Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies

Identifying along which lineages shifts in diversification rates occur is
a central goal of comparative phylogenetics; these shifts may coincide
with key evolutionary events such as the development of novel
morphological characters, the acquisition of adaptive traits,
polyploidization or other structural genomic changes, or dispersal to a
new habitat and subsequent increase in environmental niche space. However,
while multiple methods now exist to estimate diversification rates and
identify shifts using phylogenetic topologies, the appropriate use and
accuracy of these methods is hotly debated. Here we test whether five
Bayesian methods—Bayesian Analysis of Macroevolutionary Mixtures (BAMM),
two implementations of the Lineage-Specific Birth-Death-Shift model (LSBDS
and PESTO), the approximate Multi-Type Birth-Death model (MTBD;
implemented in BEAST2), and the cladogenetic diversification rate shift
model (CLaDS2)—produce comparable results. We apply each of these methods
to a set of 65 empirical time-calibrated phylogenies and compare
inferences of speciation rate, extinction rate, and net diversification
rate. We find that the five methods often infer different speciation,
extinction, and net-diversification rates. Consequently, these different
estimates may lead to different interpretations of the macroevolutionary
dynamics. The different estimates can be attributed to fundamental
differences among the compared models. Therefore, the inference of shifts
in diversification rates is strongly method-dependent. We advise
biologists to apply multiple methods to test the robustness of the
conclusions or to carefully select the method based on the validity of the
underlying model assumptions to their particular empirical system.