The Bonin Islands, comprising 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 Callicarpa 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 used double-digest restriction site–associated DNA sequencing to analyze species, ecotypes and geographical variations within Callicarpa in the Bonin Islands. We aimed to determine detailed phylogenetic relationships, investigate species and ecotype diversification patterns, estimate divergence times, and explore cryptic species using genetic and phenotypic data. Genetic analysis revealed that C. parvifolia and C. glabra formed a single, distinct genetic groups. Conversely, C. subpubescens showed seven genetic groups corresponding to different ecotypes and regions, with one ecotype derived from the hybridization of two others. Phylogenetic and population demography analyses, focusing on six Chichijima and Hahajima Islands–based species/ecotypes, indicated the divergence of an ecotype adapted to tall mesic forests approximately 170 kya, whereas the other five species/ecotypes diverged nearly simultaneously around 73–77 kya. Environmental changes during the glacial period likely contributed to this process of adaptive radiation. Moreover, leaf morphology, flowering time, and genetic analyses suggested the presence of two cryptic species within C. subpubescens.

Callicarpa subpubescens is endemic to the oceanic Ogasawara Islands, and multiple ecotypes have been suggested to exist within southern part of this group, the Hahajima Islands, each associated with unique localized habitats. We determined the habitat characteristics of each ecotype, the presence or absence of pre- and post-mating isolation, the amount of gene flow among ecotypes in adult trees and naturally pollinated seeds using EST-SSR markers, and discussed how ecotypes are maintained in this species. There were four ecotypes in the Hahajima Islands, one of which presumed to be derived from hybridization of the remaining two ecotypes. The spatial distribution and habitat of each ecotype showed distribution which have depended on the suitable environment for each ecotype, i.e. local adaptation. The leaf morphology and size distribution of each ecotype also indicated the appropriate forms for each habitat. Flowering times more or less overlap among the ecotypes, indicating that pre-mating isolation is not perfect. Artificial cross-pollination showed that no post-mating isolation exists between ecotypes. Hybridization rates in adult trees and naturally pollinated seeds were 37.2% and 26.4%, respectively, and most of the hybrids were backcrosses and few F1. The hybridization rates of each ecotype and paternal correlation indicated that the flowering synchrony and spatial distribution of ecotypes contributed to hybridization among ecotypes. The reversion to the original ecotype which adapted to the environment through backcrossing would contribute to the maintenance of the ecotypes.