title: The fossilized birth-death process for coherent calibration of divergence-time estimates.
abstract: 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 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 Middle Pliocene.
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, CA 94720;Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045;
authors.forename: Tracy A
authors.initials: TA
authors.lastname: Heath
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, CA 94720;Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
authors.forename: John P
authors.initials: JP
authors.lastname: Huelsenbeck
authors.affiliation: Department of Environmental Systems Science, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland; andDepartment of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4058 Basel, Switzerland tanja.stadler@bsse.ethz.ch.
authors.forename: Tanja
authors.initials: T
authors.lastname: Stadler
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002138:Calibration; D003198:Computer Simulation; D053476:Extinction, Biological; D005580:Fossils; D008954:Models, Biological; D013997:Time Factors; D001503:Ursidae / Q000502:physiology
keywords: Bayesian divergence time estimation; MCMC; phylogenetics; relaxed clock; time tree