Journal Article

Large-Scale Analysis of Orthologs and Paralogs under Covarion-Like and Constant-but-Different Models of Amino Acid Evolution

Romain A. Studer and Marc Robinson-Rechavi

in Molecular Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 27, issue 11, pages 2618-2627
Published in print November 2010 | ISSN: 0737-4038
Published online June 2010 | e-ISSN: 1537-1719 | DOI: http://dx.doi.org/10.1093/molbev/msq149

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Functional divergence between homologous proteins is expected to affect amino acid sequences in two main ways, which can be considered as proxies of biochemical divergence: a “covarion-like” pattern of correlated changes in evolutionary rates, and switches in conserved residues (“conserved but different”). Although these patterns have been used in case studies, a large-scale analysis is needed to estimate their frequency and distribution. We use a phylogenomic framework of animal genes to answer three questions: 1) What is the prevalence of such patterns? 2) Can we link such patterns at the amino acid level with selection inferred at the codon level? 3) Are patterns different between paralogs and orthologs? We find that covarion-like patterns are more frequently detected than “constant but different,” but that only the latter are correlated with signal for positive selection. Finally, there is no obvious difference in patterns between orthologs and paralogs.

Keywords: covarion; positive selection; whole-genome duplication; vertebrate evolution; rate shift; heterotachy

Journal Article.  6098 words.  Illustrated.

Subjects: Evolutionary Biology ; Molecular and Cell Biology

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