Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree.

ABSTRACT: Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree

SUBMITTER: Shavit Grievink L 

PROVIDER: S-EPMC2850392 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature