Abstract
The karst ecosystem in southwestern China is a global hotspot for cavefish diversity research, yet the origins and evolutionary history of this diversity remain poorly understood. To elucidate their evolutionary origins and history, we analyzed 183 cavefish species and their close relatives from ten clades. Our findings indicate that freshwater fishes began colonizing caves ~44 million years ago (Ma). Speciation was driven by in situ diversification, starting around 43.2 Ma, increasing sharply by ~35 Ma and 18 Ma, and peaking at ~8.3 Ma, 2.5 Ma, and 1.5 Ma. Distinct hydrological basins exhibited divergent diversification patterns. Dispersal between the Pearl and Yangtze River basins began by ~24.1 Ma, accelerated around 21 Ma, 13 Ma, and 9.6 Ma, and peaked at ~13 Ma, 5 Ma, and 2 Ma. We propose that river drainages in southwestern China developed stepwise from the late Eocene to early Pleistocene, with connectivity between the Pearl and Yangtze basins established by the late Oligocene ( ~ 26 Ma). The origin and diversification of cavefishes are closely linked to the evolution of karst landscapes, shaped by orogeny and monsoon-driven climate changes since the late Eocene. These insights are crucial for informing conservation strategies for these unique habitats under ongoing climate change.
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Data availability
The sequences reported in this paper have been deposited in GenBank (accession nos. ON116493–ON116532, ON148332–ON148334, OP473612–OP473909, OQ754141–OQ754145, OQ754148–OQ754150, OQ754152, OQ754154, OQ754155, OQ754157–OQ754159, PQ222367–PQ222376, PX715913–PX715924). All publicly available sequence data (e.g., GenBank accessions) used in this study are detailed in Supplementary Tables 1–8 and Supplementary Data 2–4. Source data underlying Fig. 1 are provided in Supplementary Data 1. Source data for Fig. 2 have been deposited in the Science Data Bank (https://doi.org/10.57760/sciencedb.35098)88. Source data for Figs. 3A, 3B, 3C, 3D, 3E, and 3F are provided in Supplementary Data 5, Supplementary Data 6, Supplementary Table 14, Supplementary Table 15, Supplementary Table 16, and PANGAEA39,97 (Supplementary Table 17), respectively. Source data underlying Fig. 4 are available in PANGAEA39,97 and included in Supplementary Table 17. All other datasets are provided in the supplementary information and data files associated with this publication. Source data for sequence alignments, time‑calibrated phylogenies, diversification analyses, and paleoenvironmental reconstructions are available from the Science Data Bank. (https://doi.org/10.57760/sciencedb.35098).
Code availability
All analyses were conducted using open-source software tools, with detailed parameters specified in the corresponding methods sections. Scripts used for generating the associated figures have been archived at the Science Data Bank (https://doi.org/10.57760/sciencedb.35098).
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Acknowledgements
This work was supported by the following programs: the Endangerment Processes and Mechanisms of Endangered Flagship Animals (2022YFF1301502), the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB31000000), and the Guizhou Normal University Academic Emerging Talent Fund Project (Qianshi Xin Miao [2021] 20). We are grateful to Prof. Li-Na Du for providing tissue samples of Karstsinnectes longzhouensis and Troglonectes hechiensis. We are grateful to Mr. Jia-Hu Lan for providing tissue samples of Karstsinnectes acridorsalis and Troglonectes barbatus used in this study. We also thank Chang-Ting Lan, Jing Yu, Ya-Li Wang, Xin-Rui Zhao, Xing-Liang Wang, Zhi-Xia Chen, and Ming-Le Mao for their assistance in field surveys and laboratory work. We thank LetPub (www.letpub.com.cn) for its linguistic assistance during the preparation of this manuscript.
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T.L.: Data curation, formal analysis, investigation, methodology, visualization, writing—original draft, writing—review and editing; M.Y.X.: Conceptualization, data curation, investigation, methodology, project administration, supervision, visualization, writing—review and editing; M.L. and J. J.W.: Data curation; N.X.: Writing—review and editing; J.Z.: Conceptualization, formal analysis, funding acquisition, investigation, methodology, project administration, resources, supervision, visualization, writing—review and editing. All authors gave final approval for publication and agreed to be held accountable for the work performed therein.
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Luo, T., Xiao, MY., Liao, M. et al. Evolutionary history of Chinese cavefishes parallels paleogeoclimatic and river capture processes. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09881-8
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DOI: https://doi.org/10.1038/s42003-026-09881-8
