Data from: Inferring diversification rate variation from phylogenies with fossils

Time-calibrated phylogenies of living species have been widely used to
study the tempo and mode of species diversification. However, it is
increasingly clear that inferences about species diversification —
extinction rates in particular — can be unreliable in the absence of
paleontological data. We introduce a general framework based on the
fossilized birth-death process for studying speciation-extinction dynamics
on phylogenies of extant and extinct species. Our model assumes that
phylogenies can be modeled as a mixture of distinct evolutionary rate
regimes and that a hierarchical Poisson process governs the number of such
rate regimes across a tree. We implemented the model in BAMM, a
computational framework that uses reversible jump Markov chain Monte Carlo
to simulate a posterior distribution of macroevolutionary rate regimes
conditional on the branching times and topology of a phylogeny. The
implementation we describe can be applied to paleontological phylogenies,
neontological phylogenies, and to phylogenies that include both extant and
extinct taxa. We evaluate performance of the model on datasets simulated
under a range of diversification scenarios. We find that speciation rates
are reliably inferred in the absence of paleontological data. However, the
inclusion of fossil observations substantially increases the accuracy of
extinction rate estimates. We demonstrate that the inferences are
relatively robust to at least some violations of model assumptions,
including heterogeneity in preservation rates and misspecification of the
number of occurrences in paleontological datasets.