Paleogene mass extinction and ongoing Neogene recolonization shape the tropical African flora

Tropical regions are known to host most of the global biodiversity, yet species richness varies drastically between continents. Tropical Africa has long been recognized as the "odd man out", exhibiting lower plant diversity compared to other tropical continents, but the underlying causes remain debated. Here, we use ferns as a model group to explore the processes responsible for the low diversity of African plants. We find that the current fern diversity in Africa, particularly in humid regions, is up to 84% lower than under similar climatic conditions in the Americas and Asia. Unlike on these continents, where 55-60% of extant fern diversity is the result of in-situ diversification of Gondwanan lineages, only 16% of African fern diversity originates from such lineages. This discrepancy points to significant African extinction periods during the Paleogene and mid-Miocene, likely driven by elevated temperatures and aridification. In contrast, 54% of the extant African fern diversity can be attributed to approximately 530 intercontinental dispersal events during the Neogene, indicating ongoing recolonization of Africa. Our findings provide unprecedented insight into the evolutionary forces shaping plant diversity in tropical Africa and highlight the potential risks posed by ongoing climate change to its botanical heritage.