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MBE Advance Access published online on October 13, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi015
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted October 4, 2004

Research Article

Excess of Amino Acid Substitutions Relative to Polymorphism between X-linked Duplications in Drosophila melanogaster

Kevin Thornton 1* and Manyuan Long 2

1 Committee on Genetics, University of Chicago
2 Committee on Genetics, University of Chicago; Department of Ecology and Evolution, University of Chicago

* To whom correspondence should be addressed. E-mail: kt234{at}cornell.edu.


  Abstract

We have obtained sequence polymorphism data from 13 genes belonging to 5 gene families in Drosophila melanogaster where the Ka/Ks between copies is greater than one. Twelve of these 13 loci are X-linked. In general, there is evidence of purifying selection in all families, as inferred both from levels of silent and replacement variation and insertion/deletion variation, suggesting that the loci are likely functional. Shared polymorphisms indicative of gene conversion between paralogs are rare amongst the X-linked families, in contrast to available data from autosomal duplicates. McDonald-Kreitman tests between duplicates reveal an excess of amino-acid fixations between copies in the X-linked families, suggesting that the divergence between these loci was driven by positive selection. In contrast, available data from autosomal duplicates show a deficit of fixations, consistent with gene conversion being a strong homogenizing force.

Keywords: Drosophila; gene duplicates; positive selection; pseudogenes; polymorphism; concerted evolution.
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