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doi:10.1534/genetics.106.065557
A more recent version of this article appeared on March 1, 2007.
REGULAR RESEARCH PAPERS |
Background Selection In Single Genes May Explain Patterns Of Codon Bias
Laurence Loewe 1* and Brian Charlesworth 1
1 University of Edinburgh
* To whom correspondence should be addressed. E-mail: laurence.loewe{at}evolutionary-research.net.
Submitted on September 1, 2006
Revised on November 15, 2006
Accepted on 23 December 2006
Background selection involves the reduction in effective population size caused by the removal of recurrent deleterious mutations from a population. Previous work has examined this process for large genomic regions. Here we focus on the level of a single gene or small group of genes, and investigate how the effects of background selection caused by nonsynonymous mutations are influenced by the lengths of coding sequences, the number and length of introns, intergenic distances, neighboring genes, mutation rate and recombination rate. We generate our predictions from estimates of the distribution of the fitness effects of nonsynonymous mutations, obtained from DNA sequence diversity data in Drosophila. Results for genes in regions with typical frequencies of crossing over in Drosophila melanogaster suggest that background selection may influence the effective population sizes of different regions of the same gene, consistent with observed differences in codon usage bias along genes. It may also help to cause the observed effects of gene length and introns on codon usage. Gene conversion plays a crucial role in determining the sizes of these effects. The model over-predicts the effects of background selection with large groups of non-recombining genes, because it ignores Hill-Robertson interference among the mutations involved.
Key Words: Drosophila melanogaster, background selection, deleterious mutations, effective population size, reduced codon bias
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