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Genome Biology and Evolution Advance Access published online on May 25, 2009
Genome Biology and Evolution, doi:10.1093/gbe/evp008
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© 2009 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Locus specific decoupling of base composition evolution at synonymous sites and introns along the Drosophila melanogaster and D. sechellia lineages

Vanessa L. Bauer DuMont, Nadia D. Singh, Mark H. Wright and Charles F. Aquadro*

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853

* Author for Correspondence: Charles Aquadro, Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA, telephone (607) 254-4839; fax (607)255-6249; cfa1{at}cornell.edu


  Abstract

Selection is thought to be partially responsible for patterns of molecular evolution at synonymous sites within numerous Drosophila species. Recently, "per site" and likelihood methods have been developed to detect loci for which positive selection is a major component of synonymous site evolution. An underlying assumption of these methods, however, is a homogeneous mutation process. To address this potential shortcoming we perform a complementary analysis making gene-by-gene comparisons of paired synonymous site and intron substitution rates toward and away from the nucleotides G and C, since preferred codons are G- or C- ending in Drosophila. This comparison may reduce both the false positive rate (due to broad-scale heterogeneity in mutation) and false negative rate (due to lack of power comparing small numbers of sites) of the per-site and likelihood methods. We detect loci with patterns of evolution suggestive of synonymous site selection pressures predominately favoring unpreferred and preferred codons along the D. melanogaster and D. sechellia lineages, respectively. Intron selection pressures do not appear sufficient to explain all of these results as the magnitude of the difference in synonymous and intron evolution is dependent on recombination environment and chromosomal location in a direction supporting the hypothesis of selectively driven synonymous fixations. This comparison identifies 101 loci with an apparent switch in codon preference between D. melanogaster and D. sechellia, a pattern previously only observed at the Notch locus.

Keywords: Drosophila, base composition, substitution rates

Received January 29, 2009; Revised April 10, 2009; Revised May 12, 2009; Accepted May 15, 2009


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