Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics

Systematic Biology

Volumn 52, Issue 5, 2003, Pages 665-673

  Erixon, Per ^a   Svennblad, Bodil ^b   Britton, Tom ^b   Oxelman, Bengt ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Bayesian inference; Bootstrap; Model misspecification; Phylogeny; Posterior probability; Simulations; Support; True sampling

Indexed keywords

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; COMPUTER SIMULATION; PHYLOGENY; REPRODUCIBILITY; STATISTICAL MODEL;

BAYES THEOREM; COMPUTER SIMULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; REPRODUCIBILITY OF RESULTS;

EID: 0242487486     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150390235485     Document Type: Article

References (30)

1. AGRESTI, A. 1990. Categorical data analysis. Wiley-Interscience, New York.
2. ALFARO, M. E., S. ZOLLER, AND F. LUTZONI. 2003. Bayes or bootstrap? A aimulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20:255-266.
3. BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
4. BREMER, K. 1994. Branch support and tree stability. Cladistics 10:295-304.
5. 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.
6. 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.
7. DURBIN, R., S. EDDY, A. KROGH, AND G. MITCHISON. 1998. Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge Univ. Press, Cambridge, U.K.
8. EFRON, B., E. HALLORAN, AND S. HOLMES. 1996. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Scei. USA 93:7085-7090.
9. FARRIS, J. S., V. A. ALBERT, M. KÄLLERSJÖ, D. LIPSCOMB, AND A. G. KLUGE. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124.
10. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
11. HEDGES, S. B. 1992. The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. Mol. Biol. Evol. 9:366-369.
12. 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.
13. HUELSENBECK, J. P., B. LARGET, R. E. MILLER, AND F. RONQUIST. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51:673-688.
14. HUELSENBECK, J. P., AND F. RONQUIST. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
15. HUELSENBECK, J. P., F. RONQUIST, R. NIELSEN, AND J. P. BOLLBACK. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
16. KAROL, K. G., R. M. MCCOURT, M. T. CIMINO, AND C. F. DELWICHE. 2001. The closest living relatives of land plants. Science 294:2351-2353.
17. LARGET, B., AND D. L. SIMON. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
18. LEACHÉ, A. D., AND T. W. REEDER. 2002. Molecular systematics of the eastern fence lizard Sceloporus undulatus: A comparison of parsimony, likelihood, and Bayesian approaches. Syst. Biol. 51:44-68.
19. MURPHY, W. J., E. EIZIRIK, SJ. O'BRIEN, O. MADSEN, M. SCALLY, C. J. DOUADY, E. TEELING, O. A. RYDER, M. J. STANHOPE, W. W. DE JONG, AND M.S. SPRINGER. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
20. OXELMAN, B., M. BACKLUND, AND B. BREMER. 1999. Relationships of the Buddlejaceae s.l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF and rbcL sequence data. Syst. Bot. 24:164-182.
21. PENNY, D., M. D. HENDY, AND M. A. STEEL. 1992. Progress with methods for constructing evolutionary trees. Trends Ecol. Evol. 7:73-79.
22. 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.
23. RANNALA, B., AND Z. YANG .1996. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
24. SANDERSON, M. J. 1989. Confidence limits on phylogenies: The bootstrap revisited. Cladistics 5:113-129.
25. SUZUKI, Y., G. V. GLAZKO, AND M. NEI. 2002. Overcredibility of molecular phylogenetics obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143.
26. SWOFFORD, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer, Sunderland, Massachusetts.
27. WHITTINGHAM, L. A., B. SLIKAS, D. W. WINKLER, AND F. H. SHELDON. 2002. Phylogeny of the tree swallow genus Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences. Mol. Phylogenet. Evol. 22:430-441.
28. YANG, Z. 1997. How often do wrong models produce better phylogenies? Mol. Biol. Evol. 14:105-108.
29. YANG, Z., AND B. RANNALA. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
30. ZHARKIKH, A., AND W.-H. LI. 1992. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol. Biol. Evol. 9:1119-1147.