Originally published as Genetics Published Articles Ahead of Print on December 28, 2006.

Genetics, Vol. 175, 1381-1393, March 2007, Copyright © 2007
doi:10.1534/genetics.106.065557

Background Selection in Single Genes May Explain Patterns of Codon Bias

Laurence Loewe1 and Brian Charlesworth

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom

1 Corresponding author: Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, King's Bldgs., W. Mains Rd., Edinburgh EH9 3JT, United Kingdom.
E-mail: laurence.loewe{at}evolutionary-research.net

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.


Related articles in Genetics:

ISSUE HIGHLIGHTS

Genetics 2007 175: NP. [Full Text]  



This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
A. D. Cutter, A. Dey, and R. L. Murray
Evolution of the Caenorhabditis elegans Genome
Mol. Biol. Evol., June 1, 2009; 26(6): 1199 - 1234.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
U. Friberg and W. R. Rice
Cut Thy Neighbor: Cyclic Birth and Death of Recombination Hotspots via Genetic Conflict
Genetics, August 1, 2008; 179(4): 2229 - 2238.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. Kawabe, A. Forrest, S. I. Wright, and D. Charlesworth
High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata
Genetics, June 1, 2008; 179(2): 985 - 995.
[Abstract] [Full Text] [PDF]

Home page
 Integr. Comp. Biol.Home page
D. E. Janes, T. Ezaz, J. A. Marshall Graves, and S. V. Edwards
Characterization, chromosomal location, and genomic neighborhood of a ratite ortholog of a gene with gonadal expression in mammals
Integr. Comp. Biol., April 28, 2008; (2008) icn024v1.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
K. Bullaughey, M. Przeworski, and G. Coop
No effect of recombination on the efficacy of natural selection in primates
Genome Res., April 1, 2008; 18(4): 544 - 554.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. D. Cutter, J. D. Wasmuth, and N. L. Washington
Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing
Genetics, April 1, 2008; 178(4): 2093 - 2104.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. M. Macpherson, G. Sella, J. C. Davis, and D. A. Petrov
Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila
Genetics, December 1, 2007; 177(4): 2083 - 2099.
[Abstract] [Full Text] [PDF]