Detecting positive selection within genomes: the problem of biased gene conversion
- 27 August 2010
- journal article
- research article
- Published by The Royal Society in Philosophical Transactions Of The Royal Society B-Biological Sciences
- Vol. 365 (1552), 2571-2580
- https://doi.org/10.1098/rstb.2010.0007
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.Keywords
This publication has 28 references indexed in Scilit:
- Biased Gene Conversion and the Evolution of Mammalian Genomic LandscapesAnnual Review of Genomics and Human Genetics, 2009
- Hotspots of Biased Nucleotide Substitutions in Human GenesPLoS Biology, 2009
- Patterns of Positive Selection in Six Mammalian GenomesPLoS Genetics, 2008
- High-resolution mapping of meiotic crossovers and non-crossovers in yeastNature, 2008
- The Impact of Recombination on Nucleotide Substitutions in the Human GenomePLoS Genetics, 2008
- No effect of recombination on the efficacy of natural selection in primatesGenome Research, 2008
- Adaptive Evolution of Conserved Noncoding Elements in MammalsPLoS Genetics, 2007
- Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversionGenome Research, 2007
- Fast-evolving noncoding sequences in the human genomeGenome Biology, 2007
- An RNA gene expressed during cortical development evolved rapidly in humansNature, 2006