ArticleMolecular biology and evolution2018
Accurate Detection of Convergent Amino-Acid Evolution with PCOC.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
- Direct link between convergent evolution at sequence level and phenotypic level of septal pore cap in Agaricomycotina.G3 (Bethesda, Md.) · 2026Article
- Sensing Underwater: Diversifying Selection, Convergent Evolution and Inactivation in Sensory Receptors' Genes of Aquatic Mammals.Journal of molecular evolution · 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
- MoleRate: comparing molecular relative evolutionary rates to detect convergent evolution.Evolution; international journal of organic evolution · 2026Article
- TreeProfiler: large-scale metadata profiling along gene and species trees.Molecular biology and evolution · 2026Article
- A POMT2 missense substitution contributes to hypoxia adaptation in hibernating mammals.Molecular biology and evolution · 2026Article
- INSIG1 parallel substitution drives lipid/sterol metabolic plasticity mediating desert adaptation in ungulates.Communications biology · 2026Article
- Identifying the Degree of Gene Reuse During Repeated Adaptation.Molecular ecology · 2025Review
- Detecting Convergence of Amino Acid Physicochemical Properties Underlying the Organismal Adaptive Convergent Evolution.Molecular ecology resources · 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
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- Reduction of Tooth Replacement Disproportionately Affects the Evolution of Enamel Matrix Proteins.Journal of molecular evolution · 2025Article
- Multiple transitions to high l-DOPA 4,5-dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales.The New phytologist · 2025Article
- Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon.BMC genomics · 2025Article
- Article
- Evolutionary analysis of genes associated with the sense of balance in semi-aquatic mammals.BMC ecology and evolution · 2025Article
- Molecular Phylogenetic Relationships Based on Mitogenomes of Spider: Insights Into Evolution and Adaptation to Extreme Environments.Ecology and evolution · 2025Article
- A versatile pipeline to identify convergently lost ancestral conserved fragments associated with convergent evolution of vocal learning.Briefings in bioinformatics · 2024Article
- RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution.Molecular biology and evolution · 2024Article
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4 authors.
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Abstract
In the history of life, some phenotypes have been acquired several times independently, through convergent evolution. Recently, lots of genome-scale studies have been devoted to identify nucleotides or amino acids that changed in a convergent manner when the convergent phenotypes evolved. These efforts have had mixed results, probably because of differences in the detection methods, and because of conceptual differences about the definition of a convergent substitution. Some methods contend that substitutions are convergent only if they occur on all branches where the phenotype changed toward the exact same state at a given nucleotide or amino acid position. Others are much looser in their requirements and define a convergent substitution as one that leads the site at which they occur to prefer a phylogeny in which species with the convergent phenotype group together. Here, we suggest to look for convergent shifts in amino acid preferences instead of convergent substitutions to the exact same amino acid. We define as convergent shifts substitutions that occur on all branches where the phenotype changed and such that they correspond to a change in the type of amino acid preferred at this position. We implement the corresponding model into a method named PCOC. We show on simulations that PCOC better recovers convergent shifts than existing methods in terms of sensitivity and specificity. We test it on a plant protein alignment where convergent evolution has been studied in detail and find that our method recovers several previously identified convergent substitutions and proposes credible new candidates.
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