Under-parameterized Model of Sequence Evolution Leads to Bias in the Estimation of Diversification Rates from Molecular Phylogenies

Macroevolutionary inferences from molecular phylogenies are becoming increasingly common (see Harvey et al., 1996; Mooers and Heard, 1997; Pagel, 1999; Barraclough and Nee, 2001). Many methods in which phylogenies are invoked for historical inference assume that a molecular phylogeny is an errorless representation of the underlying phylogenetic history of the included taxa (but see Lutzoni et al., 2001; Huelsenbeck et al., 2000; Huelsenbeck and Rannala, 2003). However, molecular phylogenies are estimates of this history based on a particular model of evolution; thus, there is some error associated with their estimation (Huelsenbeck and Kirkpatrick, 1996). Here we explore the effects of a particular type of error in phylogenetic branch-length estimation, that caused by assuming an underparameterized model of molecular evolution, on the γ-statistic of Pybus and Harvey (2000), a statistic that tests for changes in the rate of diversification through time. Although we restrict our attention to the estimation of diversification rates, our findings are germane to any macroevolutionary inferences relying on the accurate estimation of phylogenetic branch lengths such as molecular dating (e.g., Welch and Bromham, 2005) and probabilistic methods for ancestral state reconstruction (e.g., Ronquist, 2004).