Background Selection in Single Genes May Explain Patterns of Codon Bias
- 1 March 2007
- journal article
- research article
- Published by Oxford University Press (OUP) in Genetics
- Vol. 175 (3), 1381-1393
- https://doi.org/10.1534/genetics.106.065557
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.Keywords
This publication has 54 references indexed in Scilit:
- Direct estimation of per nucleotide and genomic deleterious mutation rates in DrosophilaNature, 2007
- Evolution of Amino-Acid Sequences and Codon Usage on the Drosophila miranda Neo-Sex ChromosomesGenetics, 2006
- Inferring the distribution of mutational effects on fitness inDrosophilaBiology Letters, 2006
- The Pattern of Polymorphism in Arabidopsis thalianaPLoS Biology, 2005
- Patterns of Selection on Synonymous and Nonsynonymous Variants in Drosophila mirandaGenetics, 2005
- Selection on Codon Usage in Drosophila americanaCurrent Biology, 2004
- Effect of Strong Directional Selection on Weakly Selected Mutations at Linked Sites: Implication for Synonymous Codon UsageMolecular Biology and Evolution, 2003
- The Genome Sequence of Drosophila melanogasterScience, 2000
- A population genetic model for the evolution of synonymous codon usage: patterns and predictionsGenetics Research, 1999
- A Mathematical Theory of Natural and Artificial Selection, Part V: Selection and MutationMathematical Proceedings of the Cambridge Philosophical Society, 1927