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. 2010 Nov;27(11):2618-27.
doi: 10.1093/molbev/msq149. Epub 2010 Jun 15.

Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution

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Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution

Romain A Studer et al. Mol Biol Evol. 2010 Nov.

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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Figures

F<sc>IG</sc>. 1.
FIG. 1.
Tree topologies studied. Boxes represent speciation events and circles represent duplication events. The branches tested are the 3R genome duplication at the basis of teleost fishes (A), the speciation between fishes and tetrapods (B), the 1R/2R genome duplications at the origin of vertebrates (C), and the speciation between insects and chordates (D).
F<sc>IG</sc>. 2.
FIG. 2.
Correlation of sites under positive selection with covarions and CBDs. (A) The histogram presents the values of the chi-square score per site for covarions. The curves are the chi-square values for different BEB intervals (posterior probability for a site to be under positive selection): black for BEB < 50%, blue for BEB < 95%, green for 99% < BEB, and red for BEB ≥ 99%. (B) The histogram represents the values of BAD scores per site for CBD. The curves are the BAD values for different BEB intervals: black for BEB < 50%, blue for BEB < 95%, green for 99% < BEB, and red for BEB ≥ 99%. The dashed curve represents BAD scores of nearly neutral simulated sequences. The dashed line at 3.5 is the 99th percentile of BAD scores for BEB < 50%.
F<sc>IG</sc>. 3.
FIG. 3.
Percentage of CBDs per families under RAS model and real data. Histograms of proportion of CBD sites with BAD score >3.5 per subtree in data simulated under a neutral model of RAS (A) and in real data (B). The dashed line at 3.9% is the 99th percentile under the neutral model.

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