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47
datasets available to search
ShareScore release 0.9.0
Dataset results
47 results for “demographic inference”
Data from: Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes
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Data from: Germ banks affect the inference of past demographic events
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Data from: Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions
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Data from: Spatial familial networks to infer demographic structure of wild populations
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Data from: Demographic inferences using short-read genomic data in an Approximate Bayesian Computation framework: in silico evaluation of power, biases, and proof of concept in Atlantic walrus
Approximate Bayesian Computation (ABC) is a powerful tool for model-based inference of demographic population histories from large genetic data sets. For most organisms its implementation has been hampered by the lack of sufficient genetic data. Genotyping-by-sequencing (GBS) provides cheap genome-scale data to fill this gap, but its potential has not fully been exploited. Here, we explored power, precision and biases of a coalescent-based ABC approach where GBS data were modeled with either a population mutation parameter (θ) or with a fixed sites (FS) approach, allowing single or several segregating sites per locus. With simulated data ranging from 500 to 50,000 loci a variety of demographic models could be reliably inferred across a range of timescales and migration scenarios. Posterior estimates were informative with 1,000 loci for migration and split time in simple population divergence models. In more complex models posterior distributions were wide and almost reverted to the uninformative prior even with 50,000 loci. ABC parameter estimates, however, were generally more accurate than an alternative composite-likelihood method. Bottleneck scenarios proved particularly difficult and only recent bottlenecks without recovery could be reliably detected and dated. Notably, minor allele frequency filters – usual practice for GBS data – negatively affected nearly all estimates. With this in mind, we used a combination of FS and θ approaches on empirical GBS data generated from the Atlantic walrus (Odobenus rosmarus rosmarus), collectively providing support for a population split before the last glacial maximum followed by asymmetrical migration and a range-wide bottleneck. Overall, this study evaluates the potential and limitations of GBS data in an ABC-coalescence framework and proposes a best-practice approach.
Data from: Demographic inferences using short-read genomic data in an Approximate Bayesian Computation framework: in silico evaluation of power, biases, and proof of concept in Atlantic walrus
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Data from: Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences
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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.