title: Detecting positive selection within genomes: the problem of biased gene conversion.
abstract: The identification of loci influenced by positive selection is a major goal of evolutionary genetics. A popular approach is to perform scans of alignments on a genome-wide scale in order to find regions evolving at accelerated rates on a particular branch of a phylogenetic tree. However, positive selection is not the only process that can lead to accelerated evolution. Notably, GC-biased gene conversion (gBGC) is a recombination-associated process that results in the biased fixation of G and C nucleotides. This process can potentially generate bursts of nucleotide substitutions within hotspots of meiotic recombination. Here, we analyse the results of a scan for positive selection on genes on branches across the primate phylogeny. We show that genes identified as targets of positive selection have a significant tendency to exhibit the genomic signature of gBGC. Using a maximum-likelihood framework, we estimate that more than 20 per cent of cases of significantly elevated non-synonymous to synonymous substitution rates ratio (d(N)/d(S)), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high d(N)/d(S) (more than 2). Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection.
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden.
authors.forename: Abhirami
authors.initials: A
authors.lastname: Ratnakumar
authors.forename: Sylvain
authors.initials: S
authors.lastname: Mousset
authors.forename: Sylvain
authors.initials: S
authors.lastname: Glémin
authors.forename: Jonas
authors.initials: J
authors.lastname: Berglund
authors.forename: Nicolas
authors.initials: N
authors.lastname: Galtier
authors.forename: Laurent
authors.initials: L
authors.lastname: Duret
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Webster
mesh_terms: D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D005785:Gene Conversion / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D011323:Primates / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics; D012641:Selection, Genetic; D016415:Sequence Alignment