Inferring the Dynamics of Diversification: A Coalescent Approach
Phylogenies simulated under a model with saturated diversity and a constant turnover rate (Model 1) have short terminal branches compared to phylogenies simulated under the pure-birth process (Yule model; Model 5). With saturated diversity but decaying turnover rates, terminal branches become longer (Model 2). Compared to the pure-birth process (Model 5), the presence of extinction pushes phylogenetic nodes towards the tips (Model 3), whereas a decay in speciation rate pushes them towards the root (Model 6). In the presence of both extinction and a decay in speciation rate (Model 4), however, these two effects counteract, producing a phylogeny that appears similar to the pure-birth model. All phylogenies were simulated with the same initial speciation rate (six speciation events per time unit). The extinction rate in Models 3 and 4a was identical (three speciation events per time unit). The exponential variation in speciation rate in Models 2, 4a, and 6 was identical (0.25 per time unit). Note the different time scales.