Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection

Thomas J. Near, Michael J. Sanderson

Research output: Contribution to journalArticlepeer-review

147 Scopus citations


Estimates of species divergence times using DNA sequence data are playing an increasingly important role in studies of evolution, ecology and biogeography. Most work has centred on obtaining appropriate kinds of data and developing optimal estimation procedures, whereas somewhat less attention has focused on the calibration of divergences using fossils. Case studies with multiple fossil calibration points provide important opportunities to examine the divergence time estimation problem in new ways. We discuss two cross-validation procedures that address different aspects of inference in divergence time estimation. 'Fossil cross-validation' is a procedure used to identify the impact of different individual calibrations on overall estimation. This can identify fossils that have an exceptionally large error effect and may warrant further scrutiny. 'Fossil-based model cross-validation' is an entirely different procedure that uses fossils to identify the optimal model of molecular evolution in the context of rate smoothing or other inference methods. Both procedures were applied to two recent studies: an analysis of monocot angiosperms with eight fossil calibrations and an analysis of placental mammals with nine fossil calibrations. In each case, fossil calibrations could be ranked from most to least influential, and in one of the two studies, the fossils provided decisive evidence about the optimal molecular evolutionary model.

Original languageEnglish (US)
Pages (from-to)1477-1483
Number of pages7
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Issue number1450
StatePublished - Oct 29 2004


  • Divergence time estimation
  • Fossil calibration
  • Molecular clock
  • Penalized likelihood

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)


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