Improving the accuracy of phylogenetic reconstruction by improving models of sequence divergence

Phylogenies provide the essential framework for understanding evolutionary processes. Critical errors in models of sequence divergence are evident from discordant results from genome scale data sets on the primate / carnivore / rodent relationship. A strong candidate is the common treatment of rate and compositional variation as independent phenomena. This is inconsistent with mutation mechanisms and the evolvability of DNA metabolism. Using a novel context dependent substitution model class we will be the first to establish whether coupling the influence of compositional and rate heterogeneity improves phylogenetic reconstruction accuracy. Furthermore, we will assess the suitability of full genome data sets for resolving phylogenies.