Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

Molecular Biology and Evolution

Volumn 23, Issue 1, 2006, Pages 212-226

  Yang, Ziheng ^a   Rannala, Bruce ^b  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bayesian method; Divergence times; MCMC; Molecular clock

Indexed keywords

ACCURACY; ALGORITHM; ANALYTICAL ERROR; ARTICLE; BAYES THEOREM; BIRTH; CALIBRATION; DEATH; FOSSIL; GENE LOCUS; GENE SEQUENCE; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MOLECULAR CLOCK; MONTE CARLO METHOD; PHYLOGENY; PRIMATE; PROBABILITY; RELIABILITY; SPECIES DIVERSITY; STATISTICAL ANALYSIS; TIME;

ANIMALS; BAYES THEOREM; CLASSIFICATION; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; FOSSILS; GENETIC SPECIATION; MODELS, GENETIC; PHYLOGENY; PRIMATES;

PRIMATES;

EID: 28944451210     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj024     Document Type: Article

References (35)

1. Aris-Brosou, S., and Z. Yang. 2002. The effects of models of rate evolution on estimation of divergence dates with a special reference to the metazoan 18S rRNA phylogeny. Syst. Biol. 51:703-714.
2. _. 2003. Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa. Mol. Biol. Evol. 20:1947-1954.
3. Brunet, M., F. Guy, D. Pilbeam et al. (37 co-authors). 2002. A new hominid from the upper Miocene of Chad, central Africa. Nature 418:145-151.
4. Cao, Y., A. Janke, P. J. Waddell, M. Westerman, O. Takenaka, S. Murata, N. Okada, S. Paabo, and M. Hasegawa. 1998. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47:307-322.
5. Cox, D. R., and D. V. Hinkley. 1974. Theoretical statistics. Chapman and Hall, London.
6. Delson, E., I. Tattersall, J. A. Van Couvering, and A. S. Brooks. ed. 2000. Encyclopedia of human evolution and prehistory. Garland, New York, pp. 166-171.
7. Drummond, A. J., G. K. Nicholls, A. G. Rodrigo, and W. Solomon. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
8. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
9. Graur, D., and W. Martin. 2004. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20:80-86.
10. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the humanape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
11. Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their application. Biometrika 57:97-109.
12. Hedges, S. B., and S. Kumar. 2004. Precision of molecular time estimates. Trends Genet. 20:242-247.
13. Ho, S. Y. W., M. J. Phillips, A. J. Drummond, and A. Cooper. 2005. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early Metazoan radiation. Mol. Biol. Evol. 22:1355-1363.
14. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
15. Kendall, D. G. 1948. On the generalized birth-and-death process. Ann. Math. Stat. 19:1-15.
16. 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.
17. Kumar, S. 1996. Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537-548.
18. Lindley, D. V. 1985. Making decisions. John Wiley, London.
19. 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.
20. Raaum, R. L., K. N. Sterner, C. M. Noviello, C. B. Stewart, and T. R. Disotell. 2005. Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J. Hum. Evol. 48:237-257.
21. Rambaut, A., and L. Bromham. 1998. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15:442-448.
22. Rannala, B., and Z. Yang. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
23. _. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656.
24. Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1232.
25. Steiper, M. E., N. M. Young, and T. Y. Sukarna. 2004. Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence. Proc. Natl. Acad. Sci. USA 101:17021-17026.
26. Suchard, M. A., R. E. Weiss, and J. S. Sinsheimer. 2003. Testing a molecular clock without an outgroup: derivations of induced priors on branch-length restrictions in a Bayesian framework. Syst. Biol. 52:48-54.
27. 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.
28. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
29. _. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
30. _. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556 (http://abacus.gene.ucl.ac.uk/ software/paml.html).
31. _. 2004. A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Acta Zool. Sin. 50:645-656.
32. Yang, Z., R. Nielsen, and M. Hasegawa. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611.
33. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
34. Yoder, A. D., and Z. Yang. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17:1081-1090.
35. 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.