Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms

Takahiro Maruki, Sudhir Kumar, Yuseob Kim

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

An improved understanding of the biological and numerical properties of measures of population differentiation across loci is becoming increasingly more important because of their growing use in analyzing genome-wide polymorphism data for detecting population structures, inferring the rates of migration, and identifying local adaptations. In a genome-wide analysis, we discovered that the estimates of population differentiation (e.g., FST, θ, and Jost's D) calculated for human single-nucleotide polymorphisms (SNPs) are strongly and positively correlated to the position-specific evolutionary rates measured from multispecies alignments. That is, genomic positions (loci) experiencing higher purifying selection (lower evolutionary rates) produce lower values for the degree of population differentiation than those evolving with faster rates. We show that this pattern is completely mediated by the negative effects of purifying selection on the minor allele frequency (MAF) at individual loci. Our results suggest that inferences and methods relying on the comparison of population differentiation estimates (FST, θ, and Jost's D) based on SNPs across genomic positions should be restricted to loci with similar MAFs and/or the rates of evolution in genome scale surveys.

Original languageEnglish (US)
Pages (from-to)3617-3623
Number of pages7
JournalMolecular Biology and Evolution
Volume29
Issue number12
DOIs
StatePublished - Dec 2012

Fingerprint

single nucleotide polymorphism
Single Nucleotide Polymorphism
polymorphism
genome
Genome
loci
Population
genomics
local adaptation
gene frequency
population structure
Gene Frequency
genetic polymorphism
allele
comparison
rate
methodology

Keywords

  • evolutionary rate
  • F
  • minor allele frequency
  • population differentiation
  • purifying selection

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms. / Maruki, Takahiro; Kumar, Sudhir; Kim, Yuseob.

In: Molecular Biology and Evolution, Vol. 29, No. 12, 12.2012, p. 3617-3623.

Research output: Contribution to journalArticle

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