Show simple item record

dc.creatorPlatt, A
dc.creatorPivirotto, A
dc.creatorKnoblauch, J
dc.creatorHey, J
dc.date.accessioned2020-12-11T20:38:21Z
dc.date.available2020-12-11T20:38:21Z
dc.date.issued2019-01-01
dc.identifier.issn1553-7390
dc.identifier.issn1553-7404
dc.identifier.doihttp://dx.doi.org/10.34944/dspace/4339
dc.identifier.other31425500 (pubmed)
dc.identifier.urihttp://hdl.handle.net/20.500.12613/4357
dc.description.abstract© 2019 Platt et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Allele age has long been a focus of population genetic research, primarily because it can be an important clue to the fitness effects of an allele. By virtue of their effects on fitness, alleles under directional selection are expected to be younger than neutral alleles of the same frequency. We developed a new coalescent-based estimator of a close proxy for allele age, the time when a copy of an allele first shares common ancestry with other chromosomes in a sample not carrying that allele. The estimator performs well, including for the very rarest of alleles that occur just once in a sample, with a bias that is typically negative. The estimator is mostly insensitive to population demography and to factors that can arise in population genomic pipelines, including the statistical phasing of chromosomes. Applications to 1000 Genomes Data and UK10K genome data confirm predictions that singleton alleles that alter proteins are significantly younger than those that do not, with a greater difference in the larger UK10K dataset, as expected. The 1000 Genomes populations varied markedly in their distributions for singleton allele ages, suggesting that these distributions can be used to inform models of demographic history, including recent events that are only revealed by their impacts on the ages of very rare alleles.
dc.format.extente1008340-e1008340
dc.language.isoen
dc.relation.haspartPLoS Genetics
dc.relation.isreferencedbyPublic Library of Science (PLoS)
dc.rightsCC BY
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectAlleles
dc.subjectBiological Variation, Population
dc.subjectDatasets as Topic
dc.subjectEvolution, Molecular
dc.subjectFemale
dc.subjectGene Frequency
dc.subjectGenetic Heterogeneity
dc.subjectGenetics, Population
dc.subjectGenome, Human
dc.subjectHumans
dc.subjectMale
dc.subjectModels, Genetic
dc.subjectSelection, Genetic
dc.subjectTime Factors
dc.titleAn estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations
dc.typeArticle
dc.type.genreJournal Article
dc.relation.doi10.1371/journal.pgen.1008340
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.date.updated2020-12-11T20:38:17Z
refterms.dateFOA2020-12-11T20:38:22Z


Files in this item

Thumbnail
Name:
An estimator of first coalescent ...
Size:
1.700Mb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record

CC BY
Except where otherwise noted, this item's license is described as CC BY