Identifiability of parameters in MCMC Bayesian inference of phylogeny

Systematic Biology

Volumn 51, Issue 5, 2002, Pages 754-760

  Rannala, Bruce ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Bayesian phylogenetic inference; Markov chain Monte Carlo; Overparameterization; Parameter id entifiability

Indexed keywords

ALGORITHM; BAYES THEOREM; BIOLOGICAL MODEL; CONFERENCE PAPER; EVOLUTION; MOLECULAR EVOLUTION; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; TIME;

ALGORITHMS; BAYES THEOREM; EVOLUTION; EVOLUTION, MOLECULAR; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY; TIME FACTORS;

EID: 0036803348     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150290102429     Document Type: Conference Paper

References (13)

1. Carlin, B. P., and T. A. Louis. 1996. Bayes and Empirical Bayes Methods for Data Analysis. Chapman and Hall, New York.
2. Casella, G., and R. Berger. 1990. Statistical Inference. Duxbury Press, Belmont, California.
3. Gilks, W. R., S. Richardson, and D. J. Spiegelhalter. 1996. Introducing Markov chain Monte Carlo. Pages 1-16 in Markov Chain Monte Carlo in Practice (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds.). Chapman and Hall, New York.
4. Gillespie, J. H. 1984. The molecular clock may be an episodic clock. Proc. Natl. Acad. Sci. USA 81:8009-8013.
5. Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-101.
6. Huelsenbeck, J. P., B. Larget, and D. Swofford. 2000. A compound poisson process for relaxing the molecular clock. Genetics 154:1879-1892.
7. 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.
8. Mau, B., M. A. Newton, and B. Larget. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1-12.
9. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equations of state calculation by fast computing machine. J. Chem. Phys. 21:1087-1091.
10. Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1232.
11. Shoemaker, J. S., I. S. Painter, and B. S. Weir. 1999. Bayesian statistics in genetics: A guide for the uninitiated. Trends Genet. 15:354-358.
12. 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.
13. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.