Long-branch attraction bias and inconsistency in bayesian phylogenetics

PLoS ONE

Volumn 4, Issue 12, 2009, Pages

  Kolaczkowski, Bryan ^a   Thornton, Joseph W ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; BAYES THEOREM; CONTROLLED STUDY; DATA ANALYSIS; LONG BRANCH ATTRACTION; MATHEMATICAL ANALYSIS; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; PHYLOGENETIC TREE; PHYLOGENY; PROBABILITY; RELIABILITY; SEQUENCE ANALYSIS; SIMULATION;

BAYES THEOREM; BIAS (EPIDEMIOLOGY); COMPUTER SIMULATION; DATABASES, GENETIC; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY;

EID: 77949525939     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007891     Document Type: Article

References (58)

1. Hillis D (1997) Biology recapitulates phylogeny. Science 276: 218-219
2. Yang Z, Rannala B (1997) Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol Biol Evol 14: 717-724
3. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314
4. Huelsenbeck JP, Larget B, Miller RE, Ronquist F (2002) Potential applications and pitfalls of bayesian inference of phylogeny. Syst Biol 51: 673-688
5. Karol KG, McCourt RM, Cimino MT, Delwiche CF (2001) The closest living relatives of land plants. Science 294: 2351-2353
6. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, et al. (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351
7. Kuhner MK, Felsenstein J (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 11: 459-468
8. Bruno WJ, Halpern AL (1999) Topological bias and inconsistency of maximum likelihood using wrong models. Mol Biol Evol 16: 564-566
9. Rogers JS (1997) On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences. Syst Biol 46: 354-357
10. Holder M, Lewis PO (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat Rev Genet 4: 275-284
11. Yang Z (2005) Bayesian inference in molecular phylogenetics. In: Gascuel O, ed. Mathematics of Evolution and Phylogeny, Oxford University Press. pp 63-90
12. Alfaro M, Holder M (2006) The posterior and the prior in Bayesian phylogenetics. Annu Rev Ecol Syst 37: 19-42
13. Felsenstein J (2004) Inferring Phylogenies. Sinauer Associates, Inc.
14. Lewis P (2001) Phylogenetic systematics turns over a new leaf. Trends Ecol Evol 16: 30-37
15. Penny D, Hendy MD, Steel MA (1992) Progress with evolutionary tree methods. Trends Ecol Evol 7: 73-79
16. Chang JT (1996) Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Mathematical Biosciences 134: 189-215
17. Rogers JS (2001) Maximum likelihood estimation of phylogenetic trees is consistent when substitution rates vary according to the invariable sites plus gamma distribution. Systematic Biology 50: 713-722
18. Spencer M, Susko E, Roger AJ (2005) Likelihood, parsimony, and heterogeneous evolution. Mol Biol Evol 22: 1161-1164
19. Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: 401-410
20. Kolaczkowski B, Thornton JW (2006) Is there a star tree paradox? Mol Biol Evol 23: 1819-1823
21. Huelsenbeck JP, Hillis DM (1993) Success of phylogenetic methods in the fourtaxon case. Syst Biol 42: 247-264
22. Huelsenbeck JP (1995) The performance of phylogenetic methods in simulation. Syst Biol 17: 17-48
23. Kolaczkowski B, Thornton JW (2004) Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431: 980-984
24. Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, et al. (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol 50: 525-539
25. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
26. Hillis DM, Huelsenbeck JP, Swofford DL (1994) Hobgoblin of phylogenetics? Nature 369: 363-364
27. Hillis DM (1996) Inferring complex phylogenies. Nature 383: 130-131
28. Lemmon AR, Moriarty EC (2004) The importance of proper model assumption in Bayesian phylogenetics. Syst Biol 53: 265-277
29. Huelsenbeck JP, Rannala B (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol 53: 904-913
30. Lewis PO, Holder MT, Holsinger KE (2005) Polytomies and Bayesian phylogenetic inference. Syst Biol 54: 241-253
31. Yang Z, Rannala B (2005) Branch-length prior influences Bayesian posterior probability of phylogeny. Syst Biol 54: 455-470
32. Kolaczkowski B, Thornton JW (2007) Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses. Mol Biol Evol 24: 2108-2118
33. Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42: 182-192
34. Suzuki Y, Glazko GV, Nei M (2002) Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci USA 99: 16138-16143
35. Alfaro ME, Zoller S, Lutzoni F (2003) Bayes or bootstrap? a simulation study comparing the performance of bayesian markov chain monte carlo sampling and bootstrapping in assessing phylogenetic confidence. Molecular Biology and Evolution 20: 255-266
36. Cummings MP, Handley SA, Myers DS, Reed DL, Rokas A, et al. (2003) Comparing bootstrap and posterior probability values in the four-taxon case. Systematic Biology 52: 477-487
37. Erixon P, Svennbald B, Britton T, Oxelman B (2003) Reliability of bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Systematic Biology 52: 665-673
38. Misawa K, Nei M (2003) Reanalysis of murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. Journal of Molecular Evolution 57: S290-S296.
39. Simmons MP, Pickett KM, Miya M (2004) How meaningful are bayesian support values? Molecular Biology and Evolution 21: 188-199
40. Taylor DJ, Piel WH (2004) An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data. Molecular Biology and Evolution 21: 1534-1537
41. Susko E (2008) On the distributions of bootstrap support and posterior distributions for a star tree. Syst Biol 57: 602-612
42. Carlin BP, Louis TA (2000) Bayes and Empirical Bayes Methods for Data Analysis. Chapman and Hall.
43. Ronquist F, Huelsenbeck J (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574
44. Lopez P, Casane D, Philippe H (2002) Heterotachy, an important process of protein evolution. Mol Biol Evol 19: 1-7
45. Inagaki Y, Susko E, Fast NM, Roger AJ (2004) Covarion shifts cause a longbranch attraction artifact that unites microsporidia and archaebacteria in EF1alpha phylogenies. Mol Biol Evol 21: 1340-1349
46. Brinkmann H, van der Giezen M, Zhou Y, de Raucourt GP, Philippe H (2005) An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol 54: 743-757
47. Kolaczkowski B, Thornton J (2008) A mixed branch length model of heterotachy improves phylogenetic accuracy. Mol Biol Evol 25: 1054-1066
48. Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375
49. Anderson FE, Swofford DL (2004) Should we be worried about long-branch attraction in real data sets? investigations using metazoan 18S rDNA. Mol Phylogenet Evol 33: 440-451
50. Bergsten J (2005) A review of long-branch attraction. Cladistics 21: 163-193
51. Mossel E, Vigoda E (2005) Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309: 2207-2209
52. Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 55: 539-552
53. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-90
54. Edwards AWF (1992) Likelihood. Johns Hopkins University Press.
55. Jeffrey RC (2004) Subjective Probability: The Real Thing. Cambridge University Press.
56. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704
57. Pagel M, Meade A (2004) A phylogenetic mixture model for detecting patternheterogeneity in gene sequence or character-state data. Syst Biol 53: 571-581
58. Akaike H (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19: 716-723.