Distinguishing between selective sweeps and demography using DNA polymorphism data

Genetics. 2005 Jul;170(3):1401-10. doi: 10.1534/genetics.104.038224. Epub 2005 May 23.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Computer Simulation
  • Demography*
  • Genetics, Population*
  • Likelihood Functions
  • Models, Genetic*
  • Mutation / genetics
  • Polymorphism, Genetic*
  • Reproducibility of Results
  • Selection, Genetic*