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

Figure 3

BAMM analyses of constant-rate phylogenies and prior on Poisson rate parameter (γ).

Histograms in (A–C) display the frequency distribution of the estimated number of processes in the model with the maximum a posteriori (MAP) probability as a function of three different priors on the Poisson rate parameter Λ (γ = 1; γ = 5; γ = 10). This “best-fit” model was simply the model that was visited most often during the MCMC simulation of the posterior. (D–F) show the distribution of posterior probabilities for the true model (M0). With a relatively flat prior on models (γ = 10), the MAP model is biased towards a model with 2 processes ( = 1 transition). However, the posterior probability of the true model M0 remains substantial (F), and M0 nonetheless had a posterior probability greater than 0.10 for the vast majority of simulations. Results are based on 500 simulated phylogenies per γ scenario.

Figure 3

doi: https://doi.org/10.1371/journal.pone.0089543.g003