|Title||Detecting positive selection within genomes: the problem of biased gene conversion|
|Publication Type||Journal Article|
|Year of Publication||2010|
|Authors||Ratnakumar, A, Mousset, S, Glémin, S, Berglund, J, Galtier, N, Duret, L, Webster, MT|
|Journal||Philosophical Transactions of the Royal Society B: Biological Sciences|
|Keywords||2010-08-22, divergence, genomics, positive selection|
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 (dN/dS), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high dN/dS (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.
Detecting positive selection within genomes: the problem of biased gene conversion
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