Figure S1: ParalogWizard pairwise distance histogram. Figure S2: Maximum likelihood ancestral range estimation of Helichrysum using the best-fit model DEC+j from BioGeoBEARS. Figure S3: ASTRAL species tree of Helichrysum. Figure S4: Frequency distributions of event counts from 100 biogeographic stochastic mappings (DEC+j model) on the Helichrysum phylogeny. Figure S5: Maximum likelihood ancestral range estimation of Helichrysum using the model DEC from BioGeoBARS. Figure S6: Frequency distributions of event counts form 100 biogeographic stochastic mappings (DEC model) on the Helichrysum phylogeny. Table S1: List of studied materials with BioSample accession numbers. Table S2: Reads recovered per species after filtering (HPM1). Table S3: Statistics from paralogy analyses using ParalogWizard. Table S4: Summary of selected loci for subsequent phylogeny reconstruction. Table S5: Summary statistics resulting from the processing of nuclear DNA data. Table S6: Summary statistics of biogeographic model testing in BioGeoBEARS. Table S7: Ancestral range probabilities of the model DEC+J for Helichrysum. Table S8: DEC+j model biogeographic stochastic mapping mean and standard deviation tables. Table S9: DEC model biogeographic stochastic mapping mean and standard deviation tables.

The Afromontane and Afroalpine areas constitute some of the main biodiversity hotspots of Africa. They are particularly rich in plant endemics, but the biogeographic origins and evolutionary processes leading to this outstanding diversity are poorly understood. We performed phylogenomic and biogeographic analyses of one of the most species-rich plant genera in these mountains, Helichrysum (Compositae-Gnaphalieae). Most previous studies have focused on Afroalpine elements of Eurasian origin, and the southern African origin of Helichrysum provides an interesting counterexample. We obtained a comprehensive nuclear dataset from 304 species (≈50% of the genus) using target-enrichment with the Compositae1061 probe set. Summary-coalescent and concatenation approaches combined with paralog recovery yielded congruent, well-resolved phylogenies. Ancestral range estimations revealed that Helichrysum originated in arid southern Africa, whereas the southern African grasslands were the source of most lineages that dispersed within and outside Africa. Colonization of the tropical Afromontane and Afroalpine areas occurred repeatedly throughout the Miocene–Pliocene. This timing coincides with mountain uplift and the onset of glacial cycles, which together may have facilitated both speciation and intermountain gene flow, contributing to the evolution of the Afroalpine flora.