ArticleMolecular biology and evolution2022
A Population-Genetic Lens into the Process of Gene Loss Following Whole-Genome Duplication.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 34 citations in OpenAlex.
- Pax6 homologs are required for patterning both visual systems of the daddy-longlegs Phalangium opilio.Molecular biology and evolution · 2026Article
- Evolutionary causes and consequences of gene duplication.Nature reviews. Genetics · 2026Review
- The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.BMC biology · 2026Article
- Article
- Genome-wide identification and characterization of theFrontiers in plant science · 2026Article
- Whole-genome duplications revealed by macronuclear genomes of five rare species of the model ciliates Paramecium.Science China. Life sciences · 2025Article
- Understanding Functional Evolution in Orthologs and Paralogs.Journal of molecular evolution · 2025Review
- Little millet genome reveals evolutionary insights into tetraploid structure and genetic basis of micronutrient density.Nature communications · 2025Article
- Gene and Genome Duplication in Spiders.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Review
- Whole-Genome Sequence of Potamopyrgus antipodarum-A Model System for the Maintenance of Sexual Reproduction-Reveals a Recent Whole-Genome Duplication.Genome biology and evolution · 2025Article
- Diploidization in a wild rice allopolyploid is both episodic and gradual.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Mutational biases favor complexity increases in protein interaction networks after gene duplication.Molecular systems biology · 2024Article
- Comparative transcriptomics reveals divergence in pathogen response gene families amongst 20 forest tree species.G3 (Bethesda, Md.) · 2023Article
- Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event.Molecular biology and evolution · 2023Article
- Review
- Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event.bioRxiv : the preprint server for biology · 2023Article
- Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae).Molecular biology and evolution · 2023Article
- Evolutionary trade-off and mutational bias could favor transcriptional over translational divergence within paralog pairs.PLoS genetics · 2023Article
- Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae.Genome biology and evolution · 2023Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Whole-genome duplications (WGDs) have occurred in many eukaryotic lineages. However, the underlying evolutionary forces and molecular mechanisms responsible for the long-term retention of gene duplicates created by WGDs are not well understood. We employ a population-genomic approach to understand the selective forces acting on paralogs and investigate ongoing duplicate-gene loss in multiple species of Paramecium that share an ancient WGD. We show that mutations that abolish protein function are more likely to be segregating in retained WGD paralogs than in single-copy genes, most likely because of ongoing nonfunctionalization post-WGD. This relaxation of purifying selection occurs in only one WGD paralog, accompanied by the gradual fixation of nonsynonymous mutations and reduction in levels of expression, and occurs over a long period of evolutionary time, "marking" one locus for future loss. Concordantly, the fitness effects of new nonsynonymous mutations and frameshift-causing indels are significantly more deleterious in the highly expressed copy compared with their paralogs with lower expression. Our results provide a novel mechanistic model of gene duplicate loss following WGDs, wherein selection acts on the sum of functional activity of both duplicate genes, allowing the two to wander in expression and functional space, until one duplicate locus eventually degenerates enough in functional efficiency or expression that its contribution to total activity is too insignificant to be retained by purifying selection. Retention of duplicates by such mechanisms predicts long times to duplicate-gene loss, which should not be falsely attributed to retention due to gain/change in function.
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