ArticleMolecular biology and evolution2022
Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- On the Origin and Evolution of Sweet Taste Mediated by Tas1r2-Tas1r3 in Vertebrates.Integrative zoology · 2026Article
- Resurrecting Full-Length Ancestral Schizorhodopsins and Heliorhodopsins with Structure-Guided, Indel-Aware Sequence Reconstruction.ACS omega · 2026Article
- The Use of dN/dS Ratios to Investigate Types of Selection in Related Sexual and Asexual Lineages.Genome biology and evolution · 2026Review
- Article
- Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity.Molecular biology and evolution · 2025Article
- Empirical substitution models of protein evolution: database, relationships, and modeling considerations.Database : the journal of biological databases and curation · 2025Article
- Article
- The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense γ-Irradiation.Molecular biology and evolution · 2024Article
- Applications of ancestral sequence reconstruction for understanding the evolution of plant specialized metabolism.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Ancestral Reconstruction and the Evolution of Protein Energy Landscapes.Annual review of biophysics · 2024Review
- Microbial Diversity and Open Questions about the Deep Tree of Life.Genome biology and evolution · 2024Article
- Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation.Journal of molecular evolution · 2024Article
- Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2024Article
- Substitution Models of Protein Evolution with Selection on Enzymatic Activity.Molecular biology and evolution · 2024Article
- Article
- Topiary: Pruning the manual labor from ancestral sequence reconstruction.Protein science : a publication of the Protein Society · 2023Article
- Proteome-Wide Structural Computations Provide Insights into Empirical Amino Acid Substitution Matrices.International journal of molecular sciences · 2023Article
- The evolution of the HIV-1 protease folding stability.Virus evolution · 2022Article
- Ancestral sequence reconstruction as a tool to study the evolution of wood decaying fungi.Frontiers in fungal biology · 2022Review
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2 authors.
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Abstract
The selection of the best-fitting substitution model of molecular evolution is a traditional step for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a few recent studies suggested that applying this procedure does not affect the accuracy of phylogenetic tree reconstruction. Here, we revisited this debate topic by analyzing the influence of selection among substitution models of protein evolution, with focus on exchangeability matrices, on the accuracy of ASR using simulated and real data. We found that the selected best-fitting substitution model produces the most accurate ancestral sequences, especially if the data present large genetic diversity. Indeed, ancestral sequences reconstructed under substitution models with similar exchangeability matrices were similar, suggesting that if the selected best-fitting model cannot be used for the reconstruction, applying a model similar to the selected one is preferred. We conclude that selecting among substitution models of protein evolution is recommended for reconstructing accurate ancestral sequences.
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