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1,598 results for “genetic diversity”
Supplementary data: Agro-morphological and molecular characterization reveal deep insights in promising genetic diversity and marker-trait associations in Fagopyrum esculentum and F. tataricum
<p>Our study focuses on the global/European buckwheat germplasm collected as part of the ECOBREDD project. The potential of this highly diverse collection for organic buckwheat breeding was evaluated at two complementary levels: phenotypic and genetic. Here, we characterized the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species <em>Fagopyrum esculentum</em> and <em>F. tataricum</em> (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers (Simple Sequence Repeats) (see publication and info sheet of the data).</p>
Data from: Genetic admixture increases phenotypic diversity in the nectar yeast Metschnikowia reukaufii,
<p>Raw data and supplementary files for the manuscript "Genetic admixture increases phenotypic diversity in the nectar yeast <em>Metschnikowia reukaufii</em>."</p> <p>-------------------</p> <p><strong>Table S5.xlsx </strong>-- Pairwise correlations between phenotypic traits of <em>Metschnikowia reukaufii</em>.</p> <p><strong>Table S6.xlsx</strong> -- Detailed results obtained in tests of phylogenetic signal for different phenotypic traits and indices of overall performance of <em>Metschnikowia reukaufii</em>.</p> <p><strong>Table S7.xlsx</strong> -- Detailed model fitting results obtained for phenotypic traits and indices of overall performance of <em>Metschnikowia reukaufii</em>.</p> <p><strong>mronlyvcf-renamed.vcf</strong> -- High coverage SNPs obtained from whole genome mapping of 73 <em>Metschnikowia reukaufii</em> strains to diploid reference (mean coverage = 47.9×, range 23 – 116×).</p> <p><strong>MR_phenotypes.xlsx</strong> -- Phenotypic data obtained for 73 <em>Metschnikowia reukaufii</em> strains.</p>
Exploring the Pocillopora cryptic diversity: a new genetic lineage in the western Indian Ocean or remnants from an ancient one?
<p>Cryptic species and lineages have been widely reported during the last decades, particularly in the marine realm. Misidentifications and ignoring species complexes imply many consequences, notably biasing biodiversity and connectivity assessments, which in turn mislead our understanding of ecosystems and impact the effective design and management of conservation plans. Focusing on the Indo-Pacific coral genus <em>Pocillopora</em>, playing key roles in reef ecosystems as one of the main bio-constructors, we report the first <em>Pocillopora</em> PSH16 (ORF53; <em>sensu</em> Gélin et al. 2017, Mol Phylogenet Evol 109:430–446) colonies (<em>N</em> = 19) in the western Indian Ocean (Nosy Tanikely, Madagascar), 6,000 km further from its current distribution. Colonies were identified according to their mitochondrial Open Reading Frame (ORF) haplotype and Bayesian assignment tests based on 13-microsatellite genotypes. Additionally, we performed genetic structure and diversity analyses with sympatric colonies from other <em>Pocillopora</em> species and <em>Pocillopora</em> PSH16 colonies from the tropical southwestern Pacific, revealing (1) a weak clonal richness, (2) a weak genetic diversity and (3) a relative isolation for the newly reported PSH16 colonies. These colonies thus represent either a new, distinct and uncommon, genetic lineage, or isolated remnants of a wider one. In any case, unless specific management measures are implemented, their long-term maintenance seems compromised due to restricted gene flow within a restricted pool of genes.</p> <p> </p> <p>This dataset contains the microsatellite genotypes analysed (98 <em>Pocillopora</em> colonies × 13 loci + ORF). Missing data are encoded as "?". The sampling marine province and the population are indicated for each individual.</p>
Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»
<p>Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (<em>Dendrocopos major</em>), lower genetic diversity was found in the specialist middle spotted woodpecker (<em>Dendrocoptes medius</em>). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.</p>
Molecular characterization and genetic diversity of four undescribed novel oleaginous Mortierella alpina strains from Libya
<p>A large number of undiscovered fungal species still exist on earth, which can be useful for bioprospecting, particularly for single cell oil (SCO) production. <em>Mortierella</em> is one of the significant genera in this field and contains about hundred species. Moreover, <em>M. alpina </em>is the main single cell oil producer / arachidonic acid producer at commercial scale under this genus.</p>
Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates
<p>Sequence data and stepwise pipeline outputs associated with the article "Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates".</p> <p>Preprint available here: <a href="https://doi.org/10.22541/au.167085544.47638352/v1">10.22541/au.167085544.47638352/v1</a></p> <p>Sequence data is deposited in fastq-format in folders by region (Palinuro.tar.gz, Livorno.tar.gz, and Rovinj.tar.gz) and a separate folder for controls (Controls.tar.gz). Each fastq-file contains sequences for a single PCR replicate named by sample and replicate number. Sample names are described in spineless_sample_names.csv. Positive control sequences are described in SM1_positive_controls.csv. Stepwise pipeline outputs are available in the folder Pipeline_outputs_stepwise.zip</p> <p>Scripts used to generate pipeline outputs as well as other aspects of the final article are available at <a href="https://github.com/thomasdotter/spineless-haplotypes">https://github.com/thomasdotter/spineless-haplotypes</a>.</p> <p> </p>
Genetic diversity, population structure, and linkage disequilibrium among tropical quality protein maize (QPM) lines assessed with high-density SNP markers
<p>The study of genetic diversity (GD), population structure, and linkage disequilibrium (LD) provides a better understanding of the genetic relationships between individuals in a population which can be utilized in crop research and improvement. Genotyping-by-sequencing (GBS) was used to detect and genotype single nucleotide polymorphisms (SNPs) in a collection of 74 quality protein maize (QPM) lines and further to characterize their genetic diversity, population structure, and linkage disequilibrium. A total of 235,214 high-quality SNPs were used for different genetic analyses except for structure analysis where 11,950 SNPs were used. Analysis of molecular variance (AMOVA) based on these SNPs revealed high genetic heterozygosity among the five populations with 1% of the total genetic variation present among the subpopulations and 99% of the variation among individuals within the populations. Population structure analysis using Bayesian-based clustering revealed that the 74 lines could be clustered into four groups. However, neighbor-joining trees indicate the lines are grouped into three major clusters. Further analysis using principal component analyses (PCA) clustered the genotypes into five groups which are concordant with the groups based on pedigree information. Higher genetic diversity was detected in population 1 with a GD value of 0.484 and the lowest in population 5 (0.396) and overall, with a mean of 0.434. The LD pattern in the quality protein maize was investigated and we observed a relatively rapid LD decay of 3.53kb and 10.66kb at r<sup>2</sup> =0.2 and r<sup>2</sup>= 0.1, respectively. Our findings provide important information for future Linkage mapping studies, genome-wide association analyses, and marker-assisted selective breeding of maize as well as genomic prediction-based selection in tropical germplasm.</p>
Large-scale longitudinal gradients of genetic diversity: a meta-analysis across six phyla in the Mediterranean basins
Predicting patterns of variation in biodiversity across the globe is a fundamental issue in ecology and evolution. Diversity within species, that is, genetic diversity, is of prime importance for understanding past and present evolutionary patterns, and highlighting areas where conservation might be a priority. However, most studies on spatial patterns of genetic diversity have not considered longitude as a potentially important ecological driver of these patterns. Therefore, we carried out a meta-analysis to examine the longitudinal patterns of genetic diversity in the Mediterranean Basin. Using published literature and a systematic review/meta-analysis framework, we collected data on the genetic diversity of species whose populations occur in the Mediterranean basin. We then calculated a coefficient of correlation between within‐population genetic diversity indices and longitude, and estimated the role of biological, ecological, biogeographic, and marker type factors on the strength and magnitude of this correlation in six phylla. The results of this study were published in the paper titled Large‐scale longitudinal gradients of genetic diversity: a meta‐analysis across six phyla in the Mediterranean basin (Conord et al. 2012).
Geographical gradients of genetic diversity and differentiation among the southernmost marginal populations of Abies sachalinensis revealed by EST-SSR polymorphism
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than do central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and methods: A total of 1,189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations; namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were highly differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.
Fig. 3 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction
Fig. 3. Haplotype network based on partial sequencing of the D-loop region (mtDNA) of 92 individuals of Brycon nattereri from the Laranjinha River. Circle sizes are pro- portional to haplotype frequency.
Data from: Neo-sex chromosomes and demography shape genetic diversity in the critically endangered Raso lark
Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Genetic diversity in the Raso lark is lower than in its mainland relatives, but is nonetheless considerably higher than anticipated given its recent population size. This is partly explained by an unusual and dramatic effect of enlarged neo-sex chromosomes, which preserve high heterozygosity across 13% of the genome in females, and account for half of the overall genetic diversity in the population. In addition, by reconstructing past demography we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Nevertheless, relatedness analyses suggest that the population is at risk of inbreeding depression. Our findings are particularly important in that they reveal the hidden effects of genome architecture in shaping diversity estimates, and hence demonstrate the value of a reference genome and population genomic analyses over conventional metrics to study diversity in non-model and endangered species.
Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile–Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground
<p></p><p>As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile–Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile–Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile–Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile–Peru.</p><p></p>
Genetic diversity of a marine foundation species, Laminaria hyperborea (Phaeophyceae Laminariales), along the coast of Ireland
<p><span><span><span><span><span><span><span><span><span><span><span>Worldwide, kelp populations are stressed by warming, increased storms and other man-driven disturbances<i>. </i>Marine population distributions are projected to retreat poleward with climate change if they cannot adapt to changing conditions, which would potentially lead to a regime shift in subtidal habitats. In Northern Europe, <i>Laminaria hyperborea</i>is a subtidal ecosystem engineer whose distribution has shifted over millennia, leaving predicted areas of high genetic diversity from the last glacial maximum (LGM) near its southern distribution limit in the Iberian Peninsula. In Ireland, <i>L. hyperborea </i>structures communities by supporting diverse faunal assemblages and producing large quantities of organic carbon throughout the year. We investigated the genetic diversity of eight populations ranging from the southern coast to the northwest of Ireland using nine microsatellite loci. Diversity was found to be highest in Lough Hyne, a Special Area of Conservation (SAC), near the predicted climate refugium. We found evidence of isolation by distance, with high connectivity between populations that were geographically close, likely driven by short range dispersal of <i>L. hyperborea</i>propagules. Genetic diversity (measured as expected heterozygosity and allelic richness) was highest at Lough Hyne, and decreased northwards, as predicted from past range shifts. Expected heterozygosity was highest at Lough Hyne (0.706) and decreased northward, with the lowest value at Bridges of Ross (0.283). Based on these patterns, further fine-scale investigation into population diversity, dispersal and potential resilience in Irish kelp forests are necessary as warming and non-native species are observed more and more frequently.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Creating small food-habituated groups might alter genetic diversity in the endangered Yunnan snub-nosed monkey. https://doi.org/10.1016/j.gecco.2020.e01422
<p>Ecotourism is increasing worldwide for financial, educational and social purposes. Organized viewing of wildlife, especially at feeding sites where wildlife is “ready-to-view”, increases the opportunities for tourists to observe animals in the wild. However, feeding sites might retain only a subsample of wild populations. We thus hypothesized that such human intervention could induce population subdivisions and alter random mating by artificially creating small groups. The endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) is an emblematic example reflecting the contradictions between conservation and ecotourism. In Gehuaqing/Xiangguqing (Yunnan, China), some individuals are maintained at feeding sites, while the rest of the monkey subpopulation wanders in a large surrounding area. Using faecal sampling and molecular analyses, we showed that this subpopulation is genetically structured into two moderately differentiated subgroups. The fed subgroup exhibited lower genetic diversity and higher relatedness than the rest of the subpopulation. Simulation model results indicated that a single translocation probably would not restore genetic diversity in fed individuals. Thus, feeding sites implementation and associated management practices might rapidly induce founder effects. We discuss the possibilities of conciliating ecotourism and the conservation of endangered animal species from this viewpoint.</p>
Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities
The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, i.e. ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesized to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.
Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests
Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus FST = 0.32, FST' = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R2 = 0.51) and higher local inbreeding (R2 = 0.22). Populations varied greatly in levels of local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.
Georeferenced data for the study Environmental suitability throughout the late Quaternary explains population genetic diversity
<p>Data filtered from GBIF (datasetKey: 50c9509d-22c7-4a22-a47d-8c48425ef4a7) Contains 150 records of the <i>Sciurus aberti </i>squirrel filtered in latitudinal windows of 5 degrees from 20 to 45 degrees N. </p>
A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years
<p>The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950's, opossum shrimp (<em>Mysis diluviana</em>) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Shrimp were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity and test for genetic divergence between populations and for evidence of adaptive evolution within the introduced populations in Colorado. We found overall very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was also little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that the population in Gross Reservoir is of hybrid origin, with an earlier founding population from an unknown source being later supplemented from another population. Despite the overall low genetic diversity we observed, F<sub>ST</sub> outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments.</p>
Insights into the genetic diversity of Listeria monocytogenes from bivalves
<p>Fasta files to 30 genomes described in a publication</p>
F I G U R E 3 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 3 A priori discriminant analysis of principal components (DAPC) plot of Camel trout. Each point represents the genotype of an individual fish, with centroids for each site labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
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Annotated Behaviour and Observability Dataset (ABODe)
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