title: Posterior predictive Bayesian phylogenetic model selection.
abstract: We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand-Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior predictive variance (GGp) and goodness-of-fit (GGg), which distinguishes this method from the posterior predictive P-value approach. The conditional predictive ordinate (CPO) method provides a site-specific measure of model fit useful for exploratory analyses and can be combined over sites yielding the log pseudomarginal likelihood (LPML) which is useful as an overall measure of model fit. CPO provides a useful cross-validation approach that is computationally efficient, requiring only a sample from the posterior distribution (no additional simulation is required). Both GG and CPO add new perspectives to Bayesian phylogenetic model selection based on the predictive abilities of models and complement the perspective provided by the marginal likelihood (including Bayes Factor comparisons) based solely on the fit of competing models to observed data.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA; AbbVie, 1 N. Waukegan Road, R436/AP9A-2, North Chicago, IL 60064, USA; Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA; and Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
authors.forename: Paul O
authors.initials: PO
authors.lastname: Lewis
authors.forename: Wangang
authors.initials: W
authors.lastname: Xie
authors.forename: Ming-Hui
authors.initials: MH
authors.lastname: Chen
authors.forename: Yu
authors.initials: Y
authors.lastname: Fan
authors.forename: Lynn
authors.initials: L
authors.lastname: Kuo
mesh_terms: D000460:Chlorophyta / Q000235:genetics; D002965:Classification / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics; D019684:Magnoliopsida / Q000235:genetics; D008954:Models, Biological; D010802:Phylogeny
chemical_list: D018744:DNA, Plant