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141 results for “population genetics analysis”
Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow
<p><span><span>Red deer (</span><span><em>Cervus elaphus</em></span><span>) throughout central Europe are</span> impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations<span>. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. </span></span><span><span>We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. </span></span><span><span>Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. </span></span></p> <p><span><span>Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.</span></span></p>
pgHMA: Application of the Heteroduplex mobility assay analysis in phylogenetics and population genetics
<p><span><span><span><span><span><span><span><span><span><span><span>The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (1) there is a significant linear relationship (R = 0.992) between heteroduplex mobility and genetic distance; (2) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies; (3) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies; (4) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size; and (5) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends.</span></span></span></span></span></span></span></span></span></span></span></p>
Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
<p><span>Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (<em>Galemys</em> <em>pyrenaicus</em>). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.</span></p>
Data from: Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in sage grouse Centrocercus urophasianus
<p><span>Sex ratio, and the extent to which it varies over time, is an important factor in the demography, management, and conservation of wildlife populations. We estimated pre-breeding sex ratio of greater sage-grouse (Centrocercus urophasianus) in a peripheral, geographically isolated population in northwestern Colorado during two consecutive winters using closed-population, robust-design, multi-state, genetic mark-recapture models in program MARK (White and Burnham 1999). This data release includes the data files (.inp format) used in those models, as described in Shyvers et al. 2023. The data include capture histories and auxiliary data for individual greater sage-grouse collected during two study seasons: Season 1 (winter 2012-2013) and Season 2 (winter 2013-2014) and are readable using program MARK or notepad. Each data row includes the unique bird identification number (GMR-ID); the bird's encounter history for n= sampling occasions coded as a static state (M = male, F = female); the group ID; and a region covariate (0 = North, 1 = South). The data were adapted from those originally developed for Shyvers et al. 2020 and applied using Closed Robust Design Multi-state (CRDMS) Huggins' p and c w/state probabilities in program MARK to obtain estimates of Omega, enabling estimation of sex ratio with associated confidence intervals (see Shyvers et al. 2023).</span></p> <p>References:</p> <p>Shyvers, J.E., Walker, B.L., Oyler-McCance, S.J., Fike, J.A. and Noon, B.R. 2023. Genetic mark-recapture analysis reveals large annual variation in pre-breeding sex ratio of greater sage-grouse. Wildlife Biology (https://doi.org/10.1002/wlb3.01085)</p> <p>Shyvers, J.E., Walker, B.L., Oyler‐McCance, S.J., Fike, J.A. and Noon, B.R., 2020. Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus. Ibis, 162(3), pp.749-765.</p> <p>White, G. C., and K. P. Burnham. 1999. Program Mark: survival estimation from populations of marked animals. – Bird Study 46:120–139.</p>
Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure
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pgHMA: Application of the Heteroduplex mobility assay analysis in phylogenetics and population genetics
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Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance
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Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow
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Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
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Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems
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Data from: High-resolution analysis of red deer (<em>Cervus elaphus</em>) management units in a Central European region of high human population density reveals severe effects on genetic diversity and differentiation
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Data from: Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in sage grouse Centrocercus urophasianus
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SNP reports of Cylindropuntia species from Dartseq used for population genetics analysis
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Data from: Association and function analysis of genetic variants and the risk of gestational diabetes mellitus in a southern Chinese population
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Data from: Meta-analysis reveals lower genetic diversity in overfished populations
While population declines can drive the loss of genetic diversity under some circumstances, it has been unclear whether this loss is a general consequence of overharvest in highly abundant marine fishes. Here, we use a phylogenetic approach across 160 species and 11,658 loci to show that allelic richness was on average 11% lower (p < 0.0001) in overharvested populations, even after accounting for the effects of body size, latitude, and other factors. Heterozygosity was 2% lower (p = 0.030). Simulations confirmed that these patterns are consistent with a recent bottleneck in abundant species and also showed that our analysis likely underestimates the loss of rare alleles by a factor of two or three. This evidence suggests that overharvest drives the decay of genetic diversity across a wide range of marine fishes. Such reductions of genetic diversity in some of the world's most abundant species may lead to a long-term impact of fishing on their evolutionary potential, particularly if abundance remains low and diversity continues to decay.
Population and landscape genetic analysis of the Malayan sun bear Helarctos malayanus
<p>Conservation genetics can provide data needed by conservation practitioners for their decisions regarding the management of vulnerable or endangered species, such as the sun bear <i>Helarctos malayanus</i>. Throughout its range, the sun bear is threatened by loss and fragmentation of its habitat and the illegal trade of both live bears and bear parts. Sharply declining population numbers and population sizes, and a lack of natural dispersal between populations all threaten the genetic diversity of the remaining populations of this species. In this first population genetics study of sun bears using microsatellite markers, we analyzed 68 sun bear samples from Cambodia to investigate population structure and genetic diversity. We found evidence for two genetically distinct populations in the West and East of Cambodia. Ongoing or recent gene flow between these populations does not appear sufficient to alleviate loss of diversity in these populations, one of which (West Cambodia) is characterized by significant inbreeding. We were able to assign 85% of sun bears of unknown origin to one of the two populations with high confidence (assignment probability ≥ 85%), providing valuable information for the release of bears. Further, our results suggest that developed land (mostly agricultural mosaics) acts as a barrier to gene flow for sun bears in Cambodia. We highlight that regional sun bear conservation action plans should consider promoting population connectivity and enforcing wildlife protection of this threatened species.</p>
Data from: New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus)
Sustainable management of sea mullet (Mugil cephalus) fisheries needs to account for recent observations of regional-scale differentiation. Population genetic analysis is sought to assess the situation of this ecologically and economically important fish species in eastern Australian waters. Here, we report (i) new population genetic markers [single nucleotide polymorphisms (SNPs) and potential microsatellites], (ii) first estimates of spatial genetic differentiation and (iii) prospective power tests for designing more comprehensive studies. Six DNA samples from three sampling regions (North Queensland, South Queensland and central New South Wales) on the eastern coast of Australia were used to prepare restriction site associated DNA (RAD) tag libraries from genomic DNA digested with EcoRI and MseI. A pooled sample of regional RAD tag libraries was sequenced using the Roche GS-FLX Titanium platform. A total of 172 837 raw reads (17.4 Mbp) were retrieved, 95 500 of which were used to discover 1267 SNPs and 1417 microsatellites. A subset of 161 SNPs was validated based on 63 additional DNA samples genotyped using the Sequenom MassArray (iPLEX Gold chemistry). Altogether 92 SNPs (57%) were confirmed, with 40% of these marking fixed variants between northern and southern sampling regions. Our preliminary findings indicate a multispecies fishery stock of M. cephalus in eastern Australian waters, but suggest that strong genetic differentiation occurs north of major fishing grounds. Low potential differentiation within major fishing grounds (e.g. FST = 0.0025) can be resolved with a likely power ≥67% by using standard sample sizes of 50 and validated subsets of available markers.
Data from: Integrating genetic analysis of mixed populations with a spatially-explicit population dynamics model
Inferring the dynamics of populations in time and space is a central challenge in ecology. Intra-specific structure (for example genetically distinct sub-populations or meta-populations) may require methods that can jointly infer the dynamics of multiple populations. This is of particular importance for harvested species, for which management must balance utilization of productive populations with protection of weak ones. Here we present a novel method for simultaneous learning about the spatio-temporal dynamics of multiple populations that combines genetic data with prior information about abundance and movement in an integrated population modelling approach. We apply the Bayesian genetic mixed stock analysis to 17 wild and 10 hatchery-reared Baltic salmon (S. salar) stocks, quantifying uncertainty in stock composition in time and space, and in population dynamics parameters such as migration timing and speed. Our results indicate that the commonly used "equal prior probabilities" assumption may not be appropriate for all mixed stock analyses. Incorporation of prior information about stock abundance and movement resulted in more precise and plausible estimates of mixture compositions in time and space. Inclusion of a population dynamics model also allowed robust interpolation of expected catch composition at areas and times with no genetic observations. The genetic data were informative about stock-specific movement patterns, updating priors for migration path, timing and speed. The model we present here forms the basis for optimizing the spatial and temporal allocation of harvest to support the management of mixed populations of migratory species.
Data from: Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers
The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering time and plant growth, suggesting that a similar approach using F. vesca might add to our understanding on the development of rosaceous species and perennials in general. As a first step, 298 F. vesca plants were analyzed using microsatellite markers with the primary aim of analyzing population structure and distribution of genetic diversity. Of the 68 markers tested, 56 were polymorphic, with an average of 4.46 alleles per locus. Our analysis partly confirms previous classification of F. vesca subspecies in North America and suggests two groups within the subsp. bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population.
Data from: Genome-wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia)
Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge–Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar-Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographical pattern. Pairwise FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor-Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population–TIK, and maximum values were observed in the most southern population–SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the late Pleistocene glaciations of Verkhoyansk Range.
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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)
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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.