Results 1  10
of
203
Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests
, 2004
"... 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 sel ..."
Abstract

Cited by 407 (8 self)
 Add to MetaCart
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 (modelaveraged 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 AICbased model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus (genus Carabus) ground beetles described by Sota and Vogler (2001).
A review of longbranch attraction
 CLADISTICS
, 2005
"... The history of longbranch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBAartifacts include excluding longbranch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LB ..."
Abstract

Cited by 137 (1 self)
 Add to MetaCart
The history of longbranch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBAartifacts include excluding longbranch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, longbranch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall wasps are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major
H: Computing Bayes factors using thermodynamic integration
 Syst Biol
"... Abstract.—In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the numerical evaluation of marginal likelihoods has often been performed using the harmonic mean ..."
Abstract

Cited by 112 (7 self)
 Add to MetaCart
(Show Context)
Abstract.—In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the numerical evaluation of marginal likelihoods has often been performed using the harmonic mean estimation procedure. In the present article, we propose to employ another method, based on an analogy with statistical physics, called thermodynamic integration. We describe the method, propose an implementation, and show on two analytical examples that this numerical method yields reliable estimates. In contrast, the harmonic mean estimator leads to a strong overestimation of the marginal likelihood, which is all the more pronounced as the model is higher dimensional. As a result, the harmonic mean estimator systematically favors more parameterrich models, an artefact that might explain some recent puzzling observations, based on harmonic mean estimates, suggesting that Bayes factors tend to overscore complex models. Finally, we apply our method to the comparison of several alternative models of aminoacid replacement. We confirm our previous observations, indicating that modeling pattern heterogeneity across sites tends to yield better models than standard empirical matrices. [Bayes factor; harmonic mean; mixture model; path sampling; phylogeny; thermodynamic integration.] Bayesian methods have become popular in molecular phylogenetics over the recent years. The simple and intuitive interpretation of the concept of probabilities
Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards
 Syst
, 2005
"... Abstract.Partitioned Bayesian analyses of ∼2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of a ..."
Abstract

Cited by 112 (7 self)
 Add to MetaCart
(Show Context)
Abstract.Partitioned Bayesian analyses of ∼2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean −lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2ln Bayes factor >10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from subSaharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from subSaharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.
Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
 SYSTEMATIC BIOLOGY
, 2007
"... The estimation of species trees has become popular as a considerable amount of multilocus molecular data is available for inferring the evolutionary history of species. However, the current phylogenetic paradigm, that reconstructs gene trees to represent the species tree suggests that commonly used ..."
Abstract

Cited by 109 (11 self)
 Add to MetaCart
(Show Context)
The estimation of species trees has become popular as a considerable amount of multilocus molecular data is available for inferring the evolutionary history of species. However, the current phylogenetic paradigm, that reconstructs gene trees to represent the species tree suggests that commonly used methods such as the concatenation method, the consensus tree method, or the gene tree parsimony method may be either inconsistent or highly biased. In this paper, we propose a Bayesian hierarchical model to estimate the phylogeny of a group of species using multiple estimated gene tree distributions such as those that arise in a Bayesian analysis of DNA sequence data. Our model employs substitution models used in traditional phylogenetics, but also uses coalescent theory to explain genealogical signals from species trees to gene trees and from gene trees to sequence data, thereby forming a stochastic model to estimate gene trees, species trees, ancestral population sizes and species divergence times simultaneously. Our model is founded on the assumption that gene trees, even of unlinked loci, are correlated due to being derived from a single species tree and therefore should be estimated jointly. We apply the method to two multilocus DNA sequences datasets. The estimates of the
AWTY (Are We There Yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics
, 2007
"... Summary: A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations—convergence diagnostics—in phylogenetics is still uncommon. Here we present a simple t ..."
Abstract

Cited by 108 (5 self)
 Add to MetaCart
Summary: A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations—convergence diagnostics—in phylogenetics is still uncommon. Here we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using traceplots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation.
Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
 SYST. BIOL
, 2004
"... What does die posterior probability of a phylogenetic tree mean? This simulation study shows that Bayesian posterior probabilities have the meaning that is typically ascribed to them; the pt>sterkir probability ot'a tree is the probability that the tree is corwct, assuming th>.it the mo ..."
Abstract

Cited by 101 (7 self)
 Add to MetaCart
What does die posterior probability of a phylogenetic tree mean? This simulation study shows that Bayesian posterior probabilities have the meaning that is typically ascribed to them; the pt>sterkir probability ot'a tree is the probability that the tree is corwct, assuming th>.it the model is correct. At the same time, the BayLsian method can be sensitive to model misspecification, and the sensitivity of the Bayesian method appears to be greater than the sensitivity ot " the nonparametric bootstrap method (using maximum likelihood to estimate trees). Although the estimatLs of phylogeny obtained by use of the method of maximum likelihood or the Bayesian method are Ukely to be similar, the assessment of the uncertainty of inferred trees via either bootstriipping (t"or maximum likelihood estimates) or petsterior probabilities (for Bayesian estimates) is not likely to be the same. We suggest that the Bayesian method be implemented with the most complex models of those currently avaiiable, as tliis should reduce the chance that the metliod will concentrate too much probability on tuo few trees. [Bayesian estimation; Markov ch^iin Monte Carlo; posterior probability; prior probability.] Quantify ing the uncertainty of a phylogcneticesti mil te is at least as important a goal as obtaining the phylogenetic estimate itself. Measures of phylogenetic reliability not only point out what parts of a tree can be trusted when interpreting the evolution of a group, but can guide
The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol
, 2007
"... Abstract.—As larger, more complex data sets are being used to infer phylogenies, accuracy of these phylogenies increasingly requires models of evolution that accommodate heterogeneity in the processes of molecular evolution. We investigated the effect of improper data partitioning on phylogenetic ac ..."
Abstract

Cited by 70 (6 self)
 Add to MetaCart
(Show Context)
Abstract.—As larger, more complex data sets are being used to infer phylogenies, accuracy of these phylogenies increasingly requires models of evolution that accommodate heterogeneity in the processes of molecular evolution. We investigated the effect of improper data partitioning on phylogenetic accuracy, as well as the type I error rate and sensitivity of Bayes factors, a commonly used method for choosing among different partitioning strategies in Bayesian analyses. We also used Bayes factors to test empirical data for the need to divide data in a manner that has no expected biological meaning. Posterior probability estimates are misleading when an incorrect partitioning strategy is assumed. The error was greatest when the assumed model was underpartitioned. These results suggest that model partitioning is important for large data sets. Bayes factors performed well, giving a 5 % type I error rate, which is remarkably consistent with standard frequentist hypothesis tests. The sensitivity of Bayes factors was found to be quite high when the acrossclass model heterogeneity reflected that of empirical data. These results suggest that Bayes factors represent a robust method of choosing among partitioning strategies. Lastly, results of tests for the inclusion of unexpected divisions in empirical data mirrored the simulation results, although the outcome of such tests is highly dependent on accounting for rate variation among classes. We conclude by discussing other approaches for partitioning data, as well as other applications of Bayes factors. [Bayes factors; Bayesian phylogenetic inference; data partitioning; model choice; posterior probabilities.] Maximum likelihood (ML) and Bayesian methods of
The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear proteincoding genes.
 Comptes Rendus Biologies
, 2005
"... Abstract Squamate reptiles number approximately 8000 living species and are a major component of the world's terrestrial vertebrate diversity. However, the established relationships of the higherlevel groups have been questioned in recent molecular analyses. Here we expand the molecular data ..."
Abstract

Cited by 55 (2 self)
 Add to MetaCart
(Show Context)
Abstract Squamate reptiles number approximately 8000 living species and are a major component of the world's terrestrial vertebrate diversity. However, the established relationships of the higherlevel groups have been questioned in recent molecular analyses. Here we expand the molecular data to include DNA sequences, totaling 6192 base pairs (bp), from nine nuclear proteincoding genes (Cmos, RAG1, RAG2, R35, HOXA13, JUN, αenolase, amelogenin and MAFB) for 19 taxa representing all major lineages. Our phylogenetic analyses yield a largely resolved phylogeny that challenges previous morphological analyses and requires a new classification. The limbless dibamids are the most basal squamates. Of the remaining taxa (Bifurcata), the gekkonids form a basal lineage. The Unidentata, squamates that are neither dibamids nor gekkonids, are divided into the Scinciformata (scincids, xantusiids, and cordylids) and the Episquamata (remaining taxa). Episquamata includes Laterata (Teiformata, Lacertiformata, and Amphisbaenia, with the latter two joined in Lacertibaenia) and Toxicofera (iguanians, anguimorphs and snakes). Our results reject several previous hypotheses that identified either the varanids, or a burrowing lineage such as amphisbaenians or dibamids, as the closest relative of snakes. Our study also rejects the monophyly of both Scleroglossa and Autarchoglossa, because Iguania, a speciesrich lineage (ca. 1440 sp.), is in a highly nested position rather than being basal among Squamata. Thus iguanians should not be viewed as representing a primitive state of squamate evolution but rather a specialized and successful clade combining lingual prehension, dependence on visual cues, and ambush foraging mode, and which feeds mainly on prey avoided by other squamates. Molecular time estimates show that the Triassic and Jurassic (from 250 to 150 Myr) were important times for squamate evolution and diversification. Résumé La phylogénie des squamates (lézards, serpents, et amphisbènes) inférée à partir de neuf gènes nucléaires codants. Les squamates comprennent environ 8000 espèces actuelles et forment une composante majeure de la faune de vertébrés terrestres. Les relations phylogénétiques entre les familles actuelles de squamates sont inférées par analyses de séquences de neuf gènes nucléaires codant pour des protéines (Cmos, RAG1, RAG2, R35, HOXA13, JUN, αénolase, amélogénine, MAFB). Notre jeu
Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol
, 2011
"... Abstract.—The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be e ..."
Abstract

Cited by 40 (1 self)
 Add to MetaCart
(Show Context)
Abstract.—The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, steppingstone sampling (SS), which uses importance sampling to estimate each ratio in a series (the “stepping stones”) bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed. [Bayes factor; harmonic mean; phylogenetics, marginal likelihood;