Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution
- PMID: 20551039
- PMCID: PMC2955734
- DOI: 10.1093/molbev/msq149
Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution
Abstract
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.
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References
-
- Abhiman S, Sonnhammer EL. Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins. 2005;60:758–768. - PubMed
-
- Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006;22:1600–1607. - PubMed
-
- Anisimova M, Liberles DA. The quest for natural selection in the age of comparative genomics. Heredity. 2007;99:567–579. - PubMed
-
- Aparicio S, Chapman J, Stupka E, et al. (41 co-authors) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002;297:1301–1310. - PubMed
-
- Bielawski JP, Yang Z. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol. 2004;59:121–132. - PubMed
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