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Philos Trans R Soc Lond B Biol Sci. 2004 Oct 29; 359(1450): 1477–1483.
PMCID: PMC1693436

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


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.

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Selected References

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  • Benton Michael J, Ayala Francisco J. Dating the tree of life. Science. 2003 Jun 13;300(5626):1698–1700. [PubMed]
  • Bremer K. Early Cretaceous lineages of monocot flowering plants. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4707–4711. [PMC free article] [PubMed]
  • Britten RJ. Rates of DNA sequence evolution differ between taxonomic groups. Science. 1986 Mar 21;231(4744):1393–1398. [PubMed]
  • Bromham Lindell, Penny David. The modern molecular clock. Nat Rev Genet. 2003 Mar;4(3):216–224. [PubMed]
  • Conti Elena, Eriksson Torsten, Schönenberger Jürg, Sytsma Kenneth J, Baum David A. Early Tertiary out-of-India dispersal of Crypteroniaceae: evidence from phylogeny and molecular dating. Evolution. 2002 Oct;56(10):1931–1942. [PubMed]
  • Graur Dan, Martin William. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 2004 Feb;20(2):80–86. [PubMed]
  • Gray Russell D, Atkinson Quentin D. Language-tree divergence times support the Anatolian theory of Indo-European origin. Nature. 2003 Nov 27;426(6965):435–439. [PubMed]
  • Hedges SB, Parker PH, Sibley CG, Kumar S. Continental breakup and the ordinal diversification of birds and mammals. Nature. 1996 May 16;381(6579):226–229. [PubMed]
  • Huelsenbeck JP, Larget B, Swofford D. A compound poisson process for relaxing the molecular clock. Genetics. 2000 Apr;154(4):1879–1892. [PMC free article] [PubMed]
  • Lee MS. Molecular clock calibrations and metazoan divergence dates. J Mol Evol. 1999 Sep;49(3):385–391. [PubMed]
  • Magallón S, Sanderson MJ. Absolute diversification rates in angiosperm clades. Evolution. 2001 Sep;55(9):1762–1780. [PubMed]
  • Marshall CR. The fossil record and estimating divergence times between lineages: maximum divergence times and the importance of reliable phylogenies. J Mol Evol. 1990 May;30(5):400–408. [PubMed]
  • Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348–2351. [PubMed]
  • Sanderson Michael J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol. 2002 Jan;19(1):101–109. [PubMed]
  • Sanderson Michael J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics. 2003 Jan 22;19(2):301–302. [PubMed]
  • Shaul Shaul, Graur Dan. Playing chicken (Gallus gallus): methodological inconsistencies of molecular divergence date estimates due to secondary calibration points. Gene. 2002 Oct 30;300(1-2):59–61. [PubMed]
  • Soltis Pamela S, Soltis Douglas E, Savolainen Vincent, Crane Peter R, Barraclough Timothy G. Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4430–4435. [PMC free article] [PubMed]
  • Springer Mark S, Murphy William J, Eizirik Eduardo, O'Brien Stephen J. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1056–1061. [PMC free article] [PubMed]
  • Takezaki N, Rzhetsky A, Nei M. Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol. 1995 Sep;12(5):823–833. [PubMed]
  • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. [PMC free article] [PubMed]
  • Thorne JL, Kishino H, Painter IS. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol. 1998 Dec;15(12):1647–1657. [PubMed]
  • van Tuinen Marcel, Dyke Gareth J. Calibration of galliform molecular clocks using multiple fossils and genetic partitions. Mol Phylogenet Evol. 2004 Jan;30(1):74–86. [PubMed]
  • Yoder AD, Yang Z. Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol. 2000 Jul;17(7):1081–1090. [PubMed]

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