ArticleGenome biology and evolution2011
Toward a general model for the evolutionary dynamics of gene duplicates.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- Understanding Functional Evolution in Orthologs and Paralogs.Journal of molecular evolution · 2025Review
- Dualistic MADS-box evolution forged legume diversity post-WGD.Frontiers in plant science · 2025Article
- Molecular Dating of the Teleost Whole Genome Duplication (3R) Is Compatible With the Expectations of Delayed Rediploidization.Genome biology and evolution · 2024Article
- Genome-wide characterization of Remorin gene family and their responsive expression to abiotic stresses and plant hormone in Brassica napus.Plant cell reports · 2024Article
- Genome-wide identification and analyses ofMolecular breeding : new strategies in plant improvement · 2024Article
- Expectations of duplicate gene retention under the gene duplicability hypothesis.BMC ecology and evolution · 2023Article
- The evolution of bitter taste receptor gene in primates: Gene duplication and selection.Ecology and evolution · 2023Article
- Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inGenome research · 2023Article
- Dosage balance acts as a time-dependent selective barrier to subfunctionalization.BMC ecology and evolution · 2023Article
- Article
- The ensemble of gene regulatory networks at mutation-selection balance.Journal of the Royal Society, Interface · 2023Article
- WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events.BMC bioinformatics · 2022Article
- Regulation of heart rate following genetic deletion of the ß1 adrenergic receptor in larval zebrafish.Acta physiologica (Oxford, England) · 2022Article
- Detecting Selection on Segregating Gene Duplicates in a Population.Journal of molecular evolution · 2021Article
- The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality.Genome biology and evolution · 2021Article
- Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data.Molecular biology and evolution · 2021Article
- Article
- The evolution of MarR family transcription factors as counter-silencers in regulatory networks.Current opinion in microbiology · 2020Review
- S100A7/Ran-binding protein 9 coevolution in mammals.Immunogenetics · 2020Article
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4 authors.
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Abstract
Gene duplication is an important process in the functional divergence of genes and genomes. Several processes have been described that lead to duplicate gene retention over different timescales after both smaller-scale events and whole-genome duplication, including neofunctionalization, subfunctionalization, and dosage balance. Two common modes of duplicate gene loss include nonfunctionalization and loss due to population dynamics (failed fixation). Previous work has characterized expectations of duplicate gene retention under the neofunctionalization and subfunctionalization models. Here, that work is extended to dosage balance using simulations. A general model for duplicate gene loss/retention is then presented that is capable of fitting expectations under the different models, is defined at t = 0, and decays to an orthologous asymptotic rate rather than zero, based upon a modified Weibull hazard function. The model in a maximum likelihood framework shows the property of identifiability, recovering the evolutionary mechanism and parameters of simulation. This model is also capable of recovering the evolutionary mechanism of simulation from data generated using an unrelated network population genetic model. Lastly, the general model is applied as part of a mixture model to recent gene duplicates from the Oikopleura dioica genome, suggesting that neofunctionalization may be an important process leading to duplicate gene retention in that organism.
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