Department of Integrative Biology, University of California, Berkeley, CA 94720;Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045;
Department of Integrative Biology, University of California, Berkeley, CA 94720;Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):E2957-66. doi: 10.1073/pnas.1319091111. Epub 2014 Jul 9.
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.
时间校准的物种系统发育对于解决进化生物学中的广泛问题至关重要，例如阐明历史生物地理学或揭示共同进化和多样化模式的问题。由于分子序列数据不能提供绝对时间的信息，因此需要外部数据（最常见的是化石年龄估计）来校准物种分歧日期的估计。对于贝叶斯分歧时间方法，使用化石信息进行校准的常见做法涉及在内部节点上任意选择参数分布，通常忽略化石记录中的大部分信息。我们引入了“化石出生-死亡”（FBD）过程——一种在贝叶斯框架下校准分歧时间估计的模型，明确承认现存物种和化石是同一宏观进化过程的一部分。在这个模型下，绝对节点年龄估计通过一个单一的多样化模型进行校准，不需要任意的校准密度。此外，FBD 模型允许包含所有可用的化石。我们对模拟数据进行了分析，结果表明，FBD 模型下的节点年龄估计产生了稳健而准确的物种分歧时间估计，具有现实的统计不确定性度量，克服了标准分歧时间估计方法的主要局限性。我们使用这个模型来估计一个由所有现存熊组成的数据集的物种形成时间，表明熊属在中新世晚期到中新世中期多样化。
