Performance of criteria for selecting evolutionary models in phylogenetics: A comprehensive study based on simulated datasets

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Luo, Arong ^a,b   Qiao, Huijie ^a,b   Zhang, Yanzhou ^a   Shi, Weifeng ^c   Ho, Simon Yw ^d,e   Xu, Weijun ^f   Zhang, Aibing ^g   Zhu, Chaodong ^a  

^a INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY COLLEGE DUBLIN   (Ireland)

^d AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^e UNIVERSITY OF SYDNEY   (Australia)

^f NANJING NORMAL UNIVERSITY   (China)

^g CAPITAL NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AKAIKE INFORMATION CRITERION; BAYESIAN ANALYSIS; DATA SET; EVOLUTIONARY BIOLOGY; MAXIMUM LIKELIHOOD ANALYSIS; MODEL TEST; PHYLOGENETICS; STATISTICAL APPLICATION;

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

BAYES THEOREM; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY;

EID: 77955290199     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-242     Document Type: Article

References (67)

1. Bayesian model adequacy and choice in phylogenetics. JP Bollback, Mol Biol Evol 2002 19 1171 1180 12082136
2. The importance of proper model assumption in Bayesian phylogenetics. AR Lemmon EC Moriarty, Syst Biol 2004 53 265 277 10.1080/10635150490423520 15205052
3. Performance-based selection of likelihood models for phylogeny estimation. V Minin Z Abdo P Joyce J Sullivan, Syst Biol 2003 52 674 683 10.1080/10635150390235494 14530134
4. Does choice in model selection affect maximum likelihood analysis? J Ripplinger J Sullivan, Syst Biol 2008 57 76 85 10.1080/10635150801898920 18275003
5. Parsimony, likelihood, and the role of models in molecular phylogenetics. M Steel D Penny, Mol Biol Evol 2000 17 839 850 10833190
6. Model selection in phylogenetics. J Sullivan P Joyce, Annu Rev Ecol Evol Syst 2005 36 445 466 10.1146/annurev.ecolsys.36.102003.152633
7. Science and statistics. GEP Box, J Am Stat Assoc 1976 71 791 799 10.2307/2286841
8. Selecting the best-fit model of nucleotide substitution. D Posada KA Crandall, Syst Biol 2001 50 580 601 10.1080/106351501750435121 12116655
9. Bayesian phylogenetic model selection using reversible jump Markov Chain Monte Carlo. JP Huelsenbeck B Larget ME Alfaro, Mol Biol Evol 2004 21 1123 1133 10.1093/molbev/msh123 15034130
10. A codon-based model of nucleotide substitution for protein-coding DNA sequences. N Goldman Z Yang, Mol Biol Evol 1994 11 725 736 7968486
11. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. SV Muse BS Gaut, Mol Biol Evol 1994 11 715 724 7968485
12. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. M Pagel A Meade, Syst Biol 2004 53 571 581 10.1080/10635150490522232 15371247
13. A hidden markov model approach to variation among sites in rate of evolution. J Felsenstein GA Churchill, Mol Biol Evol 1996 13 93 104 8583911
14. Modeling compositional heterogeneity. PG Foster, Syst Biol 2004 53 485 495 10.1080/10635150490445779 15503675
15. Heterotachy, an important process of protein evolution. P Lopez D Casane H Philippe, Mol Biol Evol 2002 19 1 7 11752184
16. Modeling the covarion hypothesis of nucleotide substitution. C Tuffley M Steel, Math Biosci 1998 147 63 91 10.1016/S0025-5564(97)00081-3 9401352
17. ModelTest: Testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953
18. jModelTest: phylogenetic model averaging. D Posada, Mol Biol Evol 2008 25 1253 1256 10.1093/molbev/msn083 18397919
19. Selection of models of DNA evolution with jModelTest. D Posada, Bioinformatics for DNA sequence analysis New York: Humama Press, Posada D, 2009 93 112 full-text
20. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. B Shapiro A Rambaut AJ Drummond, Mol Biol Evol 2006 23 7 9 10.1093/molbev/msj021 16177232
21. Tracing the decay of the historical signal in biological sequence data. SY Ho L Jermiin, Syst Biol 2004 53 623 637 10.1080/10635150490503035 15371250
22. Cases in which parsimony or compatibility methods will be positively misleading. J Felsenstein, Syst Zool 1978 27 401 410 10.2307/2412923
23. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J Sullivan DL Swofford, J Mammal Evol 1997 4 77 86 10.1023/A:1027314112438
24. Evolution of the mitochondrial cytochrome oxidase II gene in Collembola. F Frati C Simon J Sullivan DL Swofford, J Mol Evol 1997 44 145 158 10.1007/PL00006131 9069175
25. Phylogeny estimation and hypothesis testing using maximum likelihood. JP Huelsenbeck KA Crandall, Annu Rev Ecol Syst 1997 28 437 466 10.1146/annurev. ecolsys.28.1.437
26. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. J Sullivan JA Markert CW Kilpatrick, Syst Biol 1997 46 426 440 11975329
27. Information theory and an extension of the maximum likelihood principle. H Akaike, Proceedings of the Second International Symposium on Information Theory Budapest: Akademiai Kiado, Petrov BN, Csaki F, 1973 267 281
28. Phylogeny and molecular evolution in primates. M Hasegawa, Jpn J Genet 1990 65 243 266 10.1266/jjg.65.243 2223159
29. Bayes factors. RE Kass AE Raftery, J Am Stat Assoc 1995 90 773 795 10.2307/2291091
30. Computing Bayes factors using thermodynamic integration. N Lartillot H Philippe, Syst Biol 2006 55 195 207 10.1080/10635150500433722 16522570
31. Bayesian selection of continuous-time Markov chain evolutionary models. MA Suchard RE Weiss JS Sinsheimer, Mol Biol Evol 2001 18 1001 1013 11371589
32. Estimation the dimension of a model. G Schwarz, Ann Stat 1978 6 461 464 10.1214/aos/1176344136
33. Hypothesis testing and model selection. AE Raftery, Markov Chain Monte Carlo in Practice London: Chapman & Hall, Gilks WR, Richardson S, Spiegelhalter DJ, 1996 163 187
34. Bayesian model selection and model averaging. L Wasserman, J Math Psychol 2000 44 92 107 10.1006/jmps.1999.1278 10733859
35. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. N Lartillot H Brinkmann H Philippe, BMC Evol Biol 2007 7 4 10.1186/1471-2148-7-S1-S4 17288577
36. Model selection for probabilistic clustering using cross-validated likelihood. P Smyth, Stat Comput 2000 10 63 72 10.1023/A:1008940618127
37. Best-fit maximum-likelihood models for phylogenetic inference: empirical tests with known phylogenies. CW Cunningham H Zhu DM Hillis, Evolution 1998 52 978 987 10.2307/2411230
38. Empirical problems of the hierarchical likelihood ratio test for model selection. D Pol, Syst Biol 2004 53 949 962 10.1080/10635150490888868 15764562
39. Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation. Z Abdo VN Minin P Joyce J Sullivan, Mol Biol Evol 2005 22 691 703 10.1093/molbev/msi050 15548751
40. KP Burnham DA Anderson, Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach New York: Springer-Verlag 2 2002
41. Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty. ME Alfaro JP Huelsenbeck, Syst Biol 2006 55 89 96 10.1080/10635150500433565 16507526
42. PE Greenwood MS Nikulin, A Guide to Chi-Squared Testing New York: Wiley-Interscience 1996
43. 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? J Sullivan DJ Swofford, Syst Biol 2001 50 723 729 10.1080/106351501753328848 12116942
44. How often do wrong models produce better phylogenies? Z Yang, Mol Biol Evol 1997 14 105 108 9000758
45. Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris zone. ME Siddall, Cladistics 1998 14 209 220 10.1111/j.1096-0031.1998.tb00334.x
46. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. A Rambaut NC Grassly, Comput Appl Biosci 1997 13 235 238 9183526
47. Mesquite: a modular system for evolutionary analysis, version 2.6. WP Maddison DR Maddision, 2009 http://mesquiteproject.org
48. Statistical tests of models of DNA substitution. N Goldman, J Mol Evol 1993 36 182 198 10.1007/BF00166252 7679448
49. Molecular phylogenetics: state-of-the-art methods for looking into the past. S Whelan P Lio N Goldman, Trends Genet 2001 17 262 272 10.1016/S0168-9525(01)02272-7 11335036
50. Phylogenetic relationships of the North American chorus frogs (Pseudacris: Hylidae). EC Moriarty DC Cannatella, Mol Phylogenet Evol 2004 30 409 420 10.1016/S1055-7903(03)00186-6 14715232
51. PAML: a program package for phylogenetic analysis by maximum likelihood. Z Yang, Comput Appl Biosci 1997 13 555 556 9367129
52. PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.0 b 10. DL Swofford, Sunderland, MA: Sinauer Associates 2002
53. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. DP Posada TR Buckley, Syst Biol 2004 53 793 808 10.1080/10635150490522304 15545256
54. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. N Goldman S Whelan, Mol Biol Evol 2000 17 975 978 10833204
55. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. R Ota PJ Waddell M Hasegawa H Shimodaira H Kishino, Mol Biol Evol 2000 17 798 803 10779540
56. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. SG Self KY Liang, J Am Stat Assoc 1987 82 605 610 10.2307/2289471
57. On information and sufficiency. S Kullback RA Leibler, Ann Math Stat 1951 22 79 86 10.1214/aoms/1177729694
58. Multimodel inference: understanding AIC and BIC in model selection. KP Burnham DA Anderson, Sociol Methods Res 2004 33 261 304 10.1177/0049124104268644
59. Cluster analysis. J Han M Kamber, Data Mining: Concepts and Techniques. Chapter 8 San Francisco: Morgan Kaufmann, Han J, Kamber M, 1 2000 196 220
60. Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. M Arenas D Posada, BMC Bioinformatics 2007 8 458 10.1186/1471-2105-8-458 18028540
61. Evolution of protein molecules. TH Jukes CR Cantor, Mammalian Protein Metabolism New York: Academic Press, Munro HM, 1969 21 123
62. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. M Kimura, J Mol Evol 1980 16 111 120 10.1007/BF01731581 7463489
63. Estimation of evolutionary distances between nucleotide sequences. A Zharkikh, J Mol Evol 1994 9 315 329 10.1007/BF00160155
64. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Felsenstein, J Mol Evol 1981 17 368 376 10.1007/BF01734359 7288891
65. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. M Hasegawa H Kishino T Yano, J Mol Evol 1985 22 160 174 10.1007/BF02101694 3934395
66. A new molecular clock of mitochondrial DNA and the evolution of hominoids. M Hasegawa T Yano H Kishino, Proc Jpn Acad Ser B Phys Biol Sci 1984 60 95 98 10.2183/pjab.60.95
67. Some probabilistic and statistical problems in the analysis of DNA sequences. S Tavaré Lect Math Life Sci 1986 17 57 86