Encyclopedia of Scientific Dating Methods

Living Edition
| Editors: W. Jack Rink, Jeroen Thompson

Molecular Clock Calibration

  • Rachel Warnock
Living reference work entry
DOI: https://doi.org/10.1007/978-94-007-6326-5_80-1



Molecular clock calibration. The temporal information used to calibrate the molecular clock and estimate the molecular substitution rate.

The Molecular Clock

Establishing an evolutionary timeline for the tree of life (TOL) is essential for understanding the history of biodiversity. The incompleteness of the rock and fossil record means this cannot be achieved using paleontological evidence alone. The molecular clock provides the only viable means of obtaining precise estimates of evolutionary time. The mutations that arise along a gene sequence represent copy errors that accumulate randomly over time. The differences observed between the genes of two living species are therefore a function of the time since they last shared a common ancestor. If the age of the last common ancestor can be determined from the fossil record for a pair of living species, the clock can be calibratedand the...


Fossil Record Molecular Clock Tectonic Event Living Species Fossil Specimen 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in to check access.


  1. Benton, M. J., and Donoghue, P. C., 2007. Paleontological evidence to date the tree of life. Molecular Biology and Evolution, 24, 26–53.CrossRefGoogle Scholar
  2. Benton, M. J., Wills, M. A., and Hitchin, R., 2000. Quality of the fossil record through time. Nature, 403, 534–537.CrossRefGoogle Scholar
  3. Benton, M. J., Dunhill, A. M., Lloyd, G. T., and Marx, F. G., 2011. Assessing the quality of the fossil record: insights from vertebrates. Geological Society, London, Special Publications, 358, 63–94.CrossRefGoogle Scholar
  4. Bromham, L., and Penny, D., 2003. The modern molecular clock. Nature Reviews Genetics, 4, 216–224.CrossRefGoogle Scholar
  5. Clarke, J. T., Warnock, R. C. M., and Donoghue, P. C., 2011. Establishing a time-scale for plant evolution. New Phytologist, 192, 266–301.CrossRefGoogle Scholar
  6. Donoghue, P. C., and Benton, M. J., 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends in Ecology and Evolution, 22, 424–431.CrossRefGoogle Scholar
  7. Donoghue, P. C., and Purnell, M. A., 2009. Distinguishing heat from light in debate over controversial fossils. Bioessays, 31, 178–189.CrossRefGoogle Scholar
  8. Drummond, A. J., and Rambaut, A., 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.CrossRefGoogle Scholar
  9. Drummond, A. J., and Suchard, M. A., 2010. Bayesian random local clocks, or one rate to rule them all. BMC Biology, 8, 114.CrossRefGoogle Scholar
  10. Drummond, A. J., Ho, S. Y. W., Phillips, M. J., and Rambaut, A., 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.CrossRefGoogle Scholar
  11. Dunhill, A. M., 2012. Problems with using rock outcrop area as a paleontological sampling proxy: rock outcrop and exposure area compared to coastal proximity, topography, land use and lithology. Paleobiology, 38, 840–857.CrossRefGoogle Scholar
  12. Foote, M., Hunter, J. P., Janis, C. M., and Sepkoski, J. J., 1999. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science, 283, 1310–1314.CrossRefGoogle Scholar
  13. Goswami, A., and Upchurch, P., 2010. The dating game: a reply to Heads (2010). Zoologica Scripta, 39, 406–409.CrossRefGoogle Scholar
  14. Hedges, S. B., and Kumar, S., 2003. Genomic clocks and evolutionary timescales. Trends in Genetics, 19, 200–206.CrossRefGoogle Scholar
  15. Hedman, M. M., 2010. Constraints on clade ages from fossil outgroups. Paleobiology, 36, 16–31.CrossRefGoogle Scholar
  16. Ho, S. Y. W., and Phillips, M. J., 2009. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology, 58, 367–380.CrossRefGoogle Scholar
  17. Holland, S. M., 1995. The stratigraphic distribution of fossils. Paleobiology, 21, 92–109.Google Scholar
  18. Holland, S. M., 2000. The quality of the fossil record: a sequence stratigraphic perspective. Paleobiology, 26, 148–168.CrossRefGoogle Scholar
  19. Inoue, J. G., Donoghue, P. C. J., and Yang, Z., 2010. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Systematic Biology, 59, 74–89.CrossRefGoogle Scholar
  20. Kishino, H., Thorne, J. L., and Bruno, W. J., 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution, 18, 352–361.CrossRefGoogle Scholar
  21. Kodandaramaiah, U., 2011. Tectonic calibrations in molecular dating. Current Zoology, 57, 116–124.Google Scholar
  22. Marshall, C. R., 1997. Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiology, 23, 165–173.Google Scholar
  23. Müller, J., and Reisz, R. R., 2005. Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates. Bioessays, 27, 1069–1075.CrossRefGoogle Scholar
  24. Parham, J. F., Donoghue, P. C. J., Bell, C. J., et al., 2012. Best practices for justifying fossil calibrations. Systematic Biology, 61, 346–359.CrossRefGoogle Scholar
  25. Peters, S. E., 2005. Geologic constraints on the macroevolutionary history of marine animals. Proceedings of the National Academy of Sciences, 102, 12326–12331.CrossRefGoogle Scholar
  26. Peters, S. E., and Foote, M., 2001. Biodiversity in the Phanerozoic: a reinterpretation. Paleobiology, 27, 583–601.CrossRefGoogle Scholar
  27. Pyron, R. A., 2011. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic Biology, 60, 466–481.CrossRefGoogle Scholar
  28. Rannala, B., and Yang, Z., 2007. Inferring speciation times under an episodic molecular clock. Systematic Biology, 56, 453–466.CrossRefGoogle Scholar
  29. Raup, D. M., 1972. Taxonomic diversity during the Phanerozoic. Science, 177, 1065–1071.CrossRefGoogle Scholar
  30. Reisz, R. R., and Müller, J., 2004. Molecular timescales and the fossil record: a paleontological perspective. Trends in Genetics, 20, 237–241.CrossRefGoogle Scholar
  31. Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., and Huelsenbeck, J. P., 2012a. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539–542.CrossRefGoogle Scholar
  32. Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., and Rasnitsyn, A. P., 2012b. A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera. Systematic Biology, 61, 973–999.CrossRefGoogle Scholar
  33. Rota-Stabelli, O., Daley, A. C., and Pisani, D., 2013. Molecular timetrees reveal a cambrian colonization of land and a new scenario for ecdysozoan evolution. Current Biology, 23, 392–398.CrossRefGoogle Scholar
  34. Sanderson, M. J., 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218–1231.CrossRefGoogle Scholar
  35. Sanderson, M. J., 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101–109.CrossRefGoogle Scholar
  36. Sansom, R., Gabbott, S., and Purnell, M., 2010. Non-random decay of chordate characters causes bias in fossil interpretation. Nature, 463, 797–800.CrossRefGoogle Scholar
  37. Smith, A. B., 2007. The shape of the Phanerozoic marine palaeodiversity curve: how much can be predicted from the sedimentary rock record of Western Europe? Palaeontology, 50, 765–774.CrossRefGoogle Scholar
  38. Smith, A. B., and McGowan, A. J., 2007. The shape of the Phanerozoic marine palaeodiversity curve: how much can be predicted from the sedimentary rock record of Western Europe? Palaeontology, 50, 765–774.CrossRefGoogle Scholar
  39. Strauss, D., and Sadler, P. M., 1989. Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology, 21, 411–427.CrossRefGoogle Scholar
  40. Tavaré, S., Marshall, C. R., Will, O., Soligo, C., and Martin, R. D., 2002. Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature, 416, 726–729.CrossRefGoogle Scholar
  41. Thorne, J. L., and Kishino, H., 2005. Estimation of divergence times from molecular sequence data. In Nielsen, R. (ed.), Statistical Methods in Molecular Evolution. New York: Springer, pp. 233–256.CrossRefGoogle Scholar
  42. Thorne, J. L., Kishino, H., and Painter, I. S., 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution, 15, 1647–1657.CrossRefGoogle Scholar
  43. Warnock, R. C. M., Yang, Z., Donoghue, P. C. J., 2012. Exploring uncertainty in the calibration of the molecular clock. Biology Letters, 8, 156–159.CrossRefGoogle Scholar
  44. Wilkinson, R. D., Steiper, M. E., Soligo, C., Martin, R. D., Yang, Z., and Tavaré, S., 2011. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Systematic Biology, 60, 16–31.CrossRefGoogle Scholar
  45. Yang, Z., and Rannala, B., 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution, 23, 212–226.CrossRefGoogle Scholar
  46. Zuckerkandl, E., and Pauling, L., 1962. Molecular disease, evolution and genetic heterogeneity. In Kasha, M., and Pullman, B. (eds.), Horizons in Biochemistry. New York: Academic, pp. 189–225.Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.School of Earth SciencesUniversity of BristolBristolUK