biological work and resource demand. Long-standing 'rules' for how metabolism should covary with demography permeate biology, from predicting the impacts of climate change to managing fisheries. Evidence for these rules is almost exclusively indirect and in the form of among-species comparisons, while direct evidence is exceptionally rare. In a manipulative field experiment on a sessile marine invertebrate, we created experimental populations that varied systematically in population size (density) and metabolic rate, but not body size. We then tested key theoretical predictions regarding relationships between metabolism and demography by parameterising population models with lifetime performance data from our field experiment. We found populations with higher metabolisms had greater intrinsic rates of increase and lower carrying capacities, in qualitative accordance with classic theory, but we also found important departures from theory. In particular, carrying capacity declined less steeply than predicted, such that energy use at equilibrium increased with metabolic rate, violating the long-standing axiom of energy equivalence. Theory holds that energy equivalence emerges because resource supply is assumed to be independent of metabolic rate. We find this assumption to be violated under real world conditions – with potentially far-reaching consequences for the management of biological systems.</p>
Test data set for Aquaria
<p>Data sets for testing zenodo in Aquaria.</p>
Sling load - Dataset of software tests on column detection algorithm with laserscanner data
<p>This dataset contains data and scripts for plotting results of testing of the algorithm of column detection, using laserscanner data.</p>
Unprocessed data for the "Property-Based Testing of Web APIs" paper
<p>Unprocessed data for the "Property-Based Testing of Web APIs" paper. </p>
ScienceDex guides
Understand access before you commit
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.