Ginet R, Decou V. Initiation à la biologie et à l’écologie souterraines. Paris: J.-P. Delarge; 1977.
Google Scholar
Camacho AI. The natural history of biospeleology. Editorial CSIC-CSIC Press; 1992.
Soares D, Niemiller ML. Sensory adaptations of fishes to subterranean environments. Bioscience. 2013;63:274–83.
Article
Google Scholar
Yoshizawa M. Behaviors of cavefish offer insight into developmental evolution. Mol Reprod Dev. 2015;82:268–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dowling TE, Martasian DP, Jeffery WR. Evidence for multiple genetic forms with similar eyeless phenotypes in the blind cavefish, Astyanax mexicanus. Mol Biol Evol. 2002;19:446–55.
Article
CAS
PubMed
Google Scholar
Jingcheng R, Weicheng Y. A review of progress in Chinese troglofauna research. J Resour Ecol. 2015;6:237–46.
Google Scholar
Strecker U, Faúndez VH, Wilkens H. Phylogeography of surface and cave Astyanax (Teleostei) from Central and North America based on cytochrome b sequence data. Mol Phylogenet Evol. 2004;33:469–81.
Article
CAS
PubMed
Google Scholar
Zhao Y, Zhang C. Cavefishes: concept, diversity and research progress. Biodivers Sci. 2006;14:451.
Article
Google Scholar
Gross JB, Protas M, Conrad M, Scheid PE, Vidal O, Jeffery WR, et al. Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus. Proc Natl Acad Sci USA. 2008;105:20106–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Culver DC, Kane TC, Fong DW. Adaptation and natural selection in caves: the evolution of Gammarus minus. Cambridge: Harvard University Press; 1995.
Book
Google Scholar
Jeffery WR. Cavefish as a model system in evolutionary developmental biology. Dev Biol. 2001;231:1–12.
Article
CAS
PubMed
Google Scholar
Li Z, Guo B, Li J, He S, Chen Y. Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae: Sinocyclocheilus). Chin Sci Bull. 2008;53:2342–52.
CAS
Google Scholar
Yang J, Chen X, Bai J, Fang D, Qiu Y, Jiang W, et al. The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biol. 2016;14:1–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hart PB, Niemiller ML, Burress ED, Armbruster JW, Ludt WB, Chakrabarty P. Cave-adapted evolution in the North American amblyopsid fishes inferred using phylogenomics and geometric morphometrics. Evolution. 2020;74:936–49.
Article
PubMed
Google Scholar
Zhao Y, Huang Z, Huang J, Zhang C, Meng F. Phylogenetic analysis and expression differences of eye-related genes in cavefish genus Sinocyclocheilus. Integr Zool. 2020. https://doi.org/10.1111/1749-4877.12466.
Article
PubMed
PubMed Central
Google Scholar
Borowsky R. Breeding Astyanax mexicanus through natural spawning. Cold Spring Harb Protoc. 2008;2008:pdb-prot5091.
Article
Google Scholar
Lan J, Gan X, Wu T, Yang J. Cave fishes of Guangxi, China. 2013.
Huang Q, Cai Y, Xing X. Rocky desertification, antidesertification, and sustainable development in the karst mountain region of Southwest China. Ambio. 2008;37:390–2.
Article
PubMed
Google Scholar
Jiang W-S, Li J, Lei X-Z, Wen Z-R, Han Y-Z, Yang J-X, et al. Sinocyclocheilus sanxiaensis, a new blind fish from the Three Gorges of Yangtze River provides insights into speciation of Chinese cavefish. Zool Res. 2019;40:552.
Article
PubMed
PubMed Central
Google Scholar
Zhao Y, Zhang C. Endemic fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China-species diversity, cave adaptation, systematics and zoogeography. Beijing: Science Press; 2009.
Google Scholar
Romero A, Zhao Y, Chen X. The hypogean fishes of China. In: Chinese fishes. Dordrecht: Springer; 2009. p. 211–78.
Chapter
Google Scholar
Ma L, Zhao Y, Yang J. Cavefish of China. In: Encyclopedia of caves. Amsterdam: Elsevier; 2019. p. 237–54.
Chapter
Google Scholar
Li J, Li XH, Mayden RL. Sinocyclocheilus brevifinus (Teleostei: Cyprinidae), a new species of cavefish from Guangxi, China. Zootaxa. 2014;3873:37–48.
Article
PubMed
Google Scholar
Zhou J, Liu Q, Wang H, Yang L, Zhao D, Zhang T, et al. Description on a new species of Sinocyclocheilus in Guizhou. Sichuan J Zool. 2011;28:387–9.
Google Scholar
Zhu D, Zhu Y. A new species of the genus Sinocyclocheilus (Cypriniformes, Cyprinidae) from Guangxi, China. Acta Zootaxonomica Sin. 2012;37:222–6.
Google Scholar
Zheng H, Xiu L, Yang J. A new species of Barbine genus Sinocyclocheilus (Teleostei: Cyprinidae) from Zuojiang river drainage in Guangxi, China. Environ Biol Fish. 2013;96:747–51.
Article
Google Scholar
Li J, Li X-H. Sinocyclocheilus gracilis, a new species of hypogean fish from Guangxi, South China (Teleostei: Cypriniformes: Cyprinidae). Ichthyol Explor Freshw. 2014;24:249–56.
Google Scholar
Wang D, Zhao YH, Yang JX, Zhang CG. A new cavefish species from Southwest China, Sinocyclocheilus gracilicaudatus sp. nov. (Teleostei: Cypriniformes: Cyprinidae). Zootaxa. 2014;3768:583–90.
Article
PubMed
Google Scholar
Chen Y-Q, Peng C-L, Zhang E. Sinocyclocheilus guanyangensis, a new species of cavefish from the Li-Jiang basin of Guangxi, China (Teleostei: Cyprinidae). Ichthyol Explor Freshw. 2016;27:1–8.
Google Scholar
Luo F, Huang J, Liu X, Luo T, Wen Y. Sinocyclocheilus ronganensis Luo, Huang et Wen sp. nov., a new species belonging to Sinocyclocheilus Fang from Guangxi (Cypriniformes: Cyprinidae). J South Agric. 2016;47:650–5.
Google Scholar
Yang H, Li C, Chen Y, Li W. A new species of Sinocyclocheilus from Yunnan: Sinocyclocheilus wenshanensis. J Yunnan Univ Nat Sci Ed. 2017;39:507–12. https://doi.org/10.7540/j.ynu.20160534.
Article
Google Scholar
Zhou J, Li X, Hou X, Sun Z, Gao L, Zhao T. A new species of Sinocyclocheilus in Guizhou, China. Sichuan J Zool. 2009;28:321–3.
Google Scholar
Wu T, Liao Z, Gan X, Li W. Two new species of Sinocyclocheilus in Guangxi, China (Cypriniefrmes, Cyprinidae). J Guangxi Norm Univ Nat Sci Ed. 2010;28:116–20.
Google Scholar
Zhu D-G, Zhu Y, Lan J-H. Description of a new species of Barbinae, Sinocyclocheilus huangtianensis from China (Teleostei: Cypinidae). Dongwuxue Yanjiu. 2011;32(2):204–7.
CAS
PubMed
Google Scholar
Gan X, Wu T-J, Wei M-L, Yang J. A new blind barbine species, Sinocyclocheilus anshuiensis sp. nov. (Cypriniformes: Cyprinidae) from Guangxi, China. Dongwuxue Yanjiu. 2013;34(5):459–63.
PubMed
Google Scholar
Pan X-F, Li L, Yang J-X, Chen X-Y. Sinocyclocheilus xichouensis, a new species of golden-line fish from the Red River drainage in Yunnan, China (Teleostei: Cypriniformes). Dong wu xue yan jiu. 2013;34(4):368–73.
PubMed
Google Scholar
Cheng C, Pan X, Chen X, Li J, Ma L, Yang J. A new species of the genus Sinocyclocheilus (Teleostei: Cypriniformes), from Jinshajiang Drainage, Yunnan, China. Cave Res. 2015;1(2):1–4.
Google Scholar
Lan Y, Qin X, Lan J, Xiu L, Yang J. A new species of the genus Sinocyclocheilus (Cypriniformes, Cyprinidae) from Guangxi, China. J Xinyang Norm Univ (Nat Sci Ed). 2017;30:97. https://doi.org/10.3969/j.issn.1003-0972.2017.01.021.
Article
Google Scholar
Li G, Wu J, Leng Y, Zhou R, Pan X, Han F, et al. A new species Sinocyclocheilus longshanensis sp. nov. from Yunnan. Chin Agric Sci Bull. 2018;34:153–8. https://doi.org/10.11924/j.issn.1000-6850.casb17080066.
Article
Google Scholar
Xiao H, Chen S, Liu Z, Zhang R, Li W, Zan R, et al. Molecular phylogeny of Sinocyclocheilus (Cypriniformes: Cyprinidae) inferred from mitochondrial DNA sequences. Mol Phylogenet Evol. 2005;36:67–77.
Article
CAS
PubMed
Google Scholar
Jiang Y, Fu J, Zhang D, Zhao Y. Investigation on the lateral line systems of two cavefish: Sinocyclocheilus macrophthalmus and S. microphthalmus (Cypriniformes: Cyprinidae). J Bionic Eng. 2016;13:108–14.
Article
Google Scholar
Li P, Yang J. Complete mitochondrial genome and phylogenetic analysis of Sinocyclocheilus microphthalmus (Cypriniformes: Cyprinidae). Mitochondrial DNA Part B. 2019;4:3094–5.
Article
PubMed
PubMed Central
Google Scholar
Ardila A. The evolutionary concept of “preadaptation” applied to cognitive neurosciences. Front Neurosci. 2016;10:103.
Article
PubMed
PubMed Central
Google Scholar
Espinasa L, Borowsky R. Eyed cave fish in a karst window. J Cave Karst Stud. 2000;62:180–3.
Google Scholar
Culver DC, Pipan T. The biology of caves and other subterranean habitats. Oxford: Oxford University Press; 2019.
Book
Google Scholar
Trajano E, Bichuette ME, Kapoor BG. Biology of subterranean fishes. Boca Raton: CRC Press; 2010.
Book
Google Scholar
He Y, Chen X-Y, Xiao T-Q, Yang J-X. Three-dimensional morphology of the Sinocyclocheilus hyalinus (Cypriniformes: Cyprinidae) horn based on synchrotron X-ray microtomography. Dong wu xue yan jiu. 2013;34(E4–5):E128-34.
PubMed
Google Scholar
Soares D, Pluviose M, Zhao Y. Ontogenetic development of the horn and hump of the Chinese cavefish Sinocyclocheilus furcodorsalis (Cypriniformes: Cyprinidae). Environ Biol Fish. 2019;102:741–6.
Article
Google Scholar
Gallo ND, Jeffery WR. Evolution of space dependent growth in the teleost Astyanax mexicanus. PLoS ONE. 2012;7:e41443.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jeffery WR. Regressive evolution in Astyanax cavefish. Annu Rev Genet. 2009;43:25–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Protas M, Tabansky I, Conrad M, Gross JB, Vidal O, Tabin CJ, et al. Multi-trait evolution in a cave fish Astyanax mexicanus. Evol Dev. 2008;10:196–209.
Article
PubMed
Google Scholar
Bradic M, Teotónio H, Borowsky RL. The population genomics of repeated evolution in the blind cavefish Astyanax mexicanus. Mol Biol Evol. 2013;30:2383–400.
Article
CAS
PubMed
PubMed Central
Google Scholar
Casane D, Rétaux S. Evolutionary genetics of the cavefish Astyanax mexicanus. Adv Genet. 2016;95:117–59.
Article
CAS
PubMed
Google Scholar
Gross JB. The complex origin of Astyanax cavefish. BMC Evol Biol. 2012;12:1–12.
Article
Google Scholar
Hubbs CL, Innes WT. The first known blind fish of the family Characidae: a new genus from Mexico. Occas Pap Mus Zool Univ Mich. 1936;342:1–7.
Google Scholar
Gross JB, Furterer A, Carlson BM, Stahl BA. An integrated transcriptome-wide analysis of cave and surface dwelling Astyanax mexicanus. PLoS ONE. 2013;8:e55659.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carlson BM, Onusko SW, Gross JB. A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology. G3 Genes Genomes Genet. 2015;5:241–51.
Google Scholar
Powers AK, Davis EM, Kaplan SA, Gross JB. Cranial asymmetry arises later in the life history of the blind Mexican cavefish, Astyanax mexicanus. PLoS ONE. 2017;12:e0177419.
Article
PubMed
PubMed Central
CAS
Google Scholar
Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, et al. The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Mol Ecol. 2018;27:4397–416.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bradic M, Beerli P, García-de León FJ, Esquivel-Bobadilla S, Borowsky RL. Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus). BMC Evol Biol. 2012;12:9.
Article
PubMed
PubMed Central
Google Scholar
Wilkens H, Strecker U. Surface and cave populations of Mexican Astyanax. In: Evolution in the dark. Berlin: Springer; 2017. p. 37–52.
Chapter
Google Scholar
Krishnan J, Rohner N. Cavefish and the basis for eye loss. Philos Trans R Soc B. 2017;372:20150487.
Article
Google Scholar
Wilkens H. Genetics and hybridization in surface and cave Astyanax (Teleostei): a comparison of regressive and constructive traits. Biol J Lin Soc. 2016;118:911–28.
Article
Google Scholar
Staden R. The Staden sequence analysis package. Mol Biotechnol. 1996;5:233–41.
Article
CAS
PubMed
Google Scholar
Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinf. 2003. https://doi.org/10.1002/0471250953.bi0203s00.
Article
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Santorum JM, Darriba D, Taboada GL, Posada D. Jmodeltest.org: selection of nucleotide substitution models on the cloud. Bioinformatics. 2014;30:1310–1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus evolution. 2018;4:vey016.
Miller MA, Pfeiffer W, Schwartz T. The CIPRES science gateway: a community resource for phylogenetic analyses. In: Proceedings of the 2011 TeraGrid conference on extreme digital discovery - TG’11. Salt Lake City, Utah: ACM Press; 2011. p. 1. https://doi.org/10.1145/2016741.2016785.
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018;67:901.
Article
CAS
PubMed
PubMed Central
Google Scholar
Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rohlf F. tpsDig, ver 2.16: department of ecology and evolution. 2010.
Rohlf FJ. tpsUtil, file utility program, version 1.26. Department of Ecology and Evolution, State University of New York at Stony Brook. 2004.
Gunz P, Mitteroecker P. Semilandmarks: a method for quantifying curves and surfaces. Hystrix. 2013;24:103–9.
Google Scholar
Adams DC, Otárola-Castillo E. geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods Ecol Evol. 2013;4:393–9.
Article
Google Scholar
Adams DC, Rohlf FJ, Slice DE. A field comes of age: geometric morphometrics in the 21st century. Hystrix. 2013;24:7.
Google Scholar
Nielsen R. Mapping mutations on phylogenies. Syst Biol. 2002;51:729–39.
Article
PubMed
Google Scholar
Huelsenbeck JP, Nielsen R, Bollback JP. Stochastic mapping of morphological characters. Syst Biol. 2003;52:131–58.
Article
PubMed
Google Scholar
Evans ME, Smith SA, Flynn RS, Donoghue MJ. Climate, niche evolution, and diversification of the “bird-cage” evening primroses (Oenothera, sections Anogra and Kleinia). Am Nat. 2009;173:225–40.
Article
PubMed
Google Scholar
Revell LJ. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol. 2012;3:217–23.
Article
Google Scholar
Sidlauskas B. Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach. Evolution. 2008;62:3135–56.
Article
PubMed
Google Scholar
Team RC. R: A language and environment for statistical computing. 2013.
Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, et al. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS ONE. 2013;8:e69885.
Article
CAS
PubMed
PubMed Central
Google Scholar