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.
The evolutionary history of two species belonging to the genus Orthocladius van der Wulp, 1874 (Diptera: Chironomidae) from Lake Baikal was investigated using the mitochondrial gene coding the first subunit of the cytochrome c oxidase (CO1 mtDNA). The phylogenetic analysis indicated that the Baikal Orthocladius species were divided into two well-defined clades where O. (Orthocladius) gregarius Linevitsh, 1970 was a sister species to Palaearctic O. (Orthocladius) nitidoscutellatus Lundstrom, 1915 and the O. (Eudactylocladius) sp. was a sister species to Nearctic O. (Eudactylocladius) subletteorum Cranston, 1998. Divergence time estimates indicated that these species had been evolving independently for about 18 Ma (Neogene, Early Miocene), while emergence of the most recent common ancestors of the modern O. (Orthocladius) gregarius and O. (Eudactylocladius) sp. was dated to about 3.5 Ma (Neogene, Pliocene). The evolution of Baikal orthoclads occurred from the rheophilic fauna under conditions of global climate change during the geological history of the Baikal Depression in the Tertiary Period.
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