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image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Molecular Ecologyarrow_drop_down
image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
Molecular Ecology
Article . 2017 . Peer-reviewed
License: Wiley Online Library User Agreement
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Fast and robust detection of ancestral selective sweeps

Authors: Xiaoheng Cheng; Cheng Xu; Michael DeGiorgio;

Fast and robust detection of ancestral selective sweeps

Abstract

AbstractThere are few methods tailored for detecting signals of positive selection in populations directly ancestral to multiple descendent populations. We introduce the ancestral branch statistic (ABS), a four‐population summary statistic for identifying selective sweeps occurring in the direct ancestor of a pair of populations. Simulations show thatABSperforms at least as well as, and often better under model violations, than the complementary likelihood approach of 3P‐CLRacross diverse selection scenarios and parameter values. We first appliedABSto contemporary human genomic data to identify genes that may have been adaptive in ancestral East Asian populations, uncovering the well‐established candidateEDAR, as well as a novel candidateSLC35F3, which encodes a putative thiamine transporter that may have been involved in adaptation to eating polished grains. Next, we performed scans with ancient European genomic data to reexamine evidence of recent positive selection in ancestral Europeans. TheMCM6/LCTcluster and theSLC45A2andHERC2genes are strong outliers, agreeing with previous studies. Novel candidates, such asSLC30A9andCYP1A2, may have been involved in adaptation to local nutrient sufficiency and lifestyle changes. Finally, we provide open‐source software,CalcABS, which can perform genomic scans of ancestral sweeps withABSfrom population allele frequency data.

Related Organizations
Keywords

Likelihood Functions, Genome, Human, Genomics, White People, Genetics, Population, Asian People, Gene Frequency, Humans, Computer Simulation, Selection, Genetic, Software

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
29
Top 10%
Average
Top 10%
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