Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny

Systematic Biology

Volumn 51, Issue 5, 2002, Pages 703-714

  Aris Brosou, Stéphane ^a   Yang, Ziheng ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

18S rRNA; Local molecular clocks; Markov chain Monte Carlo; Metazoa; Metropolis Hastings algorithm; Molecular clock; Ornstein Uhlenbeck process; Phylogeny; Posterior Bayes factor; Rate of evolution

Indexed keywords

RNA 18S;

ALGORITHM; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; CONFERENCE PAPER; EVOLUTION; GENETICS; INVERTEBRATE; MONTE CARLO METHOD; PHYLOGENY; STATISTICAL MODEL; TIME;

ALGORITHMS; ANIMALS; BAYES THEOREM; EVOLUTION; INVERTEBRATES; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY; RNA, RIBOSOMAL, 18S; TIME FACTORS;

ANIMALIA; HOMINOIDEA; INVERTEBRATA; METAZOA;

EID: 0036804729     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150290102375     Document Type: Conference Paper

References (40)

1. Aitkin, M. 1991. Posterior Bayes factor. J. R. Stat. Soc. B 53:111-142.
2. Ayala, F. J., A. Rzhetsky, and F. J. Ayala. 1998. Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates. Proc. Natl. Acad. Sci. USA 95:606-611.
3. Bickel, D. R. 2000. Implications of fluctuations in substitution rates: Impact on the uncertainty of branch lengths and on relative-rate tests. J. Mol. Evol. 50:381-390.
4. Bromham, L. D., and M. D. Hendy. 2000. Can fast early rates reconcile molecular dates with the Cambrian explosion? Proc. R. Soc. Lond. B Biol. Sci. 267:1041-1047.
5. Bromham, L., D. Penny, A. Rambaut, and M. D. Hendy. 2000. The power of relative rates tests depends on the data. J. Mol. Evol. 50:296-301.
6. Bromham, L., A. Rambaut, R. Fortey, A. Cooper, and D. Penny. 1998. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proc. Natl. Acad. Sci. USA 95:12386-12389.
7. Conway Morris, S. 1998. Metazoan phylogenies: Falling into place or falling to pieces? A palaeontological perspective. Curr. Opin. Genet. Dev. 8:662-667.
8. Cooper, A., and R. Fortey. 1998. Evolutionary explosions and the phylogenetic fuse. Trends Ecol. Evol. 13:151-156.
9. Cutler, D. J. 2000. Estimating divergence times in the presence of an overdispersed molecular clock. Mol. Biol. Evol. 17:1647-1660.
10. Felsenstein, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22:521-565.
11. Gilks, W. R., S. Richardson, and D. J. Spiegelhalter. 1996. Markov Chain Monte Carlo in Practice. Chapman & Hall, London.
12. Gill, P. E., W. Murray, and M. H. Wright. 1981. Practical Optimization. Academic Press, London.
13. Gillespie, J. H. 1991. The Causes of Molecular Evolution. Oxford Univ. Press, Oxford, U.K.
14. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
15. Hastings, W. K. 1970. Monte Carlo sampling using Markov chains and their applications. Biometrika 57:97-109.
16. Horai, S., Y. Satta, K. Hayasaka, R. Kondo, T. Inoue, T. Ishida, S. Hayashi, and N. Takahata. 1992. Man's place in Hominoidea revealed by mitochondrial DNA genealogy. J. Mol. Evol. 35:32-43.
17. Huelsenbeck, J. P., B. Larget, and D. L. Swofford. 2000. A compound poisson process for relaxing the molecular clock. Genetics 154:1879-1892.
18. Karlin, S., and H. M. Taylor. 1981. A Secondary Course in Stochastic Processes. Academic Press, New York.
19. Kass, R. E., and A. E. Raftery. 1995. Bayes factors. J. Am. Stat. Assoc. 90:773-795.
20. Kendall, D. G. 1948. On the generalized birth-and-death process. Ann. Math. Stat. 19:1-15.
21. Kishino, H., J. L. Thorne, and W. J. Bruno. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361.
22. Metropolis, N. A., A. W. Rosenbluth, N. M. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1091.
23. Nee, S., R. M. May, and P. H. Harvey. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B Biol. Sci. 344:305-311.
24. Nei, M., and S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford Univ. Press, Oxford, U.K.
25. Nielsen, C. 1995. Animal Evolution: Interrelationships of the Living Phyla. Oxford Univ. Press, Oxford, U.K.
26. Raftery, A. E. 1996. Hypothesis testing and model selection Pages 163-187 in Marko Chain Monte Carlo in Practice (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds.). Chapman & Hall, Boca Raton.
27. Raftery, A. E., and S. M. Lewis. 1996. Implementing MCMC. Pages 115-130 in Markov Chain Monte Carlo in Practice (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds.). Chapman & Hall, London.
28. Rambaut, A., and L. Bromham. 1998. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15:442-448.
29. Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1232.
30. Sarich, V. M., and A. C. Wilson. 1967. Immunological time scale for hominid evolution. Science 158:1200-1203.
31. Soltis, P. S., D. E. Soltis, V. Savolainen, P. R. Crane, and T. G. Barraclough. 2002. Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils. Proc. Natl. Acad. Sci. USA 99:4430-4435.
32. Takezaki, N., A. Rzhetsky, and M. Nei. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
33. Thompson, E. A. 1975. Human Evolutionary Trees. Cambridge Univ. Press, Cambridge, U.K.
34. Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
35. Valentine, J. W., D. H. Erwin, and D. Jablonski. 1996. Developmental evolution of metazoan body-plans: The fossil evidence. Dev. Biol. 173:373-381.
36. Wu, C. I., and W. H. Li. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745.
37. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
38. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
39. Yoder, A. D., and Z. Yang. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17:1081-1090.
40. Zuckerkandl, E., and L. Pauling. 1965. Evolutionary divergence and convergence in proteins. Pages 97-166 in Evolving Genes and Proteins (V. Bryson and H. J. Vogel, eds.). Academic Press, New York.