Abstract
Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization has rarely been demonstrated among tree species in Amazonia, the world’s largest rainforest. We show that within Brownea, a characteristic tree genus of Amazonia, there is extensive evidence of hybridization. Using both phylogenomic and population genomic approaches we find multiple historical hybridization events within Brownea, along with contemporary hybridization among co-occurring species. Finally, we infer homogeneous rates of gene flow among different genomic loci, indicating a lack of selection against hybrids, reflecting their persistence over time. These results demonstrate that gene flow between Amazonian tree species has occurred across temporal scales and may have contributed to the evolution of the most diverse tree flora on Earth.