Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees
Phylogenies were simulated under 5 distinct evolutionary scenarios. For each simulated phylogeny, I reconstructed branch-specific speciation rates using BAMM and modeled these as a function of the true branch rates from the generating model. Frequency distributions of the estimated slope of this relationship are shown in the left column for each simulation scenario. Center column denotes corresponding r2 values from the same OLS regressions. Right column is distribution of mean relative rate differences (RRD) for each scenario. A value of 1 implies that, on average, branch-specific speciation estimates are unbiased; a value of 0.5 would imply that branch-specific estimates are, on average, equal to 50% of the true value. Results for each simulation scenario are based on 500 simulated phylogenies (thus giving 500 slopes, r2 values, and RRD values for each simulation scenario).