"The fossilized birth–death process for coherent calibration of divergence-time estimates" by Tracy A. Heath

Selected Works of Tracy Heath

Article

The fossilized birth–death process for coherent calibration of divergence-time estimates

Proceedings of the National Academy of Sciences of the United States of America (2014)

Tracy A. Heath, University of California, Berkeley
John P. Huelsenbeck, University of California, Berkeley
Tanja Stadler, Eidgenössische Technische Hochschule Zürich

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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.

Keywords

Phylogenetics,
Bayesian divergence time estimation,
Relaxed clock,
MCMC,
Time tree

Disciplines

Integrative Biology and
Evolution

Publication Date

July 22, 2014

DOI

10.1073/pnas.1319091111

Citation Information

Tracy A. Heath, John P. Huelsenbeck and Tanja Stadler. "The fossilized birth–death process for coherent calibration of divergence-time estimates" Proceedings of the National Academy of Sciences of the United States of America Vol. 111 Iss. 29 (2014) p. E2957 - E2966
Available at: http://works.bepress.com/tracy-heath/3/