Data from: Adaptive radiation of the Callicarpa genus in the Bonin Islands revealed through double-digest restriction site–associated DNA 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 Callicarpa genus that is represented by three species: Callicarpa
parvifolia and C. glabra exclusive to the Chichijima Islands, and
Callicarpa subpubescens, distributed across the entire Bonin Islands.
Notably, C. subpubescens 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 Callicarpa in the
Bonin Islands using phenotypic and genetic data (double-digest restriction
site–associated DNA sequencing). Genetic analysis revealed that C.
parvifolia and C. glabra both formed single, distinct genetic groups.
Conversely, C. subpubescens 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 C. subpubescens.