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.
5,538
datasets available to search
ShareScore release 0.9.0
Dataset results
5,538 results for “Population data”
Data from: Population responses to a historic drought across the range of the common monkeyflower (Mimulus guttatus)
<p>This dataset contains both metadata and phenotype data for both of the resurrections experiments described in Kooyers et al. 2020. Datasets are uploaded as .csv files. Please read the readme files for descriptions of the data in each .csv file.</p>
Data from: Extra-pair paternity in two populations of the socially monogamous Thorn-tailed Rayadito Aphrastura spinicauda (Passeriformes: Furnariidae)
Studies on extra-pair paternity (EPP) are key to understanding the ecological and evolutionary drivers of variation in avian mating strategies, but information is currently lacking for most tropical and sub-tropical taxa. We describe the occurrence of EPP in two populations of a South American socially monogamous bird, the Thorn-tailed Rayadito, based on data from 266 broods and 895 offspring that were sampled during six breeding seasons in north-central and southern Chile. In the northern population, 21% of the broods contained at least one extra-pair young and 14% of all offspring were sired by an extra-pair male, while in the southern population, we detected extra-pair offspring (EPO) in 14% of the broods, and 6% of all offspring were EPO. Variation in the frequency of EPP could stem from population differences in the duration of the breeding season or the density of breeding individuals. Other factors such as differences in breeding synchrony and variation in food availability need to be evaluated. More reports on EPP rates are necessary to determine the patterns of taxonomic and geographic variation in mating strategies in Neotropical birds, and to better understand the differences in ecological dynamics between northern and southern hemisphere populations.
Capturing the dynamics of small populations: A retrospective assessment using long-term data for an island reintroduction
<p>1. The art of population modelling is to incorporate factors essential for capturing a population's dynamics while otherwise keeping the model as simple as possible. However, it is unclear how optimal model complexity should be assessed, and whether this optimal complexity has been affected by recent advances in modelling methodology. This issue is particularly relevant to small populations because they are subject to complex dynamics but inferences about those dynamics are often constrained by small sample sizes.</p> <p>2. We fitted Bayesian hierarchical models to long-term data on vital rates (survival and reproduction) for the toutouwai (Petroica longipes) population reintroduced to Tiritiri Matangi, a 220-ha New Zealand island, and quantified the performance of those models in terms of their likelihood of replicating the observed population dynamics. These dynamics consisted of overall growth from 33 (± 0.3) to 160 (± 6) birds from 1992–2018, including recoveries following five harvest events for further reintroductions to other sites.</p> <p>3. We initially included all factors found to affect vital rates, which included inbreeding, post-release effects, density-dependence, sex, age and random annual variation, then progressively removed these factors. We also compared performance of models where data analysis and simulations were done simultaneously to those produced with the traditional two-step approach, where vital rates are estimated first then fed into a separate simulation model. Parametric uncertainty and demographic stochasticity were incorporated in all projections.</p> <p>4. The essential factors for replicating the population's dynamics were density-dependence in juvenile survival and post-release effects, i.e. initial depression of survival and reproduction in translocated birds. Inclusion of other factors reduced the precision of projections, and therefore the likelihood of matching observed dynamics. However, this reduction was modest when the modelling was done in an integrated framework. In contrast, projections were much less precise when done with a two-step modelling approach, and the cost of additional parameters was much higher under the two-step approach.</p> <p>5. These results suggest that minimization of complexity may be less important than accounting for covariances in parameter estimates, which is facilitated by integrating data analysis and population projections using Bayesian methods. 13-Aug-2021 --</p>
Additional data "Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network"
<p>Additional data containing chemical shift perturbations and intensity changes of Hsp90 upon client binding, intermolecular PREs, and raw scattering data of Hsp90-client complexes.</p>
Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence
<p><span><span><span><span><span><span><span><span><span><span><span>Three subspecies of Northern Bahamian Rock Iguanas, <i>Cyclura cychlura</i>, are currently recognized: <i>C. c. cychlura,</i>restricted to Andros Island, and <i>C. c. figginsi</i> and <i>C. c. inornata,</i> native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of <i>C. cychlura</i> are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: <i>C. cychlura</i> iguanas, their ticks (genus <i>Amblyomma</i>, preferentially parasitizing these reptiles), and <i>Rickettsia </i>spp. endosymbionts (within tick ectoparasites). Our results indicate that while <i>C. c. cychlura</i> on Andros is consistently supported as a separate clade, patterns of relatedness among populations of <i>C. c. figginsi</i> and <i>C. c. inornata</i> within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and <i>Rickettsia</i> spp., supports the evolutionary independence of <i>C. c. inornata</i>. Further, these patterns are also consistent with two independent evolutionarily significant units within <i>C. c. figginsi</i>. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.</span></span></span></span></span></span></span></span></span></span></span></p>
Data and code to replicate the analyses in "Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen"
<p>Data and code used to run the analyses presented in the article "Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen" published in Journal of Animal Ecology. Please cite this article if you use the data or write to the authors for a potential collaboration. If you require further details about the data please write to: andresvalenzuela.zoo@gmail or avalenzuela@ranitadedarwin.org.</p> <p>This study is part of an ongoing long-term monitoring program focused on the threatened Southern Darwin's frog (<em>Rhinoderma darwinii</em>), led by the Chilean non-profit organization ONG Ranita de Darwin (www.ranitadedarwin.org/monitoreo). This project has been funded by Zoo Leipzig, The National Geographic Society, Rufford Foundation, Weeden Foundation, Mohamed Bin Zayed Species Conservation Fund, VONA, Fundación Huilo Huilo, and Fundación MERI. We want to thank to the many volunteers that have kindly participated during this project.</p>
Data from: Increasing temperature weakens the positive effect of genetic diversity on population growth
Genetic diversity and temperature increases associated with global climate change are known to independently influence population growth and extinction risk. Whether increasing temperature may influence the effect of genetic diversity on population growth, however, is not known. We address this issue in the model protist system Tetrahymena thermophila. We test the hypothesis that at temperatures closer to the species' thermal optimum (i.e., the temperature at which population growth is maximal, or Topt), genetic diversity should have a weaker effect on population growth compared to temperatures away from the thermal optimum. To do so, we grew populations of T. thermophila with varying levels of genetic diversity at increasingly warmer temperatures and quantified their intrinsic population growth rate, r. We found that genetic diversity increases population growth at cooler temperatures, but that as temperature increases, this effect weakens. We also show that a combination of changes in the amount of expressed genetic diversity (G), plastic changes in population growth across temperatures (E), and strong GxE interactions, underlie this temperature effect. Our results uncover important but largely overlooked temperature effects that have implications for the management of small populations with depauperate genetic stocks in an increasingly warming world. --
Genetic loci associated with winter survivorship in diverse lowland switchgrass populations: SNP read count data
<p>High winter mortality is the most important factor limiting biomass yield of lowland switchgrass planted in the northern latitudes of North America. Due to the perennial growth habit and strong dependence on weather conditions to generate sufficient selection pressure to identify winter-hardy individuals, breeding of cold tolerant switchgrass cultivars requires many years. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 population with differential winter survivorship was used for BSA. A maximum of 10% of the individuals per population (8-20) was bulked to create survivor and non-survivor DNA pools. The DNA pools were evaluated using exome capture sequencing and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine QTL from tetraploid populations and seven QTL from octoploid populations. Some markers were identified in multiple populations that originated across a broad geographic landscape, while other markers were site-specific. QTL at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.</p>
Optimization used in in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>OptimizationResults contain the expanded input model for each data set, in the C field are the indices of the core reactions in the expanded input model used to build the multi-cell population for the 121 different parameters, A contains the indices of reaction in the multi-cell population model for the 121 runs, thresh the parameter setting for the cover and REI. The REI is given in %. So 5 REI means 0.05. While A might change because of alternative optimals when run on a different computer, C and the expanded Input model will remain unchanged.</p> <p> </p> <p>Multi_cell_population_CRC and Multi_cell_population_NM are the models obtained by scFASTCORMICS with the optimal setting for Dataset1 and Dataset2, respectively. </p> <p>Please, check the publication (scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data) for more details.</p>
ddRAD sequencing/nSSR data of Alnus glutinosa populations in Pannonia and the Western Carpathians
<p>ddRAD sequencing data from Stacks (SNPs) along with corresponding population information, including environmental and other data; and nSSR data with corresponding population coordinates for a selection of Pannonian and Western Carpathian Alnus glutinosa populations. Draft paper name: Interplay between tree genetic variation, plant community composition and environment in forest communities dominated by black alder (Alnus glutinosa (L.) Gaertn.)</p>
Raw data for Association of ACE2 gene functional variants with gestational diabetes mellitus risk in a southern Chinese population
<p class="MsoNormal"><span>These data were generated to investigate the association and functional analysis of angiotensin-converting enzyme 2 genetic variants with the pathogenesis of Gestational diabetes mellitus (GDM). This study conducted a case-control study involving 569 GDM patients and 735 healthy pregnant women to explore the associations between candidate variants in the ACE2 gene variants and the pathogenesis of GDM. This study collected clinical samples and data, and used logistic regression, false positive report rate, multi factor dimension reduction, functional analysis and other analysis methods to process the research data. Potential functional ACE2 gene variants (rs2106809 A>G, rs6632677 G>C, and rs2074192 C>T) were selected and genotyped using kompetitive allele-specific PCR. The strength of the associations between the studied genetic variants and the risk of GDM were evaluated using odds ratios (ORs) and corresponding 95% confidence intervals (CIs). </span><span>Finally, ACE2 gene variants are significantly associated with the risk of GDM via gene-gene and gene-environment combination. The rs2074192 C > T affects the splicing of ACE2 gene, which may be a potential mechanism leading to the altered susceptibility of individual female during pregnancy in Guilin to GDM</span></p>
Data from: Geothermal stickleback populations prefer cool water despite multigenerational exposure to a warm environment
<p>Given the threat of climate change to biodiversity, a growing number of studies are investigating the potential for organisms to adapt to rising temperatures. Earlier work has predicted that physiological adaptation to climate change will be accompanied by a shift in temperature preferences, but empirical evidence for this is lacking. Here, we test whether exposure to different thermal environments has led to changes in preferred temperatures in the wild. Our study takes advantage of a 'natural experiment' in Iceland, where freshwater populations of threespine sticklebacks (Gasterosteus aculeatus) are found in waters warmed by geothermal activity year-round (warm habitats), adjacent to populations in ambient-temperature lakes (cold habitats). We used a shuttle-box approach to measure temperature preferences of wild-caught sticklebacks from three warm-cold population pairs. Our prediction was that fish from warm habitats would prefer higher water temperatures than those from cold habitats. We found no support for this, as fish from both warm and cold habitats had an average preferred temperature of 13oC. Thus, our results challenge the assumption that there will be a shift in ectotherm temperature preferences in response to climate change. In addition, since warm-habitat fish can persist at relatively high temperatures despite a lower temperature preference, this suggests that preferred temperature alone may be a poor indicator of a population's adaptive potential to a novel thermal environment.</p>
Data and scripts from: Experimental evidence of size-selective harvest and environmental stochasticity effects on population demography, fluctuations, and nonlinearity
<p class="MsoNormal">Theory and analyses of fisheries datasets indicate that harvesting can alter population structure and destabilize nonlinear processes, which increases population fluctuations. We conducted a factorial experiment on the population dynamics of <em>Daphnia magna</em> in relation to size-selective harvesting and stochasticity of food supply. Harvesting and stochasticity treatments both increased population fluctuations. Timeseries analysis indicated that fluctuations in control populations were nonlinear, and nonlinearity increased substantially in response to harvesting. Both harvesting and stochasticity induced population juvenescence, but harvesting did so via depletion of adults whereas stochasticity increased the abundance of juveniles. A fitted fisheries model indicated that harvesting shifted populations towards higher reproductive rates and larger-magnitude damped oscillations that amplify demographic noise. These findings provide experimental evidence that harvesting increases nonlinearity of population fluctuations and that both harvesting and stochasticity increase population variability and juvenescence.</p>
ALL processed data of quantification of Total, viable and VC population
<p>Processed data set of qPCR, PMA-qPCR and agar enumeration of the article. These data are sorted according to the D2O concentration used (0%, 25%, 50% or 75%), and according to the incubation time</p>
Data for: Assessment of estimating selection coefficients in non-Wright-Fisher populations
<p>Selection coefficients are a useful parameter in evolutionary studies. Given that most tools to estimate selection coefficients assume population dynamics of a Wright-Fisher model, but most real-world populations violate Wright-Fisher model assumptions, the accuracy of these tools under more realistic scenarios of evolution is debatable. In this study, we test a common tool (WFABC) to assess estimates of selection coefficients in simulated populations which do and do not adhere to typical Wright-Fisher assumptions. Specifically, we look at simulated non-Wright-Fisher populations which experience evolutionary rescue. We see that fluctuating demography plays an important role in our ability to infer natural selection. Increased rates of sweeps due to bottlenecks increase error in estimates of selection by up to 5.45 times relative to typical WF-adhering populations. In a moderately polygenic model of adaptation, more severe bottlenecks produce harder sweeps such that selected sites interact with surrounding sites, including other selected sites, to increase error in estimates. This may lead to an erroneous excess of the estimated number of sites under selection within a population experiencing evolutionary rescue. Our results place an emphasis on thoughtful analyses of estimates of selection obtained from real-world populations which don't adhere to typical model assumptions.</p>
Data from: Evidence of low within-pair genetic relatedness in a relict population of Thorn-tailed Rayadito despite long-term isolation
<p>Investigating whether mating patterns are biased in relation to kinship in isolated populations can provide a better understanding of the occurrence of inbreeding avoidance mechanisms in wild populations. Here we report on the genetic relatedness (<em>r</em>) among breeding pairs in a relict population of Thorn-tailed Rayadito (<em>Aphrastura spinicauda</em>) in north-central Chile that has experienced a long-term history of isolation. We used simulations based on eight years of data to assess whether mating is random with respect to relatedness. We found that mean and median population values of pair relatedness tended to be lower than randomly generated values, suggesting that mating is not random with respect to kinship. We hypothesize that female-biased dispersal is the main mechanism reducing the likelihood of mating among kin, and that the proportion of related pairs (i.e., <em>r </em>> 0.125) in the study population (25%) would presumably be higher in the absence of sex-biased dispersal. The occurrence of other mechanisms such as extra-pair copulations, delayed breeding and active inbreeding avoidance through kin discrimination cannot be dismissed and require further study.</p>
Data from: Use of an exotic host plant shifts immunity, chemical defense, and viral burden in wild populations of a specialist insect herbivore
<p>Defense against natural enemies constitutes an important driver of herbivore host range evolution in the wild. Populations of the Baltimore checkerspot butterfly, <em>Euphydryas phaeton </em>(Nymphalidae), have recently incorporated an exotic plant, <em>Plantago lanceolata </em>(Plantaginaceae), into their dietary range. To understand the tritrophic consequences of utilizing this exotic host plant, we examined immune performance, chemical defense, and interactions with a natural entomopathogen (Junonia coenia densovirus, <em>Parvoviridae</em>) across wild populations of this specialist herbivore. We measured three immune parameters, sequestration of defensive iridoid glycosides (IGs), and viral infection load in field-collected caterpillars using either <em>P. lanceolata</em> or a native plant, <em>Chelone glabra </em>(Plantaginaceae). We found that larvae using the exotic plant exhibited reduced immunocompetence, compositional differences in IG sequestration, and higher <em>in situ </em>viral burdens compared to those using the native plant. On both host plants, high IG sequestration was associated with reduced hemocyte concentration in the larval hemolymph, providing the first evidence of incompatibility between sequestered chemical defenses and the immune response (i.e., the "vulnerable host" hypothesis) from a field-based study. However, despite this negative relationship between IG sequestration and cellular immunity, caterpillars with greater sequestration harbored lower viral loads. While survival of virus-infected individuals decreased with increasing viral burden, it ultimately did not differ between the exotic and native plants. These results provide evidence that (1) phytochemical sequestration may contribute to defense against pathogens even when immunity is compromised, and (2) herbivore persistence on exotic plant species may be facilitated by sequestration and its role in defense against natural enemies.</p>
Data for: Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure
<p>Distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle without understanding of genomic architecture for phenotypic traits. This study provides a high-resolution portrait of genomic variation in Chinook salmon (<em>Oncorhynchus</em> <em>tshawytscha</em>) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered dataset of ~13 million SNPs from low coverage whole genome resequencing of 53 populations (3,566 barcoded individuals), we contrasted patterns of genomic variation within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Allele frequency variation in GREB1L/ROCK1 was highly correlated with mean migration timing for early- and late-run populations within each of the lineages (r<sup>2</sup> between 0.58–0.95; P < 0.001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream-type) compared to the other two major lineages which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.</p>
Data for: Immune genotypes, immune responses, and survival in a wild bird population
<p>Individuals vary in their immune genotype, inbreeding coefficient <em>f</em>, immune responses, survival to adulthood, and adult longevity. However, whether immune genes predict survival or longevity, whether such relationships are mediated through immune responses, and how f affects immune genotype remain unclear. We use a wild song sparrow (<em>Melospiza</em> <em>melodia</em>) population in which survival to adulthood, adult longevity, and <em>f</em> were measured precisely, and in which immune responses have previously been assessed. We investigate four toll-like receptors (TLR) and the major histocompatibility complex (MHC) class IIB exon 2 genes. We test: a) whether immune genes predict fitness (survival to adulthood or adult longevity); b) whether immune genes predict immune response; c) whether immune response predicts fitness; and d) whether fitness, immune responses, or immune genotypes are correlated with <em>f</em>. We find that survival to adulthood is not associated with immune gene variation, but adult longevity is decreased by high MHC allele diversity (especially in birds that were relatively outbred), and by the presence of a specific MHC supertype. Immune responses were affected by specific immune genotypes. Survival to adulthood and adult longevity were not predicted by immune response, implying caution in the use of immune response as a predictor for fitness. We also found no relationship between <em>f</em> and immune genotype. This finding indicates that immune gene associations with longevity and immune response are not artefacts of <em>f</em>, and suggests that pathogen-mediated selection at functional loci can slow the loss of genetic variation arising from genetic drift and small population size.</p>
Data and scripts from: Exploratory analysis of multi-trait coadaptations in the light of population history
<p><span>During the process of range expansion, populations encounter a variety of environments. They respond to the local environments by modifying their mutually interacting traits. Common approaches of landscape analysis include first focusing on the genes that undergo diversifying selection or directional selection in response to environmental variation. To understand the whole history of populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to infer the multi-trait coadaptation. To this end, we propose a complementary approach; it is an exploratory analysis using up-to-date methods that integrates population genetic features and features of selection on multiple traits. First, we conduct correspondence analysis of site frequency spectra, traits and environments with auxiliary information of population-specific fixation index (FST). This visualizes the structure and the ages of populations and helps infer the history of range expansion, encountered environmental changes and selection on multiple traits. Next, we further investigate the inferred history using an admixture graph that describes the population split and admixture. Finally, principal component analysis of the </span><span>selection on edge-by-trait (SET) matrix identifies multi-trait coadaptation and the associated edges of the admixture graph. We introduce a newly defined factor loadings of environmental variables in order to identify the environmental factors that caused the coadaptation. A numerical simulation of one-dimensional stepping-stone population expansion showed that the exploratory analysis reconstructed the pattern of the environmental selection that was missed by analysis of individual traits. Analysis of a public dataset of natural populations of black cottonwood in northwestern America identified the first principal component (PC) coadaptation of photosynthesis- vs growth-related traits responding to the geographical clines of temperature and daylength. The second PC coadaptation of volume-related traits suggested that soil condition was a limiting factor for above-ground environmental selection.</span></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.