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..., Study species and sampling
Callicarpa parvifolia grows in sunny dry dwarf scrub on rocky ground in the Chichijima Islands, whereas C. glabra grows in the understory of dry scrub in the Chichijima Islands. In contrast, C. subpubescens is not listed as a threatened species and is widely distributed in the Bonin and Volcano Islands, situated approximately 150 km southwest of the Bonin Islands. Callicarpa subpubescens exhibits different ecotypes, each with distinct habitats and some with different flowering peaks. For example, the Chichijima Islands’ ecotype (S) inhabits the forest edge of mesic forests, with peak flowering in June. The Hahajima Islands have four ecotypes: the glabrescent ecotype (SG), the tall ecotype (ST), the dwarf ecotype (SD), and the hybrid ecotype (SH). The ecotype SG inhabits the understory of mesic forests. The ecotype ST forms the canopy of tall mesic forests. The ecotype SD forms the canopy of dry scrub. The ecotype SH forms the canopy of mesic scrub (cloud fores..., , # Data from: Adaptive radiation of the Callicarpa genus in the Bonin Islands revealed through double-digest restriction site–associated DNA sequencing analysis

[https://doi.org/10.5061/dryad.05qfttfc1](https://doi.org/10.5061/dryad.05qfttfc1)

This study investigated species and ecotype diversification patterns, estimated divergence times, and explored cryptic species within *Callicarpa* in the Bonin Islands using phenotypic and dagenetic data, revealing simultaneous divergence driven by aridification and identifying two cryptic species and one hybrid species within *C. subpubescens*. This data includes SNPs of 96 individuals characterized by ddRAD-Seq.

## Description of the data and file structure

MS Excel sheet **Individual_information.xlsx** contains \"Individual ID: Column A\", \"Population ID: Column B\", and \"Species/ecotype: Column C\" of 96 individuals used in this study. The abbreviations for the species and ecotypes are as follows:

P: *C. parvifolia*;
G: *C. glabra*;
S: ecotype...