Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model.

ABSTRACT: The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees. We simulated data of different alignment lengths under two different 11-taxon trees and a broad range of different branch length conditions. The data were analyzed with the true model parameters as well as with estimated and incorrect assumptions about among-site rate variation. If length differences between connected branches strongly increase, tree inference with the correct likelihood model assumptions can fail. We found that incorporating invariant sites together with Γ distributed site rates in the tree reconstruction (Γ+I) increases the robustness of maximum likelihood in comparison with models using only Γ. The results show that

SUBMITTER: Kuck P 

PROVIDER: S-EPMC3359070 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature