Skip to main content

Estimation of Divergence Times from Molecular Sequence Data

  • Chapter
Statistical Methods in Molecular Evolution

Part of the book series: Statistics for Biology and Health ((SBH))

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. C. B. Anfinsen. The Molecular Basis of Evolution. John Wiley and Sons, Inc, New York, 1959.

    Google Scholar 

  2. S. Aris-Brosou and Z. Yang. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst. Biol., 51:703–714, 2002.

    Article  Google Scholar 

  3. S. Aris-Brosou and Z. Yang. Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa. Mol. Biol. Evol., 20:1947–1954, 2003.

    Google Scholar 

  4. D. J. Cutler. Estimating divergence times in the presence of an overdispersed molecular clock. Mol. Biol. Evol., 17:1647–1660, 2002.

    Google Scholar 

  5. A. Drummond, R. Forsberg, and A. G. Rodrigo. The inference of stepwise changes in substitution rates using serial sequence samples. Mol. Biol. Evol., 18:1365–1371, 2001.

    Google Scholar 

  6. A. Drummond and A. G. Rodrigo. Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial—sample UPGMA. Mol. Biol. Evol., 17:1807–1815, 2000.

    Google Scholar 

  7. A. J. Drummond, G. K. Nicholls, A. G. Rodrigo, and W. Solomon. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics, 161:1307–1320, 2002.

    Google Scholar 

  8. B. Efron and R. J. Tibshirani. An Introduction to the Bootstrap. Chapman and Hall, London, 1993.

    Google Scholar 

  9. J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol., 17:368–376, 1981.

    Article  Google Scholar 

  10. J. Felsenstein. Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39:783–791, 1985.

    Google Scholar 

  11. J. Felsenstein. Inferring Phylogenies. Sinauer Associates, Sunderland, MA, 2004.

    Google Scholar 

  12. J. H. Gillespie. The Causes of Molecular Evolution. Oxford University Press, New York, 1991.

    Google Scholar 

  13. M. Hasegawa, H. Kishino, and T. Yano. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22:160–174, 1985.

    Google Scholar 

  14. W. K. Hastings. Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57:97–109, 1970.

    MATH  Google Scholar 

  15. J. P. Huelsenbeck, B. Larget, and D. L. Swofford. A compound Poisson process for relaxing the molecular clock. Genetics, 154:1879–1892, 2000.

    Google Scholar 

  16. J. P. Huelsenbeck and B. Rannala. Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology, 23:174–180, 1997.

    Google Scholar 

  17. J. L. Jensen and A.-M. K. Pedersen. Probabilistic models of DNA sequence evolution with context dependent rates of substitution. Adv. Appl. Prob., 32:499–517, 2000.

    MathSciNet  Google Scholar 

  18. T. H. Jukes and C. R. Cantor. Evolution of protein molecules. In H. N. Munro, editor, Mammalian Protein Metabolism. Academic Press, New York, 1969.

    Google Scholar 

  19. H. Kishino and M. Hasegawa. Converting distance to time: An application to human evolution. Methods Enzymol., 183:550–570, 1990.

    Google Scholar 

  20. H. Kishino, J. L. Thorne, and W. J. Bruno. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol., 18:352–361, 2001.

    Google Scholar 

  21. B. Korber, M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinsky, and T. Bhattacharya. Timing the ancestor of the HIV-1 pandemic strains. Science, 288:1789–1796, 2000.

    Article  Google Scholar 

  22. C. H. Langley and W. M. Fitch. An examination of the constancy of the rate of molecular evolution. J. Mol. Evol., 3:161–177, 1974.

    Article  Google Scholar 

  23. T. Leitner and J. Albert. The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc. Natl. Acad. Sci. USA, 96:10752–10757, 1999.

    Article  Google Scholar 

  24. W.-H. Li, M. Tanimura, and P. M. Sharpi. Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol., 5:313–330, 1988.

    Google Scholar 

  25. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. Equations of state calculations by fast computing machines. J. Chem. Phys., 21:1087–1092, 1953.

    Article  Google Scholar 

  26. A. M. Mood, F. A. Graybill, and D. C. Boes. Introduction to the theory of statistics. McGraw-Hill, New York, 3rd edition, 1974.

    Google Scholar 

  27. S. V. Muse and B. S. Weir. Testing for equality of evolutionary rates. Genetics, 132:269–276, 1992.

    Google Scholar 

  28. T. Ohta. Population size and rate of evolution. J. Mol. Evol., 1:305–314, 1972.

    Google Scholar 

  29. A.-M. K. Pedersen and J. L. Jensen. A dependent-rates model and an MCMC-based methodology for the maximum likelihood analysis of sequences with overlapping reading frames. Mol. Biol. Evol., 18:763–776, 2001.

    Google Scholar 

  30. A. Rambaut. Estimating the rate of molecular evolution: Incorporating non—contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics, 16:395–399, 2000.

    Article  Google Scholar 

  31. A. Rambaut and L. Bromham. Estimating divergence dates from molecular sequences. Mol. Biol. Evol., 15:442–448, 1998.

    Google Scholar 

  32. D. M. Robinson, D. T. Jones, H. Kishino, N. Goldman, and J. L. Thorne. Protein evolution with dependence among codons due to tertiary structure. Mol. Biol. Evol., 20:1692–1704, 2003.

    Google Scholar 

  33. M. J. Sanderson. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol., 14:1218–1232, 1997.

    Google Scholar 

  34. M. J. Sanderson. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol., 19:101–109, 2002.

    Google Scholar 

  35. M. J. Sanderson. R8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19:301–302, 2003.

    Article  Google Scholar 

  36. T.-K. Seo, H. Kishino, and J. L. Thorne. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol. Biol. Evol., 21(7):1201–1213, 2004.

    Google Scholar 

  37. T.-K. Seo, J. L. Thorne, M. Hasegawa, and H. Kishino. Estimation of effective population size of HIV-1 within a host: A pseudomaximum-likelihood approach. Genetics, 160:1283–1293, 2002.

    Google Scholar 

  38. T.-K. Seo, J. L. Thorne, M. Hasegawa, and H. Kishino. A viral sampling design for estimating evolutionary rates and divergence times. Bioinformatics, 18:115–123, 2002.

    Article  Google Scholar 

  39. M. S. Springer, W. J. Murphy, E. Eizirik, and S. J. O O’Brien. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. USA, 100:1056–1061, 2003.

    Google Scholar 

  40. A. Stuart and J. K. Ord. Kendall’s Advanced Theory of Statistics, volume 2. Oxford University Press, Oxford, 5th edition, 1991.

    Google Scholar 

  41. D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis. Phylogenetic inference. In D. M. Hillis, C. Moritz, and B. K. Mable, editors, Molecular Systematics. Sinauer Associates, Sunderland, MA, 2nd edition, 1996.

    Google Scholar 

  42. F. Tajima. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics, 135:599–607, 1993.

    Google Scholar 

  43. S. Tavaré, C. R. Marshall, O. Will, C. Soligo, and R. D. Martin. Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature, 416:726–729, 2002.

    Google Scholar 

  44. J. L. Thorne and H. Kishino. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol., 51:689–702.

    Google Scholar 

  45. J. L. Thorne, H. Kishino, and I. S. Painter. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol., 15:1647–1657, 1998.

    Google Scholar 

  46. M. K. Uyenoyama. A generalized least—squares estimate for the origin of sporophytic self-incompatibility. Genetics, 139:975–992, 1995.

    Google Scholar 

  47. P. J. Waddell and D. Penny. Evolutionary trees of apes and humans from DNA sequences. In Handbook of Human Symbolic Evolution. Oxford University Press, Oxford, Englan, 1996.

    Google Scholar 

  48. C.-I. Wu and W.-H. Li. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA, 82:1741–1745, 1985.

    Google Scholar 

  49. Z. H. Yang and A. D. Yoder. Comparison of likelihood and bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol., 52:705–716, 2003.

    Article  Google Scholar 

  50. A. D. Yoder and Z. H. Yang. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol., 17:1081–1090, 2000.

    Google Scholar 

  51. Q. Zheng. On the dispersion index of a Markovian molecular clock. Math. Biosc., 172:115–128, 2001.

    Article  MATH  Google Scholar 

  52. E. Zuckerkandl and L. Pauling. Molecular disease, evolution, and genic heterogeneity. In M. Kasha and B. Pullman, editors, Horizons in Biochemistry: Albert Szent-Györgyi Dedicatory Volume. Academic Press, New York, 1962.

    Google Scholar 

  53. E. Zuckerkandl and L. Pauling. Evolutionary divergence and convergence in proteins. In V. Bryson and H. J. Vogel, editors, Evolving Genes and Proteins. Academic Press, New York, 1965.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer Science+Business Media, Inc.

About this chapter

Cite this chapter

Thorne, J.L., Kishino, H. (2005). Estimation of Divergence Times from Molecular Sequence Data. In: Statistical Methods in Molecular Evolution. Statistics for Biology and Health. Springer, New York, NY. https://doi.org/10.1007/0-387-27733-1_8

Download citation

Publish with us

Policies and ethics