ArticleJournal of molecular evolution2004
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution.
Article in Journal of molecular evolution, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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135 citing papers in PubMed.
- Evolutionary Shifts in Rhodopsin Function Illuminate Dim-Light Adaptations in Birds.Integrative zoology · 2026Article
- Genetic Adaptation Accompanying the Emergence of Inkoo Virus, the European Orthobunyavirus jamestownense.Annals of the New York Academy of Sciences · 2026Article
- Evolutionary patterns in squamate mitogenomes: Are selective regimes associated with fossoriality and limblessness?Genetics and molecular biology · 2026Article
- Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.Evolution; international journal of organic evolution · 2025Article
- Comparative Mitogenomics ofInsects · 2025Article
- Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.bioRxiv : the preprint server for biology · 2025Article
- Comparative genomics provides insights into chromosomal evolution and immunological adaptation in horseshoe bats.Nature ecology & evolution · 2025Article
- Article
- Parallel Spectral Tuning of a Cone Visual Pigment Provides Evidence for Ancient Deep-Sea Adaptations in Cetaceans.Genome biology and evolution · 2024Article
- Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs.Molecular biology and evolution · 2024Article
- Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments.Molecular biology and evolution · 2024Article
- Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes.Biology letters · 2024Article
- Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage.Virus evolution · 2024Article
- Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae.G3 (Bethesda, Md.) · 2023Article
- Insights into the Genomics of Clownfish Adaptive Radiation: The Genomic Substrate of the Diversification.Genome biology and evolution · 2023Article
- Convergent evolutionary shifts in rhodopsin retinal release explain shared opsin repertoires in monotremes and crocodilians.Proceedings. Biological sciences · 2023Article
- Adaptation of Antarctic Icefish Vision to Extreme Environments.Molecular biology and evolution · 2023Article
- Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?Journal of molecular evolution · 2023Article
- Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae.bioRxiv : the preprint server for biology · 2023Article
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
75 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The tailoring of existing genetic systems to new uses is called genetic co-option. Mechanisms of genetic co-option have been difficult to study because of difficulties in identifying functionally important changes. One way to study genetic co-option in protein-coding genes is to identify those amino acid sites that have experienced changes in selective pressure following a genetic co-option event. In this paper we present a maximum likelihood method useful for measuring divergent selective pressures and identifying the amino acid sites affected by divergent selection. The method is based on a codon model of evolution and uses the nonsynonymous-to-synonymous rate ratio (omega) as a measure of selection on the protein, with omega = 1, < 1, and > 1 indicating neutral evolution, purifying selection, and positive selection, respectively. The model allows variation in omega among sites, with a fraction of sites evolving under divergent selective pressures. Divergent selection is indicated by different omega's between clades, such as between paralogous clades of a gene family. We applied the codon model to duplication followed by functional divergence of (i) the epsilon and gamma globin genes and (ii) the eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) genes. In both cases likelihood ratio tests suggested the presence of sites evolving under divergent selective pressures. Results of the epsilon and gamma globin analysis suggested that divergent selective pressures might be a consequence of a weakened relationship between fetal hemoglobin and 2,3-diphosphoglycerate. We suggest that empirical Bayesian identification of sites evolving under divergent selective pressures, combined with structural and functional information, can provide a valuable framework for identifying and studying mechanisms of genetic co-option. Limitations of the new method are discussed.
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