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PMID: 17579516 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

A new approach for using genome scans to detect recent positive selection in the human genome.

PLoS biology ·Vol. 5 ·No. 7 ·2007-07-00 ·Pages e171

Tang K, Thornton KR, Stoneking M

Abstract

Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation. Here, we present a genomic survey of recent local selective sweeps, especially aimed at those nearly or recently completed. A novel approach was developed for such signals, based on contrasting the extended haplotype homozygosity (EHH) profiles between populations. We applied this method to the genome single nucleotide polymorphism (SNP) data of both the International HapMap Project and Perlegen Sciences, and detected widespread signals of recent local selection across the genome, consisting of both complete and partial sweeps. A challenging problem of genomic scans of recent positive selection is to clearly distinguish selection from neutral effects, given the high sensitivity of the test statistics to departures from neutral demographic assumptions and the lack of a single, accurate neutral model of human history. We therefore developed a new procedure that is robust across a wide range of demographic and ascertainment models, one that indicates that certain portions of the genome clearly depart from neutrality. Simulations of positive selection showed that our tests have high power towards strong selection sweeps that have undergone fixation. Gene ontology analysis of the candidate regions revealed several new functional groups that might help explain some important interpopulation differences in phenotypic traits.

MeSH Terms
Alleles Biometry Databases, Genetic Genetic Techniques Genetics, Population Genome, Human Haplotypes Humans Models, Genetic Polymorphism, Single Nucleotide Recombination, Genetic Selection, Genetic Time Factors
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Tang Kun
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. tang@eva.mpg.de
Thornton Kevin R
Stoneking Mark
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Article Info
Journal
PLoS biology
Abbr.
PLoS Biol
ISSN
1545-7885
DOI
10.1371/journal.pbio.0050171
Email
tang@eva.mpg.de
Published
2007-07-00
Epub
2007-00-19
Pages
e171
Language
English
Region
United States
NLM ID
101183755
PMCID
PMC1892573
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pbio.0050171 PMC Full Text View journal details
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