Genetical Research



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


DANIEL SHRINER a1c1, DAVID C NICKLE a1, MARK A. JENSEN a1 and JAMES I. MULLINS a1a2
a1 Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, USA
a2 Departments of Medicine and Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195-8070, USA

Abstract

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.

(Received July 8 2002)
(Revised November 19 2002)


Correspondence:
c1 Tel: +1 206 732 6149. Fax: +1 206 732 6167. e-mail: dshriner@u.washington.edu


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