Evolutionary models of phylogenetic trees

Iosif Pinelis

Abstract

The most widely used evolutionary model for phylogenetic trees is the equal–rates Markov (ERM) model. A problem is that the ERM model predicts less imbalance than observed for trees inferred from real data; in fact, the observed imbalance tends to fall between the values predicted by the ERM model and those predicted by the proportional–to–distinguishable–arrangements (PDA) model. Here, a continuous multi–rate (MR) family of evolutionary models is presented which contains entire subfamilies corresponding to both the PDA and ERM models. Furthermore, this MR family covers an entire range from ‘completely balanced’ to ‘completely unbalanced’ models. In particular, the MR family contains other known evolutionary models. The MR family is very versatile and virtually free of assumptions on the character of evolution; yet it is highly susceptible to rigorous analyses. In particular, such analyses help to uncover adaptability, quasi–stabilization and prolonged stasis as major possible causes of the imbalance. However, the MR model is functionally simple and requires only three parameters to reproduce the observed imbalance.