Late Miocene Cooling drives range evolution in the African-Malagasy endemic <i>Tricalysia</i> (Rubiaceae: Coffeeae)

Abstract Tricalysia (Rubiaceae), a diverse genus of tropical African understory shrubs and small trees, offers a rich system to answer evolutionary questions about biogeography, speciation, and trait evolution. Phylogenetic relationships within the genus remain poorly resolved, limiting taxonomic clarity and obscuring evolutionary patterns. In this study, we use a target-capture approach using the Angiosperm 353 probe set to reconstruct a robust phylogenetic tree of Tricalysia, sampling broadly across the genus and generating data for hundreds of nuclear loci. Phylogenetic and systematic analyses using both concatenated maximum likelihood and coalescent-based species tree methods resolve Tricalysia as monophyletic and sister to the genus Empogona. They also reveal strong support for several major clades, while also indicating that current sectional classifications do not fully reflect evolutionary history. Robbrecht’s morphology-based sections are not corroborated, apart from section Probletostemon. In fact, only sections Androgyne Probletostemon are found to be monophyletic whereas sections Ephedranthera and Tricalysia are polyphyletic. The last section, Rosea, is only represented by a single species and cannot be evaluated. Biogeographic patterns indicate that diversification in Tricalysia is related to aridification during the Late Miocene Cooling event and rapid fluctuations during the glacial/interglacial cycles in the Plio-Pleistocene. Our results provide a well-supported phylogenetic hypothesis for understanding the history of Tricalysia while offering new insights into the evolutionary processes that have shaped this African genus.