Estimating the rate of evolution of the rate of molecular evolution

Molecular Biology and Evolution

Volumn 15, Issue 12, 1998, Pages 1647-1657

  Thorne, Jeffrey L ^a   Kishino, Hirohisa ^b   Painter, Ian S ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Markov chain Monte Carlo; Metropolis Hastings algorithm; Molecular clock; Phylogeny

Indexed keywords

DNA;

ALGORITHM; ARTICLE; DNA SEQUENCE; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL;

EID: 0031741182     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025892     Document Type: Article

References (25)

1. ALLISON, L., and C. S. WALLACE. 1994. The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments. J. Mol. Evol. 39:418-430.
2. CARLIN, B. P., and T. A. LOUIS. 1996. Bayes and empirical Bayes methods for data analysis. Chapman and Hall, London.
3. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
4. GAUT, B. S., S. V. MUSE, W. D. CLARK, and M. T. CLEGG. 1992. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J. Mol. Evol. 35:292-303.
5. GELMAN, A., J. B. CARLIN, H. S. STERN, and D. B. RUBIN. 1995. Bayesian data analysis. Chapman and Hall, London.
6. GILLESPIE, J. H. 1991. The causes of molecular evolution. Oxford University Press, New York.
7. GOLDMAN, N., J. L. THORNE, and D. T. JONES. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458.
8. HASTINGS, W. K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
9. JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275-282.
10. JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-32 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
11. KARLIN, S., and H. M. TAYLOR. 1975. A first course in stochastic processes. 2nd edition. Academic Press, San Diego.
12. KIMURA, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England.
13. LANGLEY, C. H., and W. M. FITCH. 1974. An examination of the constancy of the rate of molecular evolution. J. Mol. Evol. 3:161-177.
14. MAU, B., and M. A. NEWTON. 1997. Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. J. Comput. Graph. Stat. 6:122-131.
15. METROPOLIS, N., A. W. ROSENBLUTH, M. N. ROSENBLUTH, A. H. TELLER, and E. TELLER. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21: 1087-1092.
16. OHTA, T. 1987. Very slightly deleterious mutations and the molecular clock. J. Mol. Evol. 26:1-6
17. PENNY, D., R. P. MURRAY-MCINTOSH, and M. D. HENDY. 1998. Estimating times of divergence with a change of rate: the orangutan/African ape divergence. Mol. Biol. Evol. 15:608-610.
18. RANNALA, B., and Z. YANG. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
19. SANDERSON, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1232.
20. STUART, A., and J. K. ORD. 1991. Kendall's advanced theory of statistics. Vol. 2, 5th edition. Oxford University Press, New York.
21. TAJIMA, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607.
22. 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.
23. YANG, Z. 1997. Phylogenetic analysis by maximum likelihood (PAML). Version 1.3. University of California, Berkeley.
24. YANG, Z., and B. RANNALA. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
25. ZUCKERKANDL, E., and L. PAULING. 1965. Evolutionary divergence and convergence in proteins. Pp. 97-166 in V. BRYSON and H. J. VOGEL, eds. Evolving genes and proteins. Academic Press, New York.