Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative

Systematic Biology

Volumn 55, Issue 4, 2006, Pages 539-552

  Anisimova, Maria ^a,b   Gascuel, Olivier ^a  

^a LIRMM   (France)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Accuracy; Branch support; Likelihood ratio test; Phylogeny reconstruction; Power

Indexed keywords

ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER SIMULATION; METHODOLOGY; PHYLOGENY; STATISTICAL MODEL;

CLASSIFICATION; COMPUTER SIMULATION; LIKELIHOOD FUNCTIONS; MODELS, STATISTICAL; PHYLOGENY;

EID: 33745256005     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150600755453     Document Type: Article

References (55)

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. Berry, V., and O. Gascuel. 1996. On the interpretation of bootstrap trees: Appropriate threshold of clade selection and induced gain. Mol. Biol. Evol. 13:999-1011.
3. Buckley, T. R., P. Arensburger, C. Simon, and G. K. Chambers. 2002. Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera. Syst. Biol. 51:4-18.
4. Chernoff, H. 1954. On the distribution of the likelihood ratio. Ann. Math. Stat. 25:573-578.
5. Cowries, M. K. and B. P. Carlin. 1996. Markov chain Monte Carlo convergence diagnostics: A comparative review. J. Am. Stat. Assoc. 91:883-904.
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. Desper, R., and O.Gascuel.2004. Theoretical foundationof the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21:587-598.
8. Douady, C. J., F. Delsuc, Y. Boucher, W. F. Doolittle, and E. J. Douzery. 2003a. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20:248-254.
9. Douady, C. J., M. Dosay M. S. Shivji, and M. J. Stanhope. 2003b. Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol. Phylogenet. Evol. 25:215-221.
10. Durbin, R., S. Eddy, A. Krogh, and G. Mitchison. 1998. Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge University Press, UK.
11. Efron, B., E. Halloran, and S. Holmes. 1996. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. USA 93:13429-13434.
12. Efron, B., and R. Tibshirani. 1993. An introduction to the bootstrap. Chapman and Hall, New York.
13. 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.
14. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
15. Felsenstein, J. 1985. Confidence intervals on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
16. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sanderland, Massachusetts.
17. 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.
18. Galtier, N. 2004. Sampling properties of the bootstrap support in molecular phylogeny: Influence of nonindependence among sites. Syst. Biol. 53:38-46.
19. Gaut, B. S., and P. O. Lewis. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 12:152-162.
20. Geyer, C. J. 1992. Practical Markov chain Monte Carlo. Stat. Sci. 7:473-483.
21. Goldman, N., and S. Whelan. 2000. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Mol. Biol. Evol. 17:975-978.
22. Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
23. 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.
24. Huelsenbeck, J., and B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53:904-913.
25. 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.
26. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
27. 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.
28. 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.
29. 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.
30. Lewis, P. O., M. T. Holder, and K. E. Holsinger. 2005. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54:241-253.
31. Li, S. 1996. Phylogenetic reconstruction using Markov chain Monte Carlo. Ph.D. dissertation. The Ohio State University, Columbus.
32. Mau, B., M. A. Newton, and B. Larget. 1997. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Mol. Biol. Evol. 14:717-724.
33. Miller, R. G. 1981. Simultaneous statistical inference. Springer-Verlag, New York.
34. Ota, R., P. J. Waddell, M. Hasegawa, H. Shimodaira, and H. Kishino. 2000. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Mol. Biol. Evol. 17:798-803.
35. Posada, D., and K. A. Crandall. 1998. ModelTest: Testing the model of DNA substitution. Bioinformatics. 14:817-818.
36. Posada, D., and K. A. Crandall. 2001. Selecting models of nucleotide substitution: An application to human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 18:897-906.
37. Rambaut, A., and N. C. Crassly. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
38. Rannala, B., and Z. Yang. 1996. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
39. Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
40. Sanderson, M. J. 1995. Objections to bootstrapping phylogenies: A critique. Syst. Biol. 44:299-320.
41. Self, S. G., and K.-Y. Liang. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J. Am. Stat. Assoc. 82:605-610.
42. Siddall, M. E. 2002. Measures of support. Pages 80-101 in Techniques in molecular systematics and evolution (R. DeSalle, G. Giribet, and W. Wheeler, eds.). Birkhäuser Verlag, Basel.
43. Simmons, M. P., K. M. Pickett, and M. Miya. 2004. How meaningful are Bayesian support values? Mol. Biol. Evol. 21:188-199.
44. Stuart, A., J. K. Ord, and S. Arnold. 1999. Kendall's advanced theory of statistics. Oxford University Press, New York.
45. 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 pattern are violated? Syst. Biol. 50:723-729.
46. Suzuki, Y., G. Glazko, and N. Masatoshi. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143.
47. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics (D. M. Hillis, C. Moritz, and B. K. Mable, eds.) Sinauer Associates, Sunderland, Massachusetts.
48. Tateno, Y., N. Takezaki, and M. Nei. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11:261-277.
49. Taylor, D. J. and W. H. Piel. 2004. An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data. Mol. Biol. Evol. 21:1534-1537.
50. Waddell, P. J., H. Kishino, and R. Ota. 2002. Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data. Genome Inform. Ser. Workshop Genome Inform. 13:82-92.
51. 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.
52. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
53. Yang, Z., R. Nielsen, N. Goldman, and A. M. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
54. Yang, Z., and B. Rannala. 2005. Branch-length prior influences bayesian posterior probability of phylogeny. Syst. Biol. 54:455-470.
55. Zharkikh, A., and W. H. Li. 1992. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock. J. Mol. Evol. 35:356-366.