Data from: Caves as species pumps: Key innovations, isolation, and periodic introgression drive the world's largest cavefish radiation in a dynamic karstic landscape

Species diversification arises from complex interactions among multiple
drivers, such as gene flow, hybridization, key innovations, historical
climate changes, geological events, and ecological opportunities. Yet,
their relative contributions to large radiations remain inadequately
understood. We investigate the interplay among these factors in the
diversification of Sinocyclocheilus, a diverse cavefish radiation
comprising 79 species. This genus spans a continuum from surface-dwelling
forms with fully developed eyes and pigmentation to cave-dwelling forms
with regressed eyes, pigment loss, and unique traits such as horns and a
dorsal humps. Using reduced-representation genomic data (RADseq), we
detect widespread gene flow across different species, with introgression
playing a major role compared to incomplete lineage sorting in generating
phylogenetic discordance and contributing genetic variation for cave
adaptation and diversification in this group. Key traits, including eye
degeneration, reduced pigmentation, and horn development, evolved
independently multiple times as adaptations to cave environments.
Furthermore, geological and climatic shift events, such as the uplift of
the Tibetan plateau and the late Miocene cooling, significantly enhanced
their speciation rates. Demographic analyses indicate population
expansions during the Gonghe Movement and stability during the Last
Glacial Maximum, possibly due to the buffering of cave refugia. Periodic
introgression events promoted by isolation and reconnections due to the
changing climate and geological activity, combined with the repeated
evolution of key cave-adapted traits, emerge as primary drivers of this
radiation. Our findings underscore the intricate interactions of these
drivers in Sinocyclocheilus evolution, offering fresh insights into the
processes driving cave adaptation and diversification.