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Potential impact of recombination on sitewise approaches for detecting positive natural selection

Published online by Cambridge University Press:  30 April 2003

DANIEL SHRINER
Affiliation:
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, USA
DAVID C NICKLE
Affiliation:
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, USA
MARK A. JENSEN
Affiliation:
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, USA
JAMES I. MULLINS
Affiliation:
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, USA Departments of Medicine and Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195-8070, USA
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Abstract

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Current sitewise methods for detecting positive selection on gene sequences (the de facto standard being the CODEML method (Yang et al., 2000)) assume no recombination. This paper presents simulation results indicating that violation of this assumption can lead to false positive detection of sites undergoing positive selection. Through the use of population-scaled mutation and recombination rates, simulations can be performed that permit the generation of appropriate null distributions corresponding to neutral expectations in the presence of recombination, thereby allowing for a more accurate estimation of positive selection.

Type
Research Article
Copyright
© 2003 Cambridge University Press