ArticleMolecular biology and evolution2015
Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?
Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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95 citing papers in PubMed.
- Selection on PER2 Phosphorylation Regulation Underlies Atypical Mammalian Circadian Rhythms.Ecology and evolution · 2026Article
- Functional convergence of regulatory regions provides vital insights into mammalian gliding adaptation.Science China. Life sciences · 2026Article
- Comparative Genomics Reveals Convergent Evolution Between Avivorous Bats (Ia io and Nyctalus aviator).Integrative zoology · 2026Article
- Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Genomic and population analyses reveal asymmetric subgenome evolution and local adaptation in the polyploid Lycopus lucidus.Communications biology · 2026Article
- Assessing the Potential of Ancient Protein Sequences in the Study of Hominid Evolution.Genome biology and evolution · 2026Article
- Repeatability of gene expression evolution in experimental environmental adaptation.Nature communications · 2026Article
- INSIG1 parallel substitution drives lipid/sterol metabolic plasticity mediating desert adaptation in ungulates.Communications biology · 2026Article
- Estimates of molecular convergence reveal multiple genes with adaptive variation across teleost fish.Molecular biology and evolution · 2026Article
- Insights into Convergent Evolution From Studying Amino Acid Patterns in Independent Lineages of Birds.Genome biology and evolution · 2025Article
- Convergent Evolution and the Epigenome.Epigenomes · 2025Review
- Detecting Convergence of Amino Acid Physicochemical Properties Underlying the Organismal Adaptive Convergent Evolution.Molecular ecology resources · 2025Article
- Genomic Insights Into Convergent Evolution: Adaptation to Rocky Habitats in Rock-Inhabiting Fungi.Molecular biology and evolution · 2025Article
- Language models reveal a complex sequence basis for adaptive convergent evolution of protein functions.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Novel genomics insights into the molecular evolution of long-distance migratory mammals.BMC genomics · 2025Article
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- Multiple transitions to high l-DOPA 4,5-dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales.The New phytologist · 2025Article
- Evolutionary sparse learning reveals the shared genetic basis of convergent traits.Nature communications · 2025Article
- Evolution of canonical circadian clock genes underlies unique sleep strategies of marine mammals for secondary aquatic adaptation.PLoS genetics · 2025Article
35 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Convergent and parallel amino acid substitutions in protein evolution, collectively referred to as molecular convergence here, have small probabilities under neutral evolution. For this reason, molecular convergence is commonly viewed as evidence for similar adaptations of different species. The surge in the number of reports of molecular convergence in the last decade raises the intriguing question of whether molecular convergence occurs substantially more frequently than expected under neutral evolution. We here address this question using all one-to-one orthologous proteins encoded by the genomes of 12 fruit fly species and those encoded by 17 mammals. We found that the expected amount of molecular convergence varies greatly depending on the specific neutral substitution model assumed at each amino acid site and that the observed amount of molecular convergence is explainable by neutral models incorporating site-specific information of acceptable amino acids. Interestingly, the total number of convergent and parallel substitutions between two lineages, relative to the neutral expectation, decreases with the genetic distance between the two lineages, regardless of the model used in computing the neutral expectation. We hypothesize that this trend results from differences in the amino acids acceptable at a given site among different clades of a phylogeny, due to prevalent epistasis, and provide simulation as well as empirical evidence for this hypothesis. Together, our study finds no genomic evidence for higher-than-neutral levels of molecular convergence, but suggests the presence of abundant epistasis that decreases the likelihood of molecular convergence between distantly related lineages.
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