Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

Rachel C.M. Warnock*, Ziheng Yang, Philip C.J. Donoghue

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

24 Citations (Scopus)
289 Downloads (Pure)


Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions.

Original languageEnglish
Article number20170227
Number of pages10
JournalProceedings of the Royal Society B: Biological Sciences
Issue number1857
Early online date21 Jun 2017
Publication statusPublished - 28 Jun 2017


  • Fossil record
  • Sampling bias
  • Bayesian phylogenetics
  • Molecular clock

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