Exploring uncertainty in the calibration of the molecular clock
Rachel C. M. Warnock1, Ziheng Yang2 and Philip C. J. Donoghue1,*
Author Affiliations
1School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
2Department of Biology, Galton Laboratory, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
*Author for correspondence (phil.donoghue@bristol.ac.uk)
Abstract
Calibration is a critical step in every molecular clock analysis but it has been the least considered. Bayesian approaches to divergence time estimation make it possible to incorporate the uncertainty in the degree to which fossil evidence approximates the true time of divergence. We explored the impact of different approaches in expressing this relationship, using arthropod phylogeny as an example for which we established novel calibrations. We demonstrate that the parameters distinguishing calibration densities have a major impact upon the prior and posterior of the divergence times, and it is critically important that users evaluate the joint prior distribution of divergence times used by their dating programmes. We illustrate a procedure for deriving calibration densities in Bayesian divergence dating through the use of soft maximum constraints.
molecular, clock calibration, fossil record, evolution, BEAST, MCMCTREE
Footnotes
One contribution of 12 to a Special Feature on ‘Models in palaeontology’.
Received July 12, 2011.
Accepted August 2, 2011.
This journal is © 2011 The Royal Society
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