Polyploidy meets the Cape: Evolutionary dynamics of Heliophila (Brassicaceae).

The Cape Floristic Region (CFR), a global biodiversity hotspot, provides an exceptional setting for studying plant diversification. The South African genus Heliophila (Brassicaceae), notable for its species richness and morphological diversity, offers a unique system for examining the evolutionary role of polyploidy. Using an integrative framework combining phylogenomics, cytogenetics, and floral pigment biochemistry, we reconstructed the genus's evolutionary history based on ITS and 48 nuclear markers from 392 accessions representing over 120 taxa. Our analyses resolved four major clades originating during a rapid Miocene radiation (12-10 Mya) and revealed extensive chromosome number variation (2n = 16-80) shaped by descending dysploidy and recurrent neopolyploidization. Ancestral state reconstruction indicates that the common ancestor was annual and that perenniality evolved independently at least 13 times, predominantly in lineages occupying cooler and wetter habitats. Environmental analyses show strong ecological differentiation among clades, suggesting adaptation to contrasting climatic and edaphic conditions across the CFR. Floral pigment profiling uncovered multiple species with delphinidin-based anthocyanins, revealing new ornamental potential. Together, these findings demonstrate that polyploidy, genome restructuring, and ecological heterogeneity have jointly shaped the diversification of Heliophila, underscoring its value as a model for studying polyploid evolution in biodiversity hotspots and highlighting the importance of wild genetic resources for conservation and crop improvement.