Geological events and climate oscillations shaped the divergence and evolutionary history of Rehmannia species...

Unveiling the evolutionary trajectories of species is a key to understanding the mechanisms and processes of speciation. But it remains challenging due to its complexity shaped by paleogeological and paleoclimatic events. Rehmannia containing a few species with distinct distribution pattern is a good model for exploring how closely related species respond to similar environmental changes after speciation. Using three datasets (SLAF, cpDNA, and ITS markers), we detected phylogenetic incongruences among Rehmannia taxa. Cytonuclear discordance between R. chingii and R. henryi likely reflects chloroplast capture, with R. chingii probably having acquired its plastid genome via introgression from a lineage related to the diploid R. piasezkii. While our three datasets support the synonymy of R. solanifolia with R. glutinosa, future investigations employing more comprehensive approaches and trait-associated genes will be needed to fully resolve their phylogenetic affinities. The ambiguous phylogenetic placement of R. glutinosa possibly stems from differences of molecular evolution rates. The Qingling-Daba Mountains likely represent the center of origin and divergence for Rehmannia, where ongoing dispersal and vicariance played important roles in its lineage differentiation. The Miocene Climatic Optimum (MCO, 17-15 Mya) may have facilitated diversification of the genus. In turn, mountain uplifts, subsequent global cooling in the Late Miocene, Quaternary climatic oscillations, together with geological barriers likely accelerated divergence among the lineages. Collectively, these processes ultimately led to significant spatial structure and local adaptation differentiation among Rehmannia species.