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dc.contributor.authorLoh, Po-Ru
dc.contributor.authorLipson, Mark
dc.contributor.authorPatterson, Nick
dc.contributor.authorMoorjani, Priya
dc.contributor.authorPickrell, Joseph
dc.contributor.authorReich, David Emil
dc.contributor.authorBerger, Bonnie
dc.date.accessioned2013-10-17T13:23:37Z
dc.date.issued2013
dc.identifier.citationLoh, Po-Ru, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K. Pickrell, David Reich, and Bonnie Berger. 2013. Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193(4): 1233-1254.en_US
dc.identifier.issn0016-6731en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:11180376
dc.description.abstractLong-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods. We define an LD-based three-population test for admixture and identify scenarios in which it can detect admixture events that previous formal tests cannot. We further show that we can uncover phylogenetic relationships among populations by comparing weighted LD curves obtained using a suite of references. Finally, we describe several improvements to the computation and fitting of weighted LD curves that greatly increase the robustness and speed of the calculations. We implement all of these advances in a software package, ALDER, which we validate in simulations and apply to test for admixture among all populations from the Human Genome Diversity Project (HGDP), highlighting insights into the admixture history of Central African Pygmies, Sardinians, and Japanese.en_US
dc.language.isoen_USen_US
dc.publisherGenetics Society of Americaen_US
dc.relation.isversionofdoi:10.1534/genetics.112.147330en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606100/pdf/en_US
dash.licenseLAA
dc.subjectPopulation and Evolutionary Geneticsen_US
dc.subjectadmixtureen_US
dc.subjectlinkage disequilibriumen_US
dc.titleInferring Admixture Histories of Human Populations Using Linkage Disequilibriumen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalGeneticsen_US
dash.depositing.authorMoorjani, Priya
dc.date.available2013-10-17T13:23:37Z
dc.identifier.doi10.1534/genetics.112.147330*
dash.contributor.affiliatedMoorjani, Priya
dash.contributor.affiliatedPickrell, Joseph
dash.contributor.affiliatedReich, David


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