The effect of unequal transversion rates on the accuracy of evolutionary parsimony

Evolutionary parsimony is an easy-to-use method of phylogenetic inference that is based on nucleic acid sequences and that does not require the assumption that evolutionary processes in the various sites on the molecule are identical. It does, however, require a parameter constraint, known as the "balanced transversion" assumption. We show that the accuracy of the procedure is fairly insensitive to moderate violations of this assumption--and that the procedure thus is applicable under more general conditions than previously thought.