Biome shifts and recent rapid radiations in the Cape Clade of the genus Indigofera (Fabaceae: Indigofereae) explain contemporary diversity in the GCFR

• We present first phylogenomic data for Indigofera in South Africa. • Inference of multiple biome shifts leading to diversification of GCFR Indigofera . • Unidirectional shifts into the Temperate biome from Succulent and Grass biomes. • Pleistocene radiations in both Succulent and Temperate biomes result in current diversity. Indigofera is one of the most diverse genera in the Fabaceae within the Greater Cape Floristic Region (GCFR) of South Africa, with over 140 species known following extensive taxonomic research. The GCFR accounts for over 15 % of global species with one of the highest density of species by size of area. This study aimed to investigate biogeographic and edaphic patterns of specifically the Cape Clade of the genus in an attempt to better understand diversification patterns. Using Angiosperms353 target-enrichment sequencing, the first genomic data was produced for South African Indigofera . A phylogenetic tree was produced in ASTRAL, and then dated to allow for further analyses to infer biome, vegetation type and geological preferences. Cape Clade Indigofera species clustered primarily into two biomes, with evidence suggesting an origin and initial diversification in the Succulent biome, with multiple subsequent dispersals and radiations into the Temperate and Grass biomes, both at the lineage and species level. Recent and rapid radiations in both Temperate and Succulent biome lineages have contributed to the rich species diversity observed in the Cape Clade today. This study further emphasizes how the unique edaphic conditions of the GCFR contribute to emergence and diversification of the Cape Flora. This may also explain why the Cape Clade of Indigofera is so narrowly distributed in comparison to the other major global clades.