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Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

Figure 2

BAMM analysis of example tree (Figure 1).

Example tree was simulated under three distinct processes (one constant rate and two diversity dependent processes; two transitions in total). The tree was analyzed under (i) the full multi-process BAMM model with time-variable speciation; (ii) a constrained multi-process BAMM with time-constant speciation; and (iii) a fully constrained 1-process constant-rate birth-death model. (A) Log-likelihoods for thinned MCMC chains for the constant rate birth-death process (bottom), the time-constant multi-process model (middle), and the full BAMM model with time-varying speciation (top). (B) Numbers of transitions during rjMCMC sampling when model is constrained to time-constant speciation rates; sidebar gives frequency distribution of sampled states. (C) Numbers of transitions under full BAMM model with time-variable speciation processes. Black sidebar denotes true number of transitions in generating model. The true number of transitions was estimated correctly only when the assumption of time-constant rates was relaxed.

Figure 2