Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

Abstract

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).

Dispersals of Hyoscyameae and Mandragoreae (Solanaceae) from the New World to Eurasia in the early Miocene and their biogeographic diversification within Eurasia

“…Bayesian inference (Rannala and Yang, 1996) was conducted using MrBayes version 3.1.2 (Ronquist and Huelsenbeck, 2003) using the model estimated by Modeltest 3.7 (Posada and Buckley, 2004;Posada and Crandall, 1998). The Markov chain Monte Carlo (MCMC) algorithm was run for 2000,000 generations with four incrementally heated chains, starting from a random tree and sampling one out of every 100 generations.…”

Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes)

“…The maximum likelihood (ML) analysis as implemented in PAUP¤ 4.0b10 (SwoVord, 2002) with TBR branch swapping (10 random addition sequences). The best-Wtting nucleotide substitution model was selected by using Modeltest 3.7 (Posada and Crandall, 1998;Posada and Buckley, 2004). Bayesian inference of likelihood was implemented by using MrBayes version 3.1 (Ronquist and Huelsenbeck, 2003) with partitioned strategies.…”

Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology

“…We calculated the appropriate models of nucleotide substitution for each locus using Modeltest v3.7 (Posada and Crandall, 1998), and used the Akaike Information Criterion (AIC) to select the model of molecular evolution that best fit the data (Posada and Buckley, 2004). To test for saturation, we used PAUP v.…”