Distinguishing between selective sweeps and demography using DNA polymorphism data

Jeffrey Jensen, Yuseob Kim, Vanessa Bauer DuMont, Charles F. Aquadro, Carlos D. Bustamante

Research output: Contribution to journalArticle

155 Citations (Scopus)

Abstract

In 2002 Kim and Stephan proposed a promising composite-likelihood method for localizing and estimating the fitness advantage of a recently fixed beneficial mutation. Here, we demonstrate that their composite-likelihood-ratio (CLR) test comparing selective and neutral hypotheses is not robust to undetected population structure or a recent bottleneck, with some parameter combinations resulting in a false positive rate of nearly 90%. We also propose a goodness-of-fit test for discriminating rejections due to directional selection (true positive) from those due to population and demographic forces (false positives) and demonstrate that the new method has high sensitivity to differentiate the two classes of rejections.

Original languageEnglish (US)
Pages (from-to)1401-1410
Number of pages10
JournalGenetics
Volume170
Issue number3
DOIs
StatePublished - Jul 2005
Externally publishedYes

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Demography
DNA
Population
Mutation

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Distinguishing between selective sweeps and demography using DNA polymorphism data. / Jensen, Jeffrey; Kim, Yuseob; DuMont, Vanessa Bauer; Aquadro, Charles F.; Bustamante, Carlos D.

In: Genetics, Vol. 170, No. 3, 07.2005, p. 1401-1410.

Research output: Contribution to journalArticle

Jensen, J, Kim, Y, DuMont, VB, Aquadro, CF & Bustamante, CD 2005, 'Distinguishing between selective sweeps and demography using DNA polymorphism data', Genetics, vol. 170, no. 3, pp. 1401-1410. https://doi.org/10.1534/genetics.104.038224
Jensen, Jeffrey ; Kim, Yuseob ; DuMont, Vanessa Bauer ; Aquadro, Charles F. ; Bustamante, Carlos D. / Distinguishing between selective sweeps and demography using DNA polymorphism data. In: Genetics. 2005 ; Vol. 170, No. 3. pp. 1401-1410.
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