Identification of coevolving positions by ancestral reconstruction

Coevolution within proteins occurs when changes in one position affect the selective pressure in another position to preserve the protein structure or function. The identification of coevolving positions within proteins remains contentious, with most methods disregarding the phylogenetic information. Here, we present a time-efficient approach for detecting coevolving pairs, which is almost perfect in terms of precision and specificity. It is based on maximum parsimony-based ancestral reconstruction followed by the identification of pairs with a depletion on separate changes when compared to their number of concurrent changes. Our analysis of a previously characterised biological dataset shows that the coevolving pairs that we identified tend to be close in the protein sequence and structure, slightly less solvent exposed and have a higher mutation rate. We also show how the ancestral reconstruction can be used to detect favourable and unfavourable amino acid combinations. Altogether, we demonstrate how this approach is essential for identifying pairs of positions with weak covariation patterns.