Data and code from: Evaluating the impact and detectability of mass extinctions on total-evidence dating

Fossils are crucial for accurately dating phylogenetic trees because their
ages provide vital constraints on the timing of macroevolutionary events,
and their morphological characters offer key information on evolutionary
rates and phylogenetic positions. The fossilized birth-death (FBD) process
is a diversification model that incorporates both extant and extinct
species, serving as a tree prior that seamlessly integrates fossils into
phylogenetic inference. While the FBD model can account for mass
extinctions, which caused rapid, widespread organismal loss, few studies
have utilized FBD models incorporating these events in
phylogenetic inference. This is likely because the detectability of mass
extinctions and their impact on phylogenetic inference remain unclear.
Through simulations, we assessed the influence of mass extinctions on
divergence time and topology inference and evaluated the detectability of
mass extinction signals in total-evidence dating. We examined three FBD
tree priors: without mass extinction, with known mass extinction time and
survival probability, and with known mass extinction time but unknown
survival probability. Our results show that the FBD model with known mass
extinction time and unknown survival probability was able to reliably
detect mass extinctions when they occurred, and correctly refrained from
detecting mass extinctions when they were absent. Moreover, different FBD
models generate similar divergence time and tree topology errors. Even
when the FBD model used for tree inference did not explicitly account for
mass extinction events, signals of mass extinction were still detectable
on the resulting MCC trees. The accuracy of the detection was similar to
the one obtained from MCC trees inferred using an FBD model that includes
mass extinction parameters. We also reduced the fossilization rate and the
number of morphological characters, obtaining results consistent with the
aforementioned findings. However, reducing the fossilization rate
decreased the accuracy of detecting mass extinctions when they occurred,
and reducing the number of morphological characters decreased the accuracy
of divergence time inference. Furthermore, we adjusted the priors for the
existence of mass extinction and the survival probability of mass
extinction. We found that the prior for the existence of mass extinction
had no effect on inference, whereas the prior for the survival probability
of mass extinction significantly influenced both the detection of mass
extinctions and the estimation of survival probabilities. Finally, we
applied these models to empirical datasets of tetraodontiform fishes and
crinoids and found that, consistent with our simulation results, the
inclusion of a mass extinction event in the tree prior had a negligible
impact on the inferred topologies and divergence times.