ArticleMolecular ecology2022
Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes.
Article in Molecular ecology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 30 citations in OpenAlex.
- Temperature-Associated Variation in Evolutionary Rates ofAnimals : an open access journal from MDPI · 2026Article
- Integrated Histological and Transcriptomic Characterization of Prolonged Starvation Responses in the CavefishBiology · 2026Article
- Sensing Underwater: Diversifying Selection, Convergent Evolution and Inactivation in Sensory Receptors' Genes of Aquatic Mammals.Journal of molecular evolution · 2026Article
- Bony fish genomes: Status and gaps.Journal of fish biology · 2026Review
- Surprising cryptic cavefish diversity in a long-studied karst cave ecosystem of northern Alabama.Scientific reports · 2026Article
- Chromosome-level genome assembly of the obligate cave loach Troglonectes daqikongensis.Scientific data · 2025Article
- Loss of Conserved Noncoding Elements Likely Shaped the Evolution of Regressed Phenotypes in Cavefish.Genome biology and evolution · 2025Article
- A Splicing Mutation in mitfa is Involved in the Depigmentation of Cavefish Triplophysa rosa.Molecular biology and evolution · 2025Article
- Chromosome-level genome assembly of Triplophysa scleroptera.Scientific data · 2025Article
- Genetic Structure of the Cave-Dwelling CatfishAnimals : an open access journal from MDPI · 2025Article
- Telomere-to-telomere gapless genome assembly of Triplophysa yaopeizhii.Scientific data · 2025Article
- Whole-genome relaxed selection and molecular constraints in Triplophysa under adapted Qinghai-Tibetan Plateau.BMC genomics · 2025Article
- Population Genomics of Premature Termination Codons in Cavefish With Substantial Trait Loss.Molecular biology and evolution · 2025Article
- Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies.Scientific data · 2024Article
- A chromosome-scale reference genome assembly for Triplophysa lixianensis.Scientific data · 2024Article
- Gene loss and relaxed selection ofProceedings. Biological sciences · 2024Article
- Age, growth, and energy storage of the subterranean fish Triplophysa rosa (Cypriniformes: Nemacheilidae) from Chongqing, China.BMC ecology and evolution · 2023Article
- Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel GobyInternational journal of molecular sciences · 2023Article
- Loss of behavioral stress response in blind cavefish reduces energy expenditure.Zoological research · 2023Article
- Selection-driven trait loss in independently evolved cavefish populations.Nature communications · 2023Article
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5 authors at 2 institutions in 2 countries.
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Abstract
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.
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