  Time-calibrated species phylogenies are critical for addressing a wide range
of questions in evolutionary biology, such as those that elucidate historical
biogeography or uncover patterns of coevolution and diversification. Because
molecular sequence data are not informative on absolute time, external data,
most commonly fossil age estimates, are required to calibrate estimates of
species divergence dates. For Bayesian divergence-time methods, the common
practice for calibration using fossil information involves placing arbitrarily
chosen parametric distributions on internal nodes, often disregarding most of
the information in the fossil record. We introduce the 'fossilized birth-death'
(FBD) process, a model for calibrating divergence-time estimates in a Bayesian
framework, explicitly acknowledging that extant species and fossils are part of
the same macroevolutionary process. Under this model, absolute node age
estimates are calibrated by a single diversification model and arbitrary
calibration densities are not necessary. Moreover, the FBD model allows for
inclusion of all available fossils. We performed analyses of simulated data and
show that node-age estimation under the FBD model results in robust and
accurate estimates of species divergence times with realistic measures of
statistical uncertainty, overcoming major limitations of standard divergence
time estimation methods. We then used this model to estimate the speciation
times for a dataset composed of all living bears, indicating that the genus
Ursus diversified in the late Miocene to mid Pliocene.
