title: Potential impact of recombination on sitewise approaches for detecting positive natural selection.
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.
authors.affiliation: Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, USA. dshriner@u.washington.edu
authors.forename: Daniel
authors.initials: D
authors.lastname: Shriner
authors.forename: David C
authors.initials: DC
authors.lastname: Nickle
authors.forename: Mark A
authors.initials: MA
authors.lastname: Jensen
authors.forename: James I
authors.initials: JI
authors.lastname: Mullins
mesh_terms: D000465:Algorithms; D000818:Animals; D001499:Bayes Theorem; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D006801:Humans; D011995:Recombination, Genetic; D012641:Selection, Genetic