ArticleProceedings of the National Academy of Sciences of the United States of America2020
Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining.Nature communications · 2026Article
- Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein.PLoS genetics · 2026Article
- Multiple molecular and cellular properties jointly affect protein and site-specific evolutionary rates.bioRxiv : the preprint server for biology · 2026Article
- The molecular evolution of vertebrate organs.Nature ecology & evolution · 2026Review
- Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents.Cell proliferation · 2026Article
- Recurrent innovation of protein-protein interactions in the Drosophila piRNA pathway.The EMBO journal · 2026Article
- Phylogenomic Approaches to Study Adaptive Evolution in Mammals: From Aging to Aquatic Lifestyles.Annual review of genetics · 2025Review
- Epistasis among clustered lineage-specific adaptive amino acid substitutions in the Drosophila Trio protein.bioRxiv : the preprint server for biology · 2025Article
- Anticipating protein evolution with successor sequence predictor.Journal of cheminformatics · 2025Article
- Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure.Genome biology and evolution · 2024Article
- Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants.bioRxiv : the preprint server for biology · 2024Article
- Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats.Genome biology and evolution · 2023Article
- Evolutionary mechanisms underlying the diversification of nuclear factor of activated T cells across vertebrates.Scientific reports · 2023Article
- Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.Scientific data · 2023Article
- Evolution is not Uniform Along Coding Sequences.Molecular biology and evolution · 2023Article
- Faltwerk: a library for spatial exploratory data analysis of protein structures.Bioinformatics advances · 2023Article
- Article
- An Evolutionary Conservation and Druggability Analysis of Enzymes Belonging to the Bacterial Shikimate Pathway.Antibiotics (Basel, Switzerland) · 2022Article
- The oxytocin signaling complex reveals a molecular switch for cation dependence.Nature structural & molecular biology · 2022Article
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2 authors.
Funding
Abstract
Understanding the molecular basis of adaptation to the environment is a central question in evolutionary biology, yet linking detected signatures of positive selection to molecular mechanisms remains challenging. Here we demonstrate that combining sequence-based phylogenetic methods with structural information assists in making such mechanistic interpretations on a genomic scale. Our integrative analysis shows that positively selected sites tend to colocalize on protein structures and that positively selected clusters are found in functionally important regions of proteins, indicating that positive selection can contravene the well-known principle of evolutionary conservation of functionally important regions. This unexpected finding, along with our discovery that positive selection acts on structural clusters, opens previously unexplored strategies for the development of better models of protein evolution. Remarkably, proteins where we detect the strongest evidence of clustering belong to just two functional groups: Components of immune response and metabolic enzymes. This gives a coherent picture of pathogens and xenobiotics as important drivers of adaptive evolution of mammals.
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