Data for: Integrating fossils samples with heterogeneous diversification rates: a combined Multi-Type Fossilized Birth-Death model

Birth-death models are widely used to describe the diversification process
which leads to the observed species and phylogenies. When integrated into
Bayesian phylogenetic inference, birth-death models allow the joint
inference of the phylogeny and the diversification parameters from
molecular information. Two major classes of extensions of the birth-death
process are considered in this article. The first extends the phylogenetic
tree to include fossil samples alongside extant species, allowing the
inference to integrate information about the past diversity. This type of
inference uses either morphological or taxonomic information to place
fossils in the phylogeny. The second extension models diversification
rates which can vary between lineages, and is thus able to infer patterns
of variation in speciation or extinction rates. In this work, we combine
these two types of extension into a multi-type fossilized birth-death
(MTFBD) process, which can perform the joint inference of a phylogeny
including extinct and extant samples, and lineage-specific diversification
and fossil sampling rates in a Bayesian framework. The MTFBD model is
implemented as part of the phylogenetic inference framework BEAST2. Using
simulated and empirical datasets, we demonstrate the performance and
accuracy of the new model compared to a model with rate heterogeneity but
using only extant samples, and compared to a model without rate variation
including fossils. We demonstrate that including fossils improves the
accuracy of the phylogeny and diversification rates, especially extinction
rates, provided that the inference includes detailed morphological
information to accurately place the fossil samples. When this information
is not available however, MTFBD estimates are strongly driven by the
priors and are thus no better or even worse than estimates obtained only
with extant samples. With informative fossil characters, the MTFBD model
provides accurate phylogenies, and precisely characterizes how speciation,
extinction and fossil sampling rates vary as diversification proceeds.