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.
113
datasets available to search
ShareScore release 0.7.1
Dataset results
113 results for “VCF”
VCF files of loci in approximate linkage equilibrium for two common spruce budworm larval parasitoids: Apanteles fumiferanae (Hymenoptera: Braconidae) and Glypta fumiferanae (Hymenoptera: Ichneumonidae)
<p>Periodic and spatially synchronous outbreaks of insect pests have dramatic consequences for boreal and sub-boreal forests. Within these multitrophic systems, parasitoids can be stabilizing agents by dispersing toward patches containing higher host density (the so-called <i>birdfeeder effect</i>). However, we know little about the dispersal abilities of parasitoids in continuous forested landscapes, limiting our understanding of the spatiotemporal dynamics of host–parasitoid systems, and constraining our ability to predict forest resilience in the context of global changes. In this study, we investigate the spatial genetic structure and spatial variation in genetic diversity of two important species of spruce budworm larval parasitoids during outbreaks: <i>Apanteles fumiferanae</i> Viereck (Braconidae) and <i>Glypta fumiferanae </i>(Viereck) (Ichneumonidae). Using parasitoids sampled in 2014 from 26 and 29 locations across a study area of 350,000 km<sup>2</sup>, we identified 1,012 and 992 neutral SNP loci for <i>A. fumiferanae</i> (<i>N</i> = 279 individuals) and <i>G. fumiferanae</i> (<i>N</i> = 382), respectively. Using DAPC, PCA, AMOVA, and IBD analyses, we found evidence for panmixia and high genetic connectivity for both species, matching the previously described genetic structure of the spruce budworm within the same context, suggesting similar effective dispersal during outbreaks and high parasitoid population densities between outbreaks. We also found a significant negative relationship between genetic diversity and latitude for <i>A. fumiferanae</i> but not for <i>G. fumiferanae</i>, suggesting that northern range limits may vary by species within the spruce budworm parasitoid community. These spatial dynamics should be considered when predicting future insect outbreak severities in boreal landscapes.</p>
Genomic population reveals potential micro-refuge and riverine barriers in southern South American grasslands: An example in nightshade: VCF file (16,128 SNPs)
<p><b>Aim:</b> Pleistocene climate oscillations influenced the species distribution and genetic diversity in South American grasslands. Paleoclimate changes promoted expansion and contraction cycles that could lead to fragmentation and isolation of evolutionary lineages in refuges. Moreover, sea-level oscillations led to defrosting in some areas, affecting the river dynamics and influencing South American species' evolutionary history. This study aimed to infer which evolutionary processes most influenced the lineages differentiation in South American nightshade <i>Petunia</i> inhabiting subtropical grasslands in a phylogeographical context.<br> <b>Location:</b> Pampa and Chaco.<br> <b>Taxon:</b> The widely distributed herb <i>Petunia axillaris</i> subsp. <i>parodii</i> (Solanaceae)<br> <b>Methods:</b> We obtained a high-density genome coverage throughout <i>Petunia axillaris </i>subsp <i>. parodii </i>geographic distribution. We estimated the genetic diversity and structure to evaluate population differentiation and applied a model-based demographic analysis to investigate the scenarios that could have influenced the species evolutionary history. We evaluated the association between neutral and outlier polymorphisms with environmental variables to distinguish the influence of the geographic distance and environmental differences between populations.<br> <b>Results:</b> The results revealed three evolutionary lineages in <i> P. axillaris </i>subsp <i>. parodii</i>. The origin and differentiation of these lineages were related to the Pleistocene refuges and rivers acting as barriers to the gene flow. We also identified 496 outlier loci related to adaptation to environmental conditions.<br> <b>Main conclusion:</b> The Pleistocene climate changes drove lineage diversification isolated in micro-refugia. Rivers and changes in their courses may have also acted on the population divergence, serving as barriers to gene flow or even as corridors for species range expansion. These findings contribute to the knowledge of the evolutionary processes that influenced the lineage diversification of South American subtropical grassland species.</p>
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
<p class="MsoNormal"><span>We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from an F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies</span><span>. To </span><span>demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of three true albino bison and 45 wild-type pelage color bison. Through the examination of genomic </span>variants fixed in the albino cohort and absent in the controls<span>, we identified a nonsynonymous</span> single nucleotide polymorphism (SNP) <span>mutation on chromosome 29 </span>in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provide a highly robust and informative resource for <span>genomics </span>investigations for this iconic North American species.</p>
Filtered VCF files for Bombus pascuorum and B. lapidarius
Open the record for dataset details and reuse information.
Asellus aquaticus genome and VCF file from samples obtained on Gotland, Sweden
Open the record for dataset details and reuse information.
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
Open the record for dataset details and reuse information.
The filtered VCF file containing SNPs detected from the Vitis bryoniifolia clade using RAD-seq.
Open the record for dataset details and reuse information.
RAD-seq vcf files for the leaf beetle Gonioctena quinquepunctata sampled across Europe
Open the record for dataset details and reuse information.
VCF data file and code for: CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone
Open the record for dataset details and reuse information.
VCF for neutral data set in Harpagifer bispinis along the Magellan Province
Open the record for dataset details and reuse information.
VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species
Open the record for dataset details and reuse information.
VCF files of loci in approximate linkage equilibrium for two common spruce budworm larval parasitoids: Apanteles fumiferanae (Hymenoptera: Braconidae) and Glypta fumiferanae (Hymenoptera: Ichneumonidae)
Open the record for dataset details and reuse information.
Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
Open the record for dataset details and reuse information.
VCF file of multiple single-cyst-derived Ro1 and Ro2 lines of New York fields on Globodera rostochiensis genome
Open the record for dataset details and reuse information.
Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)
Open the record for dataset details and reuse information.
VCF from: Genetic evidence of female philopatry in a socially polyandrous shorebird
Open the record for dataset details and reuse information.
VCF files for D. serrata transposable elements
Open the record for dataset details and reuse information.
Genomic population reveals potential micro-refuge and riverine barriers in southern South American grasslands: An example in nightshade: VCF file (16,128 SNPs)
Open the record for dataset details and reuse information.
Diploid VCF files used for publication "Haplotype Threading: Accurate Polyploid Phasing from Long Reads"
<p>Diploid VCF files for three human samples, from which polyploid datasets were generated as evaluation data for the publication given in the title. Files contain gold standard haplotypes, which have been conducted by trio phasing from the samples themselves and their respective parents.</p>
SNP matrices and vcf files for phylogenetic, genetic structure and historical demographic analyses of Podocarpus from Hispaniola
<p><b>Aim</b><span>: </span>Hispaniola is the second largest island in the Caribbean and a hotspot of biodiversity. The island was formed by the fusion of a northern and southern palaeo-islands during the mid-Miocene (15 Ma). The historical split of Hispaniola together with repeated marine incursions during the Pleistocene are known to have influenced lineage divergence and genetic structure in a few birds and mammals, but the effect on vascular plants is less understood. The conifer genus <i>Podocarpus </i>has two species, <i>P. hispaniolensis </i>and <i>P. buchii, </i>that are endemic to the mountains of Hispaniola and are IUCN endangered. The former occurs in the mountains of the north, and the latter in the south, with a region of sympatry in the Central Cordillera. Here we evaluate the historical split of the two palaeo-islands, and repeated marine incursions as dispersal barriers to the geographical distribution of genetic diversity, genetic structure, divergence patterns, and the historical demography of the two species.</p> <p><b><span>Location</span></b><span>: Hispaniola island, Caribbean.</span></p> <p><b><span>Methods</span></b><span>: </span>Using Genotyping by Sequencing in 47 <i>Podocarpus</i> samples we identified two sets of single nucleotide polymorphisms for our analyses (74,260 and 22,657 SNPs).</p> <p><b><span>Results</span></b><span>: </span>The results show a population genetic structure that corresponds to the geographic distribution of the species in mountainous areas. <i>Podocarpus </i>in Hispaniola followed a stepping-stone colonization pattern with bottlenecks at each mountain colonization event.</p> <p><b><span>Main conclusions</span></b><span>:</span> The historical events in question did not seem to have influenced the genetic structure, diversity, or demography of <i>Podocarpus</i>, instead the current geographic barriers imposed by lowland xeric valleys did. The clear divergence between species together with the elevated within-population genetic diversity and significant genetic structure call for a multi-population <i>in situ</i> conservation of each species.</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.