ArticleMolecular biology and evolution2020
Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Evaluation of Molecular Phylogenetic Trees by an Information-Theoretic Metric.Journal of molecular evolution · 2026Article
- When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis.Journal of molecular evolution · 2026Article
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- nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models.Journal of molecular evolution · 2025Article
- Empirical substitution models of protein evolution: database, relationships, and modeling considerations.Database : the journal of biological databases and curation · 2025Article
- Reliable estimation of tree branch lengths using deep neural networks.PLoS computational biology · 2024Article
- Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation.Journal of molecular evolution · 2024Article
- Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales).Frontiers in plant science · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies.Systematic biology · 2023Article
- Hiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity inProceedings of the National Academy of Sciences of the United States of America · 2023Article
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- Article
- Bayesian Cross-Validation Comparison of Amino Acid Replacement Models: Contrasting Profile Mixtures, Pairwise Exchangeabilities, and Gamma-Distributed Rates-Across-Sites.Journal of molecular evolution · 2022Article
- Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck's Stint Calicivirus: Evidence for a New Genus withinMicroorganisms · 2022Article
- Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction.Molecular biology and evolution · 2022Article
- Lower Statistical Support with Larger Data Sets: Insights from the Ochrophyta Radiation.Molecular biology and evolution · 2022Article
- Methodologies for Microbial Ancestral Sequence Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus.Microorganisms · 2021Article
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Abstract
It is regarded as best practice in phylogenetic reconstruction to perform relative model selection to determine an appropriate evolutionary model for the data. This procedure ranks a set of candidate models according to their goodness of fit to the data, commonly using an information theoretic criterion. Users then specify the best-ranking model for inference. Although it is often assumed that better-fitting models translate to increase accuracy, recent studies have shown that the specific model employed may not substantially affect inferences. We examine whether there is a systematic relationship between relative model fit and topological inference accuracy in protein phylogenetics, using simulations and real sequences. Simulations employed site-heterogeneous mechanistic codon models that are distinct from protein-level phylogenetic inference models, allowing us to investigate how protein models performs when they are misspecified to the data, as will be the case for any real sequence analysis. We broadly find that phylogenies inferred across models with vastly different fits to the data produce highly consistent topologies. We additionally find that all models infer similar proportions of false-positive splits, raising the possibility that all available models of protein evolution are similarly misspecified. Moreover, we find that the parameter-rich GTR (general time reversible) model, whose amino acid exchangeabilities are free parameters, performs similarly to models with fixed exchangeabilities, although the inference precision associated with GTR models was not examined. We conclude that, although relative model selection may not hinder phylogenetic analysis on protein data, it may not offer specific predictable improvements and is not a reliable proxy for accuracy.
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