Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al.

Abstract

Our recent study evaluated the performance of parsimony and probabilistic models of phylogenetic inference based on categorical data [1]. We found that a Bayesian implementation of a probabilistic Markov model produced more accurate results than either of the competing parsimony approaches (the main method currently employed), and the maximum-likelihood implementation of the same model. This occurs principally because the results of Bayesian analyses are less resolved (less precise) as a measure of topological uncertainty is intrinsically recovered in this MCMC-based approach and can be used to construct a majority-rule consensus tree that reflects this. Of the three main methods, maximum likelihood performed theworst of all as a single exclusively bifurcating tree is estimated in this framework which does not integrate an intrinsic measure of support.