Data from: Bayesian total-evidence dating reveals the recent crown radiation of penguins

The total-evidence approach to divergence time dating uses molecular and
morphological data from extant and fossil species to infer phylogenetic
relationships, species divergence times, and macroevolutionary parameters
in a single coherent framework. Current model-based implementations of
this approach lack an appropriate model for the tree describing the
diversification and fossilization process and can produce estimates that
lead to erroneous conclusions. We address this shortcoming by providing a
total-evidence method implemented in a Bayesian framework. This approach
uses a mechanistic tree prior to describe the underlying diversification
process that generated the tree of extant and fossil taxa. Previous
attempts to apply the total-evidence approach have used tree priors that
do not account for the possibility that fossil samples may be direct
ancestors of other samples, that is, ancestors of fossil or extant species
or of clades. The fossilized birth–death (FBD) process explicitly models
the diversification, fossilization, and sampling processes and naturally
allows for sampled ancestors. This model was recently applied to estimate
divergence times based on molecular data and fossil occurrence dates. We
incorporate the FBD model and a model of morphological trait evolution
into a Bayesian total-evidence approach to dating species phylogenies. We
apply this method to extant and fossil penguins and show that the modern
penguins radiated much more recently than has been previously estimated,
with the basal divergence in the crown clade occurring at ∼12.7∼12.7 Ma
and most splits leading to extant species occurring in the last 2 myr. Our
results demonstrate that including stem-fossil diversity can greatly
improve the estimates of the divergence times of crown taxa. The method is
available in BEAST2 (version 2.4) software www.beast2.org with packages SA
(version at least 1.1.4) and morph-models (version at least 1.0.4)
installed.