Caves as Species Pumps: Key Innovations, Isolation and Periodic Introgression Drive the World's Largest Cavefish...

Species diversification arises from complex interactions among multiple drivers, such as gene flow, hybridisation, 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 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.