Adaptive radiation of the <i>Callicarpa</i> genus in the Bonin Islands revealed through double‐digest restriction site‐associated <scp>DNA</scp> sequencing analysis

The Bonin Islands, comprised of the Mukojima, Chichijima, and Hahajima Islands, are known for their isolated and distinctive habitats, hosting a diverse array of endemic flora and fauna. In these islands, adaptive radiation has played a remarkable role in speciation, particularly evident in the <i>Callicarpa</i> genus that is represented by three species: <i>Callicarpa parvifolia</i> and <i>C. glabra</i> exclusive to the Chichijima Islands, and <i>Callicarpa subpubescens</i>, distributed across the entire Bonin Islands. Notably, <i>C. subpubescens</i> exhibits multiple ecotypes, differing in leaf hair density, flowering time, and tree size. In this study, we aimed to investigate species and ecotype diversification patterns, estimate divergence times, and explore cryptic species within <i>Callicarpa</i> in the Bonin Islands using phenotypic and genetic data (double-digest restriction site-associated DNA sequencing). Genetic analysis revealed that <i>C. parvifolia</i> and <i>C. glabra</i> both formed single, distinct genetic groups. Conversely, <i>C. subpubescens</i> consisted of six genetic groups corresponding to different ecotypes and regions, and a hybrid group resulting from the hybridization between two of these genetic groups. Population demography analysis focusing on six Chichijima and Hahajima Islands-based species/ecotypes indicated that all species and ecotypes except one ecotype diverged simultaneously around 73-77 kya. The star-shaped neighbor-net tree also suggests the simultaneous divergence of species and ecotypes. The species and ecotypes that simultaneously diverged adapted to dry environments and understory forests, suggesting that aridification may have contributed to this process of adaptive radiation. Moreover, leaf morphology, flowering time, and genetic analyses suggested the presence of two cryptic species and one hybrid species within <i>C. subpubescens</i>.