Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales

Abstract Phylogenetic divergence time estimates inferred from trees optimized using maximum likelihood apply branch lengths. These branch lengths are influenced by the substitution model applied in the analysis, which can, in turn, affect divergence time estimates. To examine the effects of substitution models on divergence time estimates, we applied an empirical data set for Cornales that had 16 calibration point constraints in maximum likelihood analyses using 19 different substitution models to obtain topologies with branch lengths. Penalized likelihood was then used to obtain divergence time estimates for corresponding nodes of these topologies. Discrepancy in divergence time estimates among corresponding nodes of trees constructed with different models was small in most cases (falling within 95% confidence intervals based on the most supported model); however, we recovered instances of nodes differing by as much as 23.7% from times on corresponding nodes of the phylogeny reconstructed from our best-f...