MBE Advance Access published online on April 21, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm078
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Research Article |
Comparisons of Site- and Haplotype-frequency Methods for Detecting Positive Selection
State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
* Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
Corresponding author: Kai Zeng, 1101 E 57th Street, Chicago, IL 60637, U.S.A., Tel: 1-773-702-3234, Fax: 1-773-702-9740, Email: kzeng{at}uchicago.edu
Received for publication April 9, 2007. Accepted for publication April 14, 2007.
In this report, we compare the differences between various site- and haplotype-frequency tests in their power to detect positive selection by doing computer simulations. Our results are: (i) although haplotype-frequency tests that are conditional on the number of haplotypes (K) were developed for nonrecombining haplotypes, these tests are insensitive to recombination. Such tests, including the Ewens-Watterson (EW) test, can therefore be applied to recombining haplotypes. (ii) Tests conditional on the number of segregating sites (S) become overly conservative in the presence of recombination. (iii) The EW test is usually the most powerful test during the sweep phase, especially when the local recombination rate is high. (iv) The extended haplotype homozygosity (EHH) test relies heavily on the prior knowledge of the target of selection. With that knowledge, it is the most powerful test, whereas in the absence of this prior information the test has little power. We also study the sensitivities of the haplotype-frequency tests to background selection and various demographic forces. We find that these tests are sensitive to some forces other than positive selection. To alleviate the problem of low specificity, compound tests, such as the DH test (Zeng et al. 2006), may be a solution. In the companion paper (Zeng et al. submitted), we use the EW test to devise two compound tests which are more powerful in detecting positive selection than DH, but are also relatively insensitive to demography.
Key Words: positive selection • haplotype-frequency tests • site-frequency tests
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