Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 28, Issue 5, Pages 1731-1743Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msq354
Keywords
codon usage; D; pseudoobscura; D; miranda; D; melanogaster; selective constraints; selective sweeps
Funding
- Natural Environment Research Council of the United Kingdom
- e-Science Data, Information and Knowledge Transformation (eDIKT) initiative
- Royal Society of Edinburgh
- Caledonian Research Foundation
- NERC [NE/D00232X/1] Funding Source: UKRI
- Natural Environment Research Council [NE/D00232X/1] Funding Source: researchfish
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We estimated the intensity of selection on preferred codons in Drosophila pseudoobscura and D. miranda at X-linked and autosomal loci, using a published data set on sequence variability at 67 loci, by means of an improved method that takes account of demographic effects. We found evidence for stronger selection at X-linked loci, consistent with their higher levels of codon usage bias. The estimates of the strength of selection and mutational bias in favor of unpreferred codons were similar to those found in other species, after taking into account the fact that D. pseudoobscura showed evidence for a recent expansion in population size. We examined correlates of synonymous and nonsynonymous diversity in these species and found no evidence for effects of recurrent selective sweeps on nonsynonymous mutations, which is probably because this set of genes have much higher than average levels of selective constraints. There was evidence for correlated effects of levels of selective constraints on protein sequences and on codon usage, as expected under models of selection for translational accuracy. Our analysis of a published data set on D. melanogaster provided evidence for the effects of selective sweeps of nonsynonymous mutations on linked synonymous diversity, but only in the subset of loci that experienced the highest rates of nonsynonymous substitutions (about one-quarter of the total) and not at more slowly evolving loci. Our correlational analysis of this data set suggested that both selective constraints on protein sequences and recurrent selective sweeps affect the overall level of codon usage.
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