Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees
For each simulation, the estimated number of processes was simply the model that was most frequently sampled during MCMC simulation of the posterior distribution. Black bars denote true number of processes in generating model. For example, 84% of trees simulated under a single-shift exponential change model (exp2; top panel; two processes in the generating model) were correctly inferred to have been generated under a two-process model. For a diversity-dependent model with five processes (DD5), power to detect the true number of processes is lower, although though most analyses (80.4%) recovered either 4 or 5 process models as the MAP model. Results for each model are based on 500 simulated phylogenies and used a conservative γ = 1 prior on the expected number of non-root processes (see Figure 3).