Frequentist properties of bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models

Systematic Biology

Volumn 53, Issue 6, 2004, Pages 904-913

  Huelsenbeck, John P ^a   Rannala, Bruce ^b  

^a University of California San Diego   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; PHYLOGENY; THEORETICAL MODEL;

ANIMALS; BAYES THEOREM; MODELS, THEORETICAL; PHYLOGENY;

EID: 11144277878     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150490522629     Document Type: Article

References (50)

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. Bremer, K. 1988. The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
3. Bremer, K. 1994. Branch support and tree stability. Cladistics 10:295-304.
4. Burnham, K. P., and D. R. Anderson. 1998. Model selection and inference. Springer-Verlag, New York.
5. Castoe, T. A., T. M. Doan, and C. L. Parkinson. 2004.Data partitions and complex models in Bayesian analysis: The phylogeny of Gymnophthalmid lizards. Syst. Biol. 53:448-470.
6. 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.
7. DeBry, R. 2001. Improving interpretation of the decay index for DNA sequences. Syst. Biol. 50:742-752.
8. Douady, C. J., F. Delsuc, Y. Boucher, W. F. Doolittle, and E. J. P. Douzery. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20:248-254.
9. Efron, B. 1979. Bootstrap methods: Another look at the jackknife. Ann. Stat. 7:1-26.
10. Efron, B., E. Halloran, and S. Holmes. 1996. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. USA 93:13429-13434.
11. Efron, B., and R. Tibshirani. 1993. An introduction to the bootstrap. Chapman & Hall, London.
12. 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.
13. Faith, D. P. 1991. Cladistic permutation tests for monophyly and non-monophyly. Syst. Zool. 40:366-375.
14. Farris, J. S., V. A. Albert, M. Kallersjo, D. Lipscomb, and A. G. Kluge. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124.
15. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
16. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
17. Felsenstein, J. 2003. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
18. Felsenstein, J., and G. A. Churchill. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93-104.
19. Felsenstein, J., and H. Kishino. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42:193-200.
20. Goldman, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:725-736.
21. Hillis, D. M., and J. J. Bull. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
22. Holmes, S. 2003. Bootstrapping phylogenetic trees: Theory and methods. Stat. Sci. 2:241-255.
23. Huelsenbeck, J. P 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
24. Huelsenbeck, J. P., and D. M. Hillis. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-265.
25. Huelsenbeck, J. P., B. Larget, and M. E. Alfaro. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21:1123-1133.
26. Huelsenbeck, J. P., B. Larget, and D. L. Swofford. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879-1892.
27. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
28. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pages 21-123 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
29. Künsch, H. R. 1989. The jackknife and the bootstrap for general stationary observations. Ann. Stat. 17:1217-1241.
30. Larget, B., and D. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
31. Lemmon, A. R., and E. C. Moriarty. 2004. The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol. 53:265-277.
32. Lin, C. P., B. N. Danforth, and T. K. Wood. 2004. Molecular phylogenetics and evolution of maternal care in membracine treehoppers. Syst. Biol. 53:400-422.
33. Mueller, L. D., and F. J. Ayala. 1982. Estimation and interpretation of genetic distance in empirical studies. Genet. Res. Camb. 40:127-137.
34. Murphy, W. J., E. Eizirik, S. J. O'Brien, O. Madsen, M. Scally, C. Douady, E. C. Teeling, O. A. Ryder, M. Stanhope, W. W. De Jong, and M. S. Springer. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
35. Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53:47-68.
36. Rodrigo, A. 1993. Calibrating the bootstrap test of monophyly. Int. J. Parasitol. 23:507-514.
37. Sanderson, M. J., and M. F. Wojciechowski. 2000. Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Syst. Biol. 49:671-685.
38. Sullivan, J., and D. L. Swofford. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution patternare violated? Syst. Biol. 50:723-729.
39. Suzuki, Y., G. V. Glazko, and M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:15138-16143.
40. Swofford, D. L., J. L. Thorne, J. Felsenstein, and B. M. Wiegmann. 1996. The topology-dependent permutation test for monophyly does not test for monophyly. Syst. Biol. 45:575-579.
41. Tavaré, S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Pages 57-86 in Lectures in mathematics in the life sciences, vol. 17. American Mathematical Society.
42. Tuffley, C., and M. Steel. 1997. Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147:63-91.
43. Waddell, P. J., H. Kishino, and R. Ota. 2002. Very fast algorithms for evaluating the stabilityof ML and Bayesian phylogenetic trees from sequence data. Genome Informatics 13:82-92.
44. 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.
45. Yang, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
46. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
47. Yang, Z. 1995. A space-time process model for the evolution of DNA sequences. Genetics 139:993-1005.
48. Zharkikh, A., and W.-H. Li. 1992a. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol. Biol. Evol. 9:1119-1147.
49. Zharkikh, A., and W.-H. Li. 1992b. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. II. Four taxa without a molecular clock. J. Mol. Evol. 35:356-366.
50. Zharkikh, A., and W.-H. Li. 1995. Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4:44-63.