Macroevolutionary analysis of discrete character evolution using parsimony-informed likelihood

AO_SCPLOWBSTRACTC_SCPLOWRates of character evolution in macroevolutionary datasets are typically estimated by maximizing the likelihood function of a continuous-time Markov chain (CTMC) model of character evolution over all possible histories of character state change, a technique known as maximum average likelihood. An alternative approach is to estimate ancestral character states independently of rates using parsimony and to then condition likelihood-based estimates of transition rates on the resulting ancestor-descendant reconstructions. We use maximum parsimony reconstructions of possible pathways of evolution to implement this alternative approach for single-character datasets simulated on empirical phylogenies using a two-state CTMC. We find that transition rates estimated using parsimonious ancestor-descendant reconstructions have lower mean squared error than transition rates estimated by maximum average likelihood. Although we use a binary state character for exposition, the approach remains valid for an arbitrary number of states. Finally, we show how this method can be used to rapidly and easily detect phylogenetic variation in tempo and mode of character evolution with two empirical examples from squamates. These results highlight the mutually informative roles of parsimony and likelihood when testing hypotheses of character evolution in macroevolution.