Data from: 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 Oligocene (~26 Ma) and undergoing repeated connections thereafter.
The origin and diversification of cavefishes are intrinsically 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 the conservation of these unique karst habitats amidst ongoing
climate change.