Evolutionary history of Chinese cavefishes parallels paleogeoclimatic and river capture processes

The karst ecosystems of southwestern China are a global hotspot of cavefish diversity. To elucidate their evolutionary origins and diversification history, we analyzed 183 cave species and their close relatives from ten clades. Our findings reveal that freshwater fishes started colonizing caves ~44 million years ago (Ma). The primary driver of speciation was in situ diversification, which began around 43.8 Ma, increased sharply by ~25 Ma, and showed peaks at ~10 Ma and 2.4 Ma, with a valley at ~3.3 Ma. Distinct hydrological basins exhibited divergent diversification patterns. Dispersal from the Pearl River to the Yangtze River and vice versa began around 23.8 Ma and 12.6 Ma, accelerated at ~13 Ma and 8.2 Ma, and peaked at 16 Ma, 2 Ma, and 5 Ma, respectively. We propose that the river drainages of southwestern China developed stepwise from the late Eocene to early Pleistocene, with the Pearl and Yangtze River basins potentially establishing connectivity as early as the late Oligocen..., , , # Evolutionary history of Chinese cavefishes parallels paleogeoclimatic and river capture processes [https://doi.org/10.5061/dryad.ht76hdrqx](https://doi.org/10.5061/dryad.ht76hdrqx) ## Description of the data and file structure Title: Origin and diversification history of underground fishes in a biodiversity hotspot in China. Author list: Tao Luo, Ming-Yuan Xiao, Jia-Jia Wang, Mei Liao, Ning Xiao, Jiang Zhou BEAST_alignment.zip: Alignments for phylogenetic analyses of 10 clades investigated. BEAST_settings.zip: Settings for divergence time estimation of 10 clades investigated. BEAST_timetrees.zip: Timetrees for the 10 clades investigated. , ,