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

Figure 1

Example of tree simulated under mixture of three distinct evolutionary processes.

(A) Clade diversification under constant-rate “background” diversification process with λ = 0.032 and μ = 0. (B) Shift to new adaptive zone with subsequent diversity-dependent regulation of speciation and diversity-independent extinction (blue branches; λ0 = 0.395; K = 66; μ = 0.041). (C) Another lineage shifts to diversity-dependent speciation regime (red branches; λ0 = 0.21; K = 97; μ = 0.012). Total tree depth is 100 time units. Despite undergoing two distinct diversity-dependent slowdowns in the rate of speciation, the overall gamma statistic [63] for the tree is positive (γ = 2.51) and provides no evidence for changes in the rate of speciation through time. Note that a tree with three distinct processes contains two distinct transitions between processes.

Figure 1

doi: https://doi.org/10.1371/journal.pone.0089543.g001