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Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods

https://doi.org/10.1093/molbev/msq168
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
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Information Theory and an Extension of the Maximum Likelihood Principle
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Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA
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Statistical tests of models of DNA substitution
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Evolutionary trees from DNA sequences: A maximum likelihood approach
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola
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Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power Using Marginal Tests
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Comparison of phylogenetic trees
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Mammalian Protein Metabolism
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Evolution of Protein Molecules
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Model use in phylogenetics: nine key questions
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A tenth crucial question regarding model use in phylogenetics
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Evolutionary history of the greater white-toothed shrew (Crocidura russula) inferred from analysis of mtDNA, Y, and X chromosome markers
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Modeling the covarion hypothesis of nucleotide substitution
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Molecular phylogenetics: state-of-the-art methods for looking into the past
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Phytophthora pistaciae sp. nov. and P. melonis: the principal causes of pistachio gummosis in Iran
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Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America
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Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics
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Estimation of evolutionary distances between homologous nucleotide sequences.
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Parametric Phylogenetics?
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Exploring Among-Site Rate Variation Models in a Maximum Likelihood Framework Using Empirical Data: Effects of Model Assumptions on Estimates of Topology, Branch Lengths, and Bootstrap Support
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Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods
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Should We Use Model-Based Methods for Phylogenetic Inference When We Know That Assumptions About Among-Site Rate Variation and Nucleotide Substitution Pattern Are Violated?
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Molecular Phylogenetics of Allodapine Bees, with Implications for the Evolution of Sociality and Progressive Rearing
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Performance-Based Selection of Likelihood Models for Phylogeny Estimation
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The Importance of Proper Model Assumption in Bayesian Phylogenetics
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Modeling Compositional Heterogeneity
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Data Partitions and Complex Models in Bayesian Analysis: The Phylogeny of Gymnophthalmid Lizards
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Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests
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Under-parameterized Model of Sequence Evolution Leads to Bias in the Estimation of Diversification Rates from Molecular Phylogenies
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An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction
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Statistical Methods in Molecular Evolution
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The Importance of Data Partitioning and the Utility of Bayes Factors in Bayesian Phylogenetics
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Does Choice in Model Selection Affect Maximum Likelihood Analysis?
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Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
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MODELTEST: testing the model of DNA substitution.
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/genetics/155.1.431openalex-snapshot
Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
inferredcites →https://doi.org/10.1093/molbev/msi050openalex-snapshot
Accounting for Uncertainty in the Tree Topology Has Little Effect on the Decision-Theoretic Approach to Model Selection in Phylogeny Estimation
inferredcites →https://doi.org/10.1093/molbev/msi129openalex-snapshot
Evaluating the Performance of a Successive-Approximations Approach to Parameter Optimization in Maximum-Likelihood Phylogeny Estimation
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004128openalex-snapshot
Testing a Covariotide Model of DNA Substitution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004175openalex-snapshot
Bayesian Model Adequacy and Choice in Phylogenetics
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040023openalex-snapshot
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
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Recovering evolutionary trees under a more realistic model of sequence evolution.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040153openalex-snapshot
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040183openalex-snapshot
Success of maximum likelihood phylogeny inference in the four-taxon case.
inferredcites →https://doi.org/10.1093/sysbio/27.4.401openalex-snapshot
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
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Phylogeography and Molecular Systematics of the Peromyscus Aztecus Species Group (Rodentia: Muridae) Inferred Using Parsimony and Likelihood
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Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamanderDicamptodon aterrimus
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FACTORS DETERMINING THE ACCURACY OF CLADOGRAM ESTIMATION: EVALUATION USING COMPUTER SIMULATION
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Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
inferredcites →https://doi.org/10.1126/science.288.5475.2349openalex-snapshot
Accommodating Phylogenetic Uncertainty in Evolutionary Studies
inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.102003.152633openalex-snapshot
Model Selection in Phylogenetics
inferredcites →https://doi.org/10.1214/aos/1176344136openalex-snapshot
Estimating the Dimension of a Model
inferredcites →https://doi.org/10.1214/aos/1176346785openalex-snapshot
Bayesianly Justifiable and Relevant Frequency Calculations for the Applied Statistician
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Cases in which Parsimony or Compatibility Methods Will be Positively Misleading

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria
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High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function
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Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
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Model selection may not be a mandatory step for phylogeny reconstruction
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Impact of the tree prior on estimating clock rates during epidemic outbreaks
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Model Adequacy and the Macroevolution of Angiosperm Functional Traits
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Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation
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A Novel Test for Absolute Fit of Evolutionary Models Provides a Means to Correctly Identify the Substitution Model and the Model Tree
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Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics
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Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life
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Likelihood-Based Tests of Species Tree Hypotheses
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Approximating Model Probabilities in Bayesian Information Criterion and Decision-Theoretic Approaches to Model Selection in Phylogenetics
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MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
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Statistics and Truth in Phylogenomics
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SPIn: Model Selection for Phylogenetic Mixtures via Linear Invariants
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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
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Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
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Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales
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The Devil in the Details: Interactions between the Branch-Length Prior and Likelihood Model Affect Node Support and Branch Lengths in the Phylogeny of the Psoraceae
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Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data
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Posterior Predictive Bayesian Phylogenetic Model Selection
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Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit
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Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?
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Phylodynamic Model Adequacy Using Posterior Predictive Simulations
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How Well Does Your Phylogenetic Model Fit Your Data?
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Relative model fit does not predict topological accuracy in single-gene protein phylogenetics
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Neglecting model selection alters phylogenetic inference
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Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences
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Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models
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Environmental Pressure Drives the Acquisition of Aetokthonotoxin Genes: A Bioinformatic Study of Avian Vacuolar Myelinopathy Origin
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Statistical comparison of DEC and DEC+J is identical to comparison of two ClaSSE submodels, and is therefore valid
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Model-based approaches to discovering diversity : new implementations, tests of adequacy and an empirical application to central American Diptera
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