ArticleSystematic biology2013
A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.
Article in Systematic biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- Phylogenetic Accuracy Under Non-stationary and Non-homogeneous Conditions: A Simulation Study.Systematic biology · 2026Article
- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors.Nature microbiology · 2025Article
- The effectiveness of selection in a species affects the direction of amino acid frequency evolution.bioRxiv : the preprint server for biology · 2025Article
- The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense γ-Irradiation.Molecular biology and evolution · 2024Article
- Is Over-parameterization a Problem for Profile Mixture Models?Systematic biology · 2024Article
- Rooting Species Trees Using Gene Tree-Species Tree Reconciliation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study.Molecular biology and evolution · 2021Article
- Ancestral state reconstruction of metabolic pathways across pangenome ensembles.Microbial genomics · 2020Article
- A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics.NAR genomics and bioinformatics · 2020Article
- Article
- The Prevalence and Impact of Model Violations in Phylogenetic Analysis.Genome biology and evolution · 2019Article
- Review
- A Surrogate Function for One-Dimensional Phylogenetic Likelihoods.Molecular biology and evolution · 2018Article
- The growing tree of Archaea: new perspectives on their diversity, evolution and ecology.The ISME journal · 2017Review
- Improved mitochondrial amino acid substitution models for metazoan evolutionary studies.BMC evolutionary biology · 2017Article
- Integrative modeling of gene and genome evolution roots the archaeal tree of life.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data.Genome biology and evolution · 2017Article
- RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.Systematic biology · 2016Article
- A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology.Systematic biology · 2015Article
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3 authors.
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Abstract
Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.
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