Phylogenomic Analysis Using Bayesian Congruence Measuring

Phylogenomic analysis of large sets of molecular characters, primarily DNA and proteins, provides great opportunities to estimate and understand important evolutionary processes. However, molecular phylogenies inferred from individual loci often differ. This incongruence among phylogenies can be the result of systematic error, but can also be the result of different evolutionary histories. We propose a new method, based on Bayesian hierarchical clustering and posterior probability, to measure congruence between genes and to identify sets of congruent loci within which the genes or proteins share identical evolutionary history. We demonstrate the method on a sequence data of 10 nuclear genes from 20 ray-finned fish (Actinopterygii) species.