Evaluation of the models handling heterotachy in phylogenetic inference

Background  

The evolutionary rate at a given homologous position varies across time. When sufficiently pronounced, this phenomenon – called heterotachy – may produce artefactual phylogenetic reconstructions under the commonly used models of sequence evolution. These observations have motivated the development of models that explicitly recognize heterotachy, with research directions proposed along two main axes: 1) the covarion approach, where sites switch from variable to invariable states; and 2) the mixture of branch lengths (MBL) approach, where alignment patterns are assumed to arise from one of several sets of branch lengths, under a given phylogeny.