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PMID: 17194784 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Background selection in single genes may explain patterns of codon bias.

Genetics ·Vol. 175 ·No. 3 ·2007-03-00 ·Pages 1381-93

Loewe L, Charlesworth B

Abstract

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 overpredicts the effects of background selection with large groups of nonrecombining genes, because it ignores Hill-Robertson interference among the mutations involved.

MeSH Terms
Animals Codon/genetics Computer Simulation Drosophila/genetics Gene Components Gene Conversion/genetics Genes/genetics Models, Genetic Mutation/genetics Selection, Genetic
Chemicals
Codon
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Loewe Laurence
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom. [email protected]
Charlesworth Brian
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Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
DOI
10.1534/genetics.106.065557
Email
[email protected]
Published
2007-03-00
Epub
2006-00-28
Pages
1381-93
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC1840058
Subset
IM
External Links
PubMed source DOI: 10.1534/genetics.106.065557 PMC Full Text View journal details
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