Empirical and methodological challenges to the model-based inference of diversification rates in extinct clades

Changes in speciation and extinction rates are key to the dynamics of
clade diversification, but attempts to infer them from phylogenies of
extant species face challenges. Methods capable of synthesizing
information from extant and fossil species have yielded novel insights
into diversification rate variation through time, but little is known
about their behavior when analyzing entirely extinct clades. Here, we use
empirical and simulated data to assess how two popular methods, PyRate and
Fossil BAMM, perform in this setting. We inferred the first tip-dated
trees for ornithischian dinosaurs, and combined them with fossil
occurrence data to test whether the clade underwent an end-Cretaceous
decline. We then simulated phylogenies and fossil records under empirical
constraints to determine whether macroevolutionary and preservation rates
can be teased apart under paleobiologically realistic conditions. We
obtained discordant inferences about ornithischian macroevolution
including a long-term speciation rate decline (BAMM), mostly flat rates
with (PyRate) or without (BAMM) a steep diversification drop, and episodes
of implausibly accelerated speciation and extinction (PyRate). Simulations
revealed little to no conflation between speciation and preservation, but
yielded spuriously correlated speciation and extinction estimates while
time-smearing tree-wide shifts (BAMM) or overestimating their number
(PyRate). Our results indicate that the small phylogenetic
datasets available to vertebrate paleontologists and the assumptions
made by current model-based methods combine to hinder inferences
about the diversification of extinct clades. We provide
guidelines for interpreting the results of the existing approaches
in light of their limitations, and suggest how the latter may be
mitigated.