Empirical evaluation of a prior for Bayesian phylogenetic inference

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 363, Issue 1512, 2008, Pages 4031-4039

  Yang, Ziheng ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Bayesian inference; Clade probabilities; Prior; Species sampling; Substitution model

Indexed keywords

BAYESIAN ANALYSIS; CLADISTICS; COMPARATIVE STUDY; MODELING; PHYLOGENY;

CETACEA; MYSTICETI;

EID: 57149088633     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2008.0164     Document Type: Article

References (46)

1. Bourlat, S. J. et al. 2006 Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85-88.
2. Buckley, T. R. 2002 Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51, 509-523.
3. Cummings, M. P., Handley, S. A., Myers, D. S., Reed, D. L., Rokas, A. & Winka, K. 2003 Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 52, 477-487.
4. Dawid, A. P. 1999 The trouble with Bayes factors. Research report 202, Department of Statistical Science, University College London.
5. Douady, C. J., Delsuc, F., Boucher, Y., Doolittle, W. F. & Douzery, E. J. 2003 Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20, 248-254.
6. Erixon, P., Svennblad, B., Britton, T. & Oxelman, B. 2003 Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52, 665-673.
7. Felsenstein, J. 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
8. Goldman, N. & Yang, Z. 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725-736.
9. Goldman, N., Anderson, J. P. & Rodrigo, A. G. 2000 Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49, 652-670.
10. Green, P. J. 1995 Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82, 711-732.
11. Guindon, S. & Gascuel, O. 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704.
12. Hasegawa, M., Kishino, H. & Yano, T. 1985 Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
13. Holder, M. T., Lewis, P. O., Swofford, D. L. & Larget, B. 2005 Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics. Syst. Biol. 54, 961-965.
14. Huelsenbeck, J. P. & Rannala, B. 2004 Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53, 904-913.
15. Huelsenbeck, J. P. & Ronquist, F. 2001 MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
16. Jukes, T. H. & Cantor, C. R. 1969 Evolution of protein molecules. In Mammalian protein metabolism (ed. H. N. Munro), pp. 21-123. New York, NY: Academic Press.
17. Kishino, H. & Hasegawa, M. 1989 Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29, 170-179.
18. Lemmon, A. R. & Moriarty, E. C. 2004 The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol. 53, 265-277.
19. Lewis, P. O., Holder, M. T. & Holsinger, K. E. 2005 Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54, 241-253.
20. Li, S., Pearl, D. & Doss, H. 2000 Phylogenetic tree reconstruction using Markov chain Monte Carlo. J. Am. Stat. Assoc. 95, 493-508.
21. Lindley, D. V. 1957 A statistical paradox. Biometrika 44, 187-192.
22. Mau, B. & Newton, M. A. 1997 Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. J. Comput. Graph. Stat. 6, 122-131.
23. O'Hagan, A. & Forster, J. 2004 Kendall's advanced theory of statistics: Bayesian inference. London, UK: Arnold.
24. Rannala, B. & Yang, Z. 1996 Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304-311.
25. Rannala, B. & Yang, Z. 2003 Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164, 1645-1656.
26. Rannala, B. & Yang, Z. 2008 Phylogenetic inference using whole genomes. Annu. Rev. Genom. Hum. Genet. 9, 217-231
27. Ronquist, F. & Huelsenbeck, J. P. 2003 MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
28. Sasaki, T. et al. 2005 Mitochondrial phylogenetics and evolution of mysticete whales. Syst. Biol. 54, 77-90.
29. Shimodaira, H. & Hasegawa, M. 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
30. Simmons, M. P., Pickett, K. M. & Miya, M. 2004 How meaningful are Bayesian support values? Mol. Biol. Evol. 21, 188-199.
31. Stamatakis, A., Ludwig, T. & Meier, H. 2005 RAXML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21, 456-463.
32. Steel, M. & Matsen, F. A. 2007 The Bayesian "star paradox" persists for long finite sequences. Mol. Biol. Evol. 24, 1075-1079.
33. Susko, E. 2008 On the distributions of bootstrap support and posterior distributions for a star tree. Syst. Biol. 57, 602-612.
34. Suzuki, Y., Glazko, G. V. & Nei, M. 2002 Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl Acad. Sci. USA 99, 16 138-16 143.
35. Takahata, N. 1989 Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122, 957-966.
36. Wheeler, W. C. & Pickett, K. M. 2008 Topology-Bayes versus clade-Bayes in phylogenetic analysis. Mol. Biol. Evol. 25, 447-453.
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. 1995 A space-time process model for the evolution of DNA sequences. Genetics 139, 993-1005.
39. Yang, Z. 1996 Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42, 587-596.
40. Yang, Z. 2006 Computational molecular evolution. Oxford, UK: Oxford University Press.
41. Yang, Z. 2007a Fair-balance paradox, star-tree paradox and Bayesian phylogenetics. Mol. Biol. Evol. 24, 1639-1655.
42. Yang, Z. 2007b PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591.
43. Yang, Z. & Rannala, B. 1997 Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14, 717-724.
44. Yang, Z. & Rannala, B. 2005 Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol. 54, 455-470.
45. Yang, Z., Goldman, N. & Friday, A. 1994 Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11, 316-324.
46. Yang, Z., Nielsen, R. & Hasegawa, M. 1998 Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15, 1600-1611.