PMID: 18205620Jan 22, 2008Paper

Effect of co-evolving amino acid residues on topology of phylogenetic trees

Biochemistry. Biokhimii︠a︡
D Yu Sherbakov, T I Triboy

Abstract

The presence in proteins of amino acid residues that change in concert during evolution is associated with keeping constant the protein spatial structure and functions. As in the case with morphological features, correlated substitutions may become the cause of homoplasies--the independent evolution of identical non-homological adaptations. Our data obtained on model phylogenetic trees and corresponding sets of sequences have shown that the presence of correlated substitutions distorts the results of phylogenetic reconstructions. A method for accounting for co-evolving amino acid residues in phylogenetic analysis is proposed. According to this method, only a single site from the group of correlated amino acid positions should remain, whereas other positions should not be used in further phylogenetic analysis. Simulations performed have shown that replacement on the average of 8% of variable positions in a pair of model sequences by coordinately evolving amino acid residues is able to change the tree topology. The removal of such amino acid residues from sequences before phylogenetic analysis restores the correct topology.

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Citations

Feb 17, 2019·The Journal of Animal Ecology·Vojtěch BrlíkPetr Procházka

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