Co-evolution is Incompatible with the Markov Assumption in Phylogenetics

TL;DR

This paper shows that co-evolution between proteins can violate the Markov assumption in phylogenetic models, highlighting the need for alternative probabilistic approaches in such cases.

Contribution

It demonstrates that co-evolutionary relationships can conflict with the Markov assumption in phylogenetics, based on analysis of fungal orthologs.

Findings

Co-evolution can violate the Markov assumption in phylogenetic models.

Analysis of fungal orthologs reveals incompatibility between co-evolution and Markov models.

Results suggest the need for alternative models in cases of extreme co-evolution.

Abstract

Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of orthologous sets of three fungi and their co-evolutionary relations, we demonstrate that co-evolutionary assumption may violate the Markov assumption. Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution.