ArticleBMC biology2016
The Sinocyclocheilus cavefish genome provides insights into cave adaptation.
Article in BMC biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
110 citing papers in PubMed, 398 citations in OpenAlex.
- Loss, persistence and reversal of phenotypic traits.Biological reviews of the Cambridge Philosophical Society · 2026Review
- A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.Genome research · 2026Article
- Morphological adaptations of cavefish support enhanced hydrodynamic perception for underwater environmental monitoring.Environmental science and ecotechnology · 2026Article
- Phylogenetic evidence reveals the classification and evolutionary history of endemic cavefish in China.BMC ecology and evolution · 2026Article
- Stage dependent plasticity and the evolution of a non-obligate cave dwelling life cycle in frogs.BMC biology · 2026Article
- Evolutionary diversification and immunoprofiling of cathepsin L toolkit in common carp.Frontiers in cellular and infection microbiology · 2026Article
- The telomere-to-telomere genome assembly of the Triplophysa erythraea (Nemacheilidae hypogean fishes).Scientific data · 2025Article
- Chromosome-level genome assembly of the obligate cave loach Troglonectes daqikongensis.Scientific data · 2025Article
- Rapid speciation of Chinese hypogean fishes driven by paleogeoclimatic and morphological adaptations.Current zoology · 2025Article
- Loss of Conserved Noncoding Elements Likely Shaped the Evolution of Regressed Phenotypes in Cavefish.Genome biology and evolution · 2025Article
- Convergent subgenome dominance but with lineage-specific functional divergence of homoeologs during cave adaptation: insights from full-length transcriptomes of Sinocyclocheilus species.Frontiers in zoology · 2025Article
- Article
- A Splicing Mutation in mitfa is Involved in the Depigmentation of Cavefish Triplophysa rosa.Molecular biology and evolution · 2025Article
- Convergent Evolution in Amblyopsid Cavefishes and the Age of Eastern North American Subterranean Ecosystems.Molecular biology and evolution · 2025Article
- Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing.Scientific data · 2025Article
- Chromosome-level assembly and annotation of the yellow-shelled fish (Barbodes Wynaadensis).Scientific data · 2025Article
- Full-Length Transcriptome Sequencing and hsp Gene Family Analysis Provide New Insights into the Stress Response Mechanisms ofBiology · 2025Article
- Evolution of the Nonvisual and Visual Opsin Gene Repertoire in Ray-Finned Fishes.Genome biology and evolution · 2025Article
- Genetic Structure of the Cave-Dwelling CatfishAnimals : an open access journal from MDPI · 2025Article
- Chromosome-level genome assembly reveals adaptive evolution of the invasive Amazon sailfin catfish (Pterygoplichthys pardalis).Communications biology · 2025Article
50 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
41 authors at 9 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAn emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively.
resultsThe assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes.
conclusionAs the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.