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.
92
datasets available to search
ShareScore release 0.9.0
Dataset results
92 results for “pedigrees”
Data from: Mate choice and the genetic basis for color variation in a polymorphic dart frog: inferences from a wild pedigree
Open the record for dataset details and reuse information.
Data from: Evaluating the reintroduction project of Przewalski’s horse in China using genetic and pedigree data
Open the record for dataset details and reuse information.
An evaluation of inbreeding measures using a whole genome sequenced cattle pedigree
Open the record for dataset details and reuse information.
Genotypes, variants and pedigree from a human parent-offspring trio (NA12878)
<p>This dataset includes whole genome sequencing data, produced at the French National Research Center for Human Genomics (CNRGH), with known pedigree information:<br> - The VCF file contains genotypes and variants from a CEU parent-offspring trio comprising NA12878 (child), NA12891 (father) and NA12892 (mother).<br> For each member, 150-bp paired-end whole genome sequencing data were generated on the Illumina HiSeq X system, from a PCR-free library (40x).<br> - The TFAM file contains pedigree information of this CEU parent-offspring trio.</p>
Genomic SSR and EST-SSR markers for phylogenetic and pedigree reconstruction: A comparison in sea buckthorn
<p>Simple sequence repeat (SSR) markers play an important role in genetic and molecular breeding programs, especially for non-model species. We identified SSRs from expressed sequence tags (EST-SSRs) and whole genome sequences (gSSRs), by analyzing the transcriptome and genome of the Mongolian sea buckthorn (<i>Hippophae rhamnoides</i> subsp. <i>Mongolica</i>) cultivar 'Sunny'<i>.</i> Using the same number of loci, EST-SSRs showed higher transferability to <i>Hippophae </i>than gSSRs, and phylogenetic trees based on EST-SSRs demonstrated higher resolution for classifying <i>Hippophae </i>species and subspecies into clades, possibly due to high conservatism and/or existence of adaptive divergence between species/subspecies in coding sequence regions. In contrast, parentage analyses showed that gSSRs were more effective at resolving parentage than EST-SSRs due to higher level of polymorphism in gSSRs. The markers developed in this study can be used in the identification and pedigree reconstruction of species/subspecies of sea buckthorn, while their usage in clarifying phylogenetic relationship among species remains to be discussed. The comparison between EST-SSRs and gSSRs would provide insight into the trade-off between differentiation and polymorphism in marker selection for breeding programs.</p>
Data from: A high quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal
Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical by descent (IBDg) whereas in theory with enough molecular markers realised IBDg can be quantified directly. We therefore investigated inbreeding depression for multiple life-history traits in a wild population of banded mongooses using pedigree-based inbreeding coefficients (fped) and standardised multilocus heterozygosity (sMLH) measured at 35-43 microsatellites. Within an information theoretic framework, we evaluated support for either fped or sMLH as inbreeding terms and used sequential regression to determine whether the residuals of sMLH on fped explain fitness variation above and beyond fped. We found no evidence of inbreeding depression for survival, either before or after nutritional independence. By contrast, inbreeding was negatively associated with two quality related traits, yearling body mass and annual male reproductive success. Yearling body mass was associated with fped but not sMLH, while male annual reproductive success was best explained by both fped and residual sMLH. Thus, our study not only uncovers variation in the extent to which different traits show inbreeding depression, but also reveals trait-specific differences in the ability of pedigrees and molecular markers to explain fitness variation and suggests that for certain traits genetic markers may capture variation in realised IBDg above and beyond the pedigree expectation.
Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer
<p>Assessing the evolutionary potential of animal populations in the wild is crucial to understanding how they may respond to selection mediated by rapid environmental change (e.g. habitat loss and fragmentation). A growing number of studies have investigated the adaptive role of behaviour, but assessments of its genetic basis in a natural setting remain scarce. We combined intensive biologging technology with genome-wide data and a pedigree-free quantitative genetic approach to quantify repeatability, heritability and evolvability for a suite of behaviours related to the risk avoidance-resource acquisition trade-off in a wild roe deer (Capreolus capreolus) population inhabiting a heterogeneous, human-dominated landscape. These traits, linked to the stress response, movement and space-use behaviour, were all moderately to highly repeatable. Furthermore, the repeatable among-individual component of variation in these traits was partly due to additive genetic variance, with heritability estimates ranging from 0.19±0.07 to 0.71±0.11 and evolvability ranging from 1.1 to 4.3%. Changes in the trait mean can therefore occur under hypothetical directional selection over just a few generations. To the best of our knowledge, this is the first empirical demonstration of additive genetic variation in space-use behaviour in a free-ranging population based on genomic relatedness data. We conclude that wild animal populations may have the potential to adjust their spatial behaviour to human-driven environmental modifications through micro-evolutionary change.</p>
Data from: Pedigree analysis reveals a generational decline in reproductive success of captive Tasmanian devil (Sarcophilus harrisii): implications for captive management of threatened species
Captive breeding programs are an increasingly popular tool to augment the conservation of threatened wild populations. Many programs keep detailed pedigrees, which are used to prescribe breeding targets to meet demographic and genetic goals. Annual breeding targets are based on previous productivity, but do not account for changes in reproductive success that may occur over generations in captivity and which may impair the ability of a program to meet its goals. We utilise a large studbook from the Tasmanian devil (Sarcophilus harrisii) captive breeding program to investigate biological, genetic and environmental factors that affect variation in reproductive success among individuals and over generations of captive breeding. Reproductive success declined with increasing generations in captivity: wild-born females had a 56.5% chance of producing a litter compared to a 2.8% chance for generation 5 captive-born females (N = 182) and when they did, wild-born females produced more offspring (3.1 joeys, 95% CI: 2.76 - 3.38, compared to 2.7 joeys, 95% CI: 2.55 - 2.90, in captive-born females [N = 105]). Reproductive success also declined as dam age at first breeding increased. Our results reveal a conflict with the widely-cited conservation strategy to limit opportunity for selection by extending generation length through delaying reproduction, as captive breeding programs that delay female breeding with this goal in mind risk reduced productivity. Our data demonstrate the benefit of pedigree analysis to identify biological processes that reveal crucial trade-offs with conservation best-practice.
Data from: Characterization of class I- and II-like major histocompatibility complex loci in pedigrees of North Atlantic right whales
Open the record for dataset details and reuse information.
Data from: Pedigree analysis reveals a generational decline in reproductive success of captive Tasmanian devil (Sarcophilus harrisii): implications for captive management of threatened species
Open the record for dataset details and reuse information.
Data from: Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding
Open the record for dataset details and reuse information.
Genomic SSR and EST-SSR markers for phylogenetic and pedigree reconstruction: A comparison in sea buckthorn
Open the record for dataset details and reuse information.
Data from: A high quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal
Open the record for dataset details and reuse information.
Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer
Open the record for dataset details and reuse information.
Data from: Cattle sex-specific recombination and genetic control from a large pedigree analysis
Open the record for dataset details and reuse information.
Data from: How well do molecular and pedigree relatedness correspond, in populations with variable mating systems, and types and quantities of molecular and demographic data?
Open the record for dataset details and reuse information.
Copy number variation of human intestinal stem cells with different passage in culture (two pedigrees, passage 5, 10, 15 and 20)
GEO Series GSE66747. Homo sapiens. 9 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Genomic analysis of hESC pedigrees enables identification of de novo genetic alterations and determination of the timing and origin of mutational events
GEO Series GSE49452. Homo sapiens. 21 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Gene expression and intragenic polymorphism in a Populus trichocarpa and Populus deltoides pseudo-backcross pedigree
GEO Series GSE12623. Populus trichocarpa; Populus trichocarpa x Populus deltoides. 178 samples. Type: Expression profiling by genome tiling array.
Characterization of genome-methylome interactions in 22 nuclear pedigrees
GEO Series GSE47614. Homo sapiens. 96 samples. Type: Methylation profiling by high throughput sequencing.
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.