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

Warnock RCM, Yang Z, Donoghue PCJ (2017)

Publication Type: Journal article

Publication year: 2017

Journal

Proceedings of the Royal Society of London, Series B: Biological Sciences Royal Society of London

Book Volume: 284

Article Number: 20170227

Journal Issue: 1857

DOI: 10.1098/rspb.2017.0227

Abstract

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.

Authors with CRIS profile

Rachel Warnock

Involved external institutions

University of Bristol GB United Kingdom (GB) University College London (UCL) GB United Kingdom (GB)

How to cite

APA:

Warnock, R.C.M., Yang, Z., & Donoghue, P.C.J. (2017). Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution. Proceedings of the Royal Society of London, Series B: Biological Sciences, 284(1857). https://doi.org/10.1098/rspb.2017.0227

MLA:

Warnock, Rachel C. M., Ziheng Yang, and Philip C. J. Donoghue. "Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution." Proceedings of the Royal Society of London, Series B: Biological Sciences 284.1857 (2017).

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