Ancient hybridization drives arid adaptation and species diversification in Caragana (Fabaceae)

The genus Caragana (Fabaceae), comprising predominantly xerophytic shrubs, is ecologically important in arid ecosystems across Asia and Eastern Europe. Hybridization is increasingly recognized as a critical evolutionary mechanism, yet its role in arid adaptation and lineage diversification remains underexplored. Here, we test the hypothesis that ancient hybridization-facilitated ecological expansion and diversification in Caragana. We generated a chromosome-level genome assembly for Caragana arborescens and conducted genome-wide resequencing of 98 individuals across 73 species, representing the full taxonomic breadth of the genus. Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages. These hybridization events coincided with late Oligocene aridification and were temporally associated with sharp increases in diversification rates. Introgressed genomic regions were significantly enriched for genes involved in drought tolerance, including those regulating root development, osmoregulation, and hormone signaling. Key gene families, such as late embryogenesis abundant (LEA), sulfate transporters (SULTR), NAM-ATAF-CUC (NAC), and nitrate transporter 1 / peptide transporter family (NPF), exhibited duplications and evolutionary rate shifts in hybrid lineages. Furthermore, Aridity Index data confirmed that hybrid lineages occupy more arid habitats than either parent, highlighting a link between introgression and ecological breadth. Our findings demonstrate that ancient hybridization served as a catalyst for adaptive innovation and diversification in Caragana, offering a genomic mechanism for rapid radiation in response to climatic aridification. This study underscores the evolutionary significance of hybridization in enabling plant lineages to colonize and thrive in extreme environments.