Bayesian model adequacy and choice in phylogenetics

J.P. Bollback, Molecular Biology and Evolution 19 (2002) 1171–80.

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Abstract
Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.
Publishing Year
Date Published
2002-03-25
Journal Title
Molecular Biology and Evolution
Volume
19
Issue
7
Page
1171 - 80
IST-REx-ID

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Bollback JP. Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. 2002;19(7):1171-1180.
Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution, 19(7), 1171–1180.
Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.” Molecular Biology and Evolution 19, no. 7 (2002): 1171–80.
J. P. Bollback, “Bayesian model adequacy and choice in phylogenetics,” Molecular Biology and Evolution, vol. 19, no. 7, pp. 1171–80, 2002.
Bollback JP. 2002. Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. 19(7), 1171–80.
Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.” Molecular Biology and Evolution, vol. 19, no. 7, Oxford University Press, 2002, pp. 1171–80.

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