Phylogenomics reveals taxonomic challenges in Calibrachoa (Solanaceae) and sheds light on the origins of cultivated million bells.

Phylogenies are essential for understanding evolutionary relationships, testing species boundaries, and defining species status. However, hybridization and incomplete lineage sorting (ILS) can obscure these relationships in recently diversified plant lineages by creating conflicting signals across the genome and reducing phylogenetic resolution. Calibrachoa (million bells), a Neotropical genus of ornamental plants with high ecological diversity, underwent rapid diversification during the Pleistocene, leading to extensive ILS and interspecific hybridization. In this study, we sampled multiple individuals from all recognized species, a potential new species, and a commercial cultivar of Calibrachoa. We used genome-wide genotyping to investigate phylogenetic relationships, species cohesion, hybridization, and the origin of one commercial cultivar. Our results confirm the division of the genus into two subgenera: Calibrachoa sensu stricto and Stimomphis. Within Stimomphis, we observed paraphyly and polyphyly, with low support for several phylogenetic nodes. This uncertainty likely reflects challenges in species delimitation, high ILS due to recent diversification, and ongoing hybridization. We also confirm the hybrid origin of the commercial cultivar. Our findings provide new insights into the evolutionary history of Calibrachoa, improving our understanding of its taxonomy and hybridization dynamics. These results illustrate the need to account for reticulate evolution and ILS when resolving phylogenies in rapidly diversifying plant groups.