Subtropical East Asian caves are characterized by high levels of biodiversity and endemism but most do not fall within protected areas. Here, we investigate the timing and mode of cave colonization through a multi-taxon meta-analysis combined with investigation of paleoenvironmental dynamics. We show that most cave colonization events occurred after the Oligocene-Miocene boundary. Importantly, we document that biotic colonization of subtropical East Asian caves was not a random process, but was subject to periods of acceleration and decrease, in association with the climate and vegetational changes and the establishment of seasonal climate in subtropical East Asia. Our results provide insights into how subterranean biodiversity in subtropical East Asia has been shaped over time and also have implications for biodiversity conservation.

Caves are home to unique and fragile biotas with high levels of endemism. However, little is known about how the biotic colonization of caves has developed over time, especially in caves from middle and low latitudes. Subtropical East Asia holds the world’s largest karst landform with numerous ancient caves, which harbor a high diversity of cave-dwelling organisms and are regarded as a biodiversity hotspot. Here, we assess the temporal dynamics of biotic colonization of subtropical East Asian caves through a multi-taxon analysis with representatives of green plants, animals, and fungi. We then investigate the consequences of paleonviromental changes on the colonization dynamics of these caves in combination with reconstructions of vegetation, temperature, and precipitation. We discover that 88% of cave colonization events occurred after the Oligocene-Miocene boundary, and organisms from the surrounding forest were a major source for subtropical East Asian cave biodiversity. Biotic colonization of subtropical East Asian caves during the Neogene was subject to periods of acceleration and decrease, in conjunction with large-scale, seasonal climatic changes and evolution of local forests. This study highlights the long-term evolutionary interaction between surface and cave biotas; our climate-vegetation-relict model proposed for the subtropical East Asian cave biota may help explain the evolutionary origins of other mid-latitude subterranean biotas.