Evolutionary history of Chinese cavefishes parallels paleogeoclimatic and river capture processes.

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.