Are unequal clade priors problematic for Bayesian phylogenetics?

Systematic Biology

Volumn 55, Issue 1, 2006, Pages 138-146

  Brandley, Matthew ^a   Leaché, Adam ^a   Warren, Dan ^b   McGuire, Jimmy ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; METHODOLOGY; PHYLOGENY; SHORT SURVEY;

BAYES THEOREM; CLASSIFICATION; COMPUTER SIMULATION; MODELS, BIOLOGICAL; PHYLOGENY;

EID: 33644589951     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150500431155     Document Type: Short Survey

References (23)

1. Alfaro, M. E., S. Zoller, and F. Lutzoni. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20:255-266.
2. Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas, and K. Winka. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 52:477-487.
3. Douady C. J., F. Delsuc, Y. Boucher, W. Doolittle, and E. J. P. Douzery. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20:248-254.
4. Erixon, P., B. Svennblad, T. Britton, and B. Oxelman. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52:665-673.
5. Felsentstein, J. 1968. Statistical inference and the estimation of phylogenies. Ph.D. Dissertation, University of Chicago, Chicago.
6. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: Maximum likelihood approach. J. Mol. Evol. 17:368-376.
7. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts, U.S.A.
8. Goloboff, P. A., and D. Pol. 2005. Parsimony and Bayesian phylogenetics. Pages 148-162 in Parsimony, phylogeny, and genomics (V. A. Albert, ed.). Oxford University Press, Oxford, United Kingdom.
9. Huelsenbeck, J. P., and N. S. Imennov. 2002. Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison. Syst. Biol. 51:155-165.
10. Huelsenbeck, J. P., and B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53:904-910.
11. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
12. Kass, R. E., and L. Wasserman. 1996. The selection of prior distributions by formal rules. J. Am. Stat. Assoc. 91:1343-1370.
13. Lemmon, A. R., and E. C. Moriarty. 2004. The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol. 53:265-277.
14. Lewis, P. O. 2001a. Phylogenetic systematics turns over a new leaf. Trends Ecol. Evol. 16:30-37.
15. Lewis, P. O. 2001b. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913-925.
16. Lewis, P. O., M. T. Holder, and K. E. Holsinger. 2005. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54:241-253.
17. Pickett, K. M., and C. P. Randle. 2005. Strange bayes indeed: Uniform topological prior simply non-uniform clade priors. Mol. Phylogenet. Evol. 34:203-211.
18. Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
19. Suzuki, Y., G. V., Glazko, and M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Nat. Acad. Sci. USA 99:16138-16143.
20. Tuffley, C., and M. Steel. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull. Math. Biol. 59:581-607.
21. Warren, D. L., J. Wilgenbusch, and D. L. Swofford. 2003. Converge: A program for implementing MCMC convergence diagnostics. Available from the authors at danwarren@ucdavis.edu.
22. Wilcox, T. P., D. J. Zwickl, T. A. Heath, and D. M. Hillis. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25:361-371.
23. Zwickl, D. J., and M. T. Holder. 2004. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53:877-888.