ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2019
Detecting adaptive convergent amino acid evolution.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2019. 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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Who cites it
20 citing papers in PubMed.
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Estimates of molecular convergence reveal multiple genes with adaptive variation across teleost fish.Molecular biology and evolution · 2026Article
- Structural and Functional Variations of Enzymes Indicate Latitudinal Adaptations of Subarctic and Arctic Sea Urchins.Ecology and evolution · 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
- What Does It Mean to Be(Come) Arctic? Functional and Genetic Traits of Arctic- and Temperate-Adapted Diatoms.Global change biology · 2025Article
- Homospermidine synthase evolution and the origin(s) of pyrrolizidine alkaloids in Apocynaceae.American journal of botany · 2025Article
- Review
- Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor.Genome biology and evolution · 2024Article
- Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate.Plant communications · 2024Review
- Signatures of Extreme Longevity: A Perspective from Bivalve Molecular Evolution.Genome biology and evolution · 2023Article
- CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions.Bioinformatics (Oxford, England) · 2023Article
- Article
- CytochromeThe Journal of biological chemistry · 2020Article
- A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Convergent evolution in the genomics era: new insights and directions.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- The perils of intralocus recombination for inferences of molecular convergence.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Detecting adaptive convergent amino acid evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Detecting genetic interactions using parallel evolution in experimental populations.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes-including in the presence of a change in the efficacy of selection-and on empirical alignments. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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