Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty

Systematic Biology
Michael E Alfaro, John P Huelsenbeck

Abstract

Reversible-jump Markov chain Monte Carlo (RJ-MCMC) is a technique for simultaneously evaluating multiple related (but not necessarily nested) statistical models that has recently been applied to the problem of phylogenetic model selection. Here we use a simulation approach to assess the performance of this method and compare it to Akaike weights, a measure of model uncertainty that is based on the Akaike information criterion. Under conditions where the assumptions of the candidate models matched the generating conditions, both Bayesian and AIC-based methods perform well. The 95% credible interval contained the generating model close to 95% of the time. However, the size of the credible interval differed with the Bayesian credible set containing approximately 25% to 50% fewer models than an AIC-based credible interval. The posterior probability was a better indicator of the correct model than the Akaike weight when all assumptions were met but both measures performed similarly when some model assumptions were violated. Models in the Bayesian posterior distribution were also more similar to the generating model in their number of parameters and were less biased in their complexity. In contrast, Akaike-weighted models were more d...Continue Reading

References

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Oct 8, 2003·Systematic Biology·Vladimir MininJack Sullivan
Mar 23, 2004·Molecular Biology and Evolution·John P HuelsenbeckMichael E Alfaro

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Citations

Mar 6, 2008·Molecular Biology and Evolution·Bryan Kolaczkowski, Joseph W Thornton
Apr 10, 2008·Molecular Biology and Evolution·David Posada
Nov 2, 2007·BMC Evolutionary Biology·Yan ZhouHervé Philippe
Feb 16, 2008·Systematic Biology·Jennifer Ripplinger, Jack Sullivan
Jun 9, 2010·Systematic Biology·Kenneth G RossD DeWayne Shoemaker
Sep 13, 2007·Systematic Biology·Nicolas RodrigueNicolas Lartillot
Jul 27, 2007·Proteomics·Gil AlterovitzMarco F Ramoni
Oct 2, 2014·PloS One·Bastien BoussauJohn P Huelsenbeck
Apr 19, 2018·Genetics, Selection, Evolution : GSE·Gabriela Padilla-JacoboMaría G Zavala-Páramo
Oct 20, 2017·Nature Ecology & Evolution·Alex DornburgThomas J Near
Feb 6, 2017·BMC Bioinformatics·James C WilgenbuschKyle A Gallivan
Oct 20, 2006·Trends in Ecology & Evolution·Scot A Kelchner, Michael A Thomas
Sep 8, 2010·Molecular Phylogenetics and Evolution·Federico Plazzi, Marco Passamonti

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