On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations

Jeffrey Jensen, Kevin R. Thornton, Carlos D. Bustamante, Charles F. Aquadro

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site-frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic (ωmax) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.

Original languageEnglish (US)
Pages (from-to)2371-2379
Number of pages9
JournalGenetics
Volume176
Issue number4
DOIs
StatePublished - Aug 2007
Externally publishedYes

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Linkage Disequilibrium
Population
Population Genetics
Drosophila melanogaster
Demography

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. / Jensen, Jeffrey; Thornton, Kevin R.; Bustamante, Carlos D.; Aquadro, Charles F.

In: Genetics, Vol. 176, No. 4, 08.2007, p. 2371-2379.

Research output: Contribution to journalArticle

Jensen, Jeffrey ; Thornton, Kevin R. ; Bustamante, Carlos D. ; Aquadro, Charles F. / On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. In: Genetics. 2007 ; Vol. 176, No. 4. pp. 2371-2379.
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