Co-Evolution of Amino Acid Residues in Proteins Impedes Phylogenetic Inferences
Some amino acid residues evolve in concerted fashion due to the necessity for maintenance of robust spatial structure of proteins as well as maintenance of their functions. As in the case of morphological traits, concerted amino acid sub-stitutions may result in elevated number of homoplasies due to independent generation of similar but non-homolo-gous adaptations. We used simulated sets of amino acid sequences to show that concerted amino acid substitutions distort topologies of inferred trees if not taken into account. We propose an approach allowing one to remove this effect from phylogenetic analysis by representing a group of amino acid positions evolving concertedly, with a single site. The rest of the members of such set are excluded from further analysis. Simulations allowed us to show that if amino acid sequences contain 8% or more of concertedly evolving sites, the topology of the inferred tree is likely to be wrong. Removing these sites recovers the correct tree topology.