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The diversity of life is not evenly distributed across the planet. A few areas, so-called biodiversity hotspots, harbour the majority of all species. Although this pattern is well-described, a central question of evolution remains unresolved: What are the drivers shaping high biodiversity, particularly in tropical rainforests? Answering the question was impossible thus far, because at least one of three essential components was not available for study. These are: 1) a fossil record as logfile of species’ histories, 2) past climate data, needed to reconstruct habitat changes, and 3) knowledge about the ability of species to adapt to changing environments. Recent methodological advances enable us now for the first time to investigate these three components simultaneously in a biodiversity hotspot where they are all attainable: the Sunda Shelf in Southeast Asia (SE Asia). By combining climate reconstructions, molecular genetic data and species distribution data from the Late Pleistocene (126-13.7 thousand years ago; kya) to the present we can evaluate the impact of two key drivers shaping biodiversity: gradual climate change versus a single catastrophic event. The results also allow us to assess the long-term consequences of the current (man-made) biodiversity crisis.