© 2004 Society of Systematic Biologists
Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests
1 Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo Vigo 36200, Spain; E-mail: dposada{at}uvigo.es
2 Landcare Research Private Bag 92170, Auckland, New Zealand; E-mail: BuckleyT{at}LandcareResearch.co.nz
Edited by Jeffrey Thorne: Associate Editor
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Abstract |
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Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus (genus Carabus) ground beetles described by Sota and Vogler (2001).
Keywords: AIC; Bayes factors; BIC; likelihood ratio tests; model averaging; model uncertainty; model selection; multimodel inference
Received November 25, 2003; Revised January 29, 2004; Accepted June 10, 2004
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|
|
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|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
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|
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|
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|
|
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|
|
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|
|
|
|
|
|
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|
|
|
|
 |
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|
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|
|
|
|
|
|
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|
|
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|
|
|
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|
|
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G. Giribet, A. Okusu, A. R. Lindgren, S. W. Huff, M. Schrodl, and M. K. Nishiguchi Evidence for a clade composed of molluscs with serially repeated structures: Monoplacophorans are related to chitons PNAS, May 16, 2006; 103(20): 7723 - 7728. [Abstract] [Full Text] [PDF]
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 T. Vladusich, M. P. Lucassen, and F. W. Cornelissen Do Cortical Neurons Process Luminance or Contrast to Encode Surface Properties? J Neurophysiol, April 1, 2006; 95(4): 2638 - 2649. [Abstract] [Full Text] [PDF]
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C. Jridi, J.-F. Martin, V. Marie-Jeanne, G. Labonne, and S. Blanc Distinct Viral Populations Differentiate and Evolve Independently in a Single Perennial Host Plant J. Virol., March 1, 2006; 80(5): 2349 - 2357. [Abstract] [Full Text] [PDF]
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P. Catalan, J. G. Segarra-Moragues, M. Palop-Esteban, C. Moreno, and F. Gonzalez-Candelas A Bayesian Approach for Discriminating Among Alternative Inheritance Hypotheses in Plant Polyploids: The Allotetraploid Origin of Genus Borderea (Dioscoreaceae) Genetics, March 1, 2006; 172(3): 1939 - 1953. [Abstract] [Full Text] [PDF]
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S. A. Jansa, F. K. Barker, and L. R. Heaney The Pattern and Timing of Diversification of Philippine Endemic Rodents: Evidence from Mitochondrial and Nuclear Gene Sequences Syst Biol, February 1, 2006; 55(1): 73 - 88. [Abstract] [Full Text] [PDF]
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M. E. Alfaro and J. P. Huelsenbeck Comparative Performance of Bayesian and AIC-Based Measures of Phylogenetic Model Uncertainty Syst Biol, February 1, 2006; 55(1): 89 - 96. [Abstract] [Full Text] [PDF]
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B. Shapiro, A. Rambaut, and A. J. Drummond Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences Mol. Biol. Evol., January 1, 2006; 23(1): 7 - 9. [Abstract] [Full Text] [PDF]
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M. Perez-Losada, R. P. Viscidi, J. C. Demma, J. Zenilman, and K. A. Crandall Population Genetics of Neisseria gonorrhoeae in a High-Prevalence Community Using a Hypervariable Outer Membrane porB and 13 Slowly Evolving Housekeeping Genes Mol. Biol. Evol., September 1, 2005; 22(9): 1887 - 1902. [Abstract] [Full Text] [PDF]
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L. A. Real, J. C. Henderson, R. Biek, J. Snaman, T. L. Jack, J. E. Childs, E. Stahl, L. Waller, R. Tinline, and S. Nadin-Davis Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus PNAS, August 23, 2005; 102(34): 12107 - 12111. [Abstract] [Full Text] [PDF]
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Y.-x. Luan, J. M. Mallatt, R.-d. Xie, Y.-m. Yang, and W.-y. Yin The Phylogenetic Positions of Three Basal-Hexapod Groups (Protura, Diplura, and Collembola) Based on Ribosomal RNA Gene Sequences Mol. Biol. Evol., July 1, 2005; 22(7): 1579 - 1592. [Abstract] [Full Text] [PDF]
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F. Abascal, R. Zardoya, and D. Posada ProtTest: selection of best-fit models of protein evolution Bioinformatics, May 1, 2005; 21(9): 2104 - 2105. [Abstract] [Full Text] [PDF]
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D. Pol Empirical Problems of the Hierarchical Likelihood Ratio Test for Model Selection Syst Biol, December 1, 2004; 53(6): 949 - 962. [Abstract] [Full Text] [PDF]
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