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doi:10.1534/genetics.104.033068
A more recent version of this article appeared on March 1, 2005.
REGULAR RESEARCH PAPERS |
Patterns of Selection on Synonymous and Non-Synonymous Variants in Drosophila miranda
Carolina Bartolome 1*, Xulio Maside 2, Soojin Yi 3, Anna L. Grant 1 and Brian Charlesworth 1
1 University of Edinburgh
2 Complexo Hospitalario Universitario de Santiago de Compostela
3 University of Chicago
* To whom correspondence should be addressed. E-mail: carolina.bartolome{at}ed.ac.uk.
Submitted on June 30, 2004
Revised on September 5, 2004
Accepted on 2 November 2004
We have investigated patterns of within-species polymorphism and between-species divergence for synonymous and non-synonymous variants at a set of autosomal and X-linked loci of Drosophila miranda. D. pseudoobscura and D. affinis were used for the between-species comparisons. The results suggest the action of purifying selection on polymorphic, non-synonymous variants. Among synonymous polymorphisms, there is a significant excess of synonymous mutations from preferred to unpreferred codons, and of GC to AT mutations. There was no excess of GC to AT mutations among polymorphisms at non-coding sites. This suggests that selection is acting to maintain the use of preferred codons. Indirect evidence suggests that biased gene conversion in favour of GC basepairs is also likely to be operating. The joint intensity of selection and biased gene conversion, in terms of the product of effective population size and the sum of the selection and conversion coefficients, was estimated to be approximately 0.65.
Key Words: Drosophila miranda, biased gene conversion, codon usage, purifying selection, synonymous variation
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