Journal
GENETICS
Volume 170, Issue 3, Pages 1401-1410Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.104.038224
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Funding
- NIGMS NIH HHS [GM36431, R01 GM036431] Funding Source: Medline
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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 clue 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.
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