期刊
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
卷 371, 期 1699, 页码 -出版社
ROYAL SOC
DOI: 10.1098/rstb.2015.0128
关键词
phylogeny; divergence time; molecular clock; time prior; Bayesian method; birth-death process
类别
资金
- Biotechnology and Biological Sciences Research Council (BBSRC, UK) [BB/J009709/1]
- BBSRC [BB/N000609/1, BB/J009709/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/N000609/1, BB/J009709/1] Funding Source: researchfish
Constructing a multi-dimensional prior on the times of divergence (the node ages) of species in a phylogeny is not a trivial task, in particular, if the prior density is the result of combining different sources of information such as a speciation process with fossil calibration densities. Yang & Rannala (2006 Mol. Biol. Evol. 23, 212-226. (doi:10.1093/molbev/msj024)) laid out the general approach to combine the birth-death process with arbitrary fossil-based densities to construct a prior on divergence times. They achieved this by calculating the density of node ages without calibrations conditioned on the ages of the calibrated nodes. Here, I show that the conditional density obtained by Yang & Rannala is misspecified. The misspecified density can sometimes be quite strange-looking and can lead to unintentionally informative priors on node ages without fossil calibrations. I derive the correct density and provide a few illustrative examples. Calculation of the density involves a sum over a large set of labelled histories, and so obtaining the density in a computer program seems hard at the moment. A general algorithm that may provide a way forward is given. This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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