ArticleMolecular biology and evolution2025
A General Substitution Matrix for Structural Phylogenetics.
Article in Molecular biology and evolution, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Article
- From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses.Journal of virology · 2026Review
- Protein Structure Characters in the Light of Phylogenetic Systematics.Genome biology and evolution · 2026Article
- Interface swapping orchestrates carbon transfer in the archaeal acetyl-CoA decarbonylase/synthase.bioRxiv : the preprint server for biology · 2026Article
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Balancing under constraint: Structural insights into norovirus evolution and antigenic innovation.PLoS pathogens · 2026Article
- The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking.Nature communications · 2026Article
- Protein folds and catalytic strategies at the origin of biological CO2 fixation.FEMS microbiology ecology · 2026Article
- Toward a genomic understanding of the tree of life.Molecular biology and evolution · 2026Article
- Genome assembly and protein structure modeling reveal key molecular features of divergentMicrobiology spectrum · 2026Article
- Exploring the protein universe with distant similarity detection methods.Protein science : a publication of the Protein Society · 2026Review
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
- The Evolutionary History and Modern Diversity of Triterpenoid Cyclases.Molecular biology and evolution · 2025Article
- DPANN Archaea and CPR Bacteria: insights into early cellular evolution?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- The evolutionary history and modern diversity of triterpenoid cyclases.bioRxiv : the preprint server for biology · 2025Article
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics.Molecular biology and evolution · 2025Article
- Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes.Genome biology and evolution · 2025Article
- Archaeal hemeFrontiers in microbiology · 2025Article
- Exploring the Structural Diversity and Evolution of the D1 Subunit of Photosystem II Using AlphaFold and Foldtree.Physiologia plantarumArticle
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2 authors.
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Abstract
Sequence-based maximum likelihood phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the evolutionary histories of proteins and the organisms that harbor them. However, modern implementations with sophisticated models of sequence evolution struggle to resolve deep evolutionary relationships, which can be obscured by excessive sequence divergence and substitution saturation. Structural phylogenetics has emerged as a promising alternative because protein structure evolves much more slowly than protein sequences. Recent developments in protein structure prediction using AI have made it possible to predict protein structures for entire protein families and then to translate these structures into a sequence representation-the 3Di structural alphabet-that can in theory be directly fed into existing sequence-based phylogenetic software. To unlock the full potential of this idea, however, requires the inference of a general substitution matrix for structural phylogenetics, which has so far been missing. Here, we infer this matrix from large datasets of protein structures and show that it results in a better fit to empirical datasets than previous approaches. We then use this matrix to re-visit the question of the root of the tree of life. Using structural phylogenies of universal paralogs, we provide the first unambiguous evidence for a root between archaea and bacteria. Finally, we discuss some practical and conceptual limitations of structural phylogenetics. Our 3Di substitution matrix provides a starting point for revisiting many deep phylogenetic problems that have so far been extremely difficult to solve.
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