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MBE Advance Access published online on June 8, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm119
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Compound Tests for the Detection of Hitchhiking Under Positive Selection

Kai Zeng{dagger}, Suhua Shi{dagger} and Chung-I Wu*

{dagger} State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
* 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. Revision received June 1, 2007. Accepted for publication June 4, 2007.

Many statistical tests have been developed for detecting positive selection. Most of these tests draw conclusions based on significant deviations from the patterns of polymorphism predicted by the neutral model. However, many non-equilibrium forces may cause similar deviations, and thus the tests usually have low statistical specificity to positive selection. The main challenge is hence to construct test statistics that are reasonably powerful in detecting positive selection, but are relatively insensitive to other forces. Recently, Zeng et al. (2006) proposed a new test, DH, which is a compound of Tajima's D and Fay and Wu's H, and showed that DH has reasonably high statistical specificity to positive selection. In this report, we expand the idea of a compound test by combining Fay and Wu's H or DH with the Ewens-Watterson (EW) test. We refer to these two new tests as HEW and DHEW, respectively. Compared to the DH test, HEW and DHEW are more robust against the presence of recombination, and are also more powerful in detecting positive selection. Furthermore, the DHEW test, similar to DH, is also relatively insensitive to background selection and demography. The HEW test, on the other hand, tends to be somewhat less conservative than DH and DHEW in some cases.

Key Words: compound tests • positive selection • demography • background selection


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