Adaptive radiation of the Callicarpa genus in the Bonin Islands revealed through double-digest restriction site-associated DNA sequencing analysis

Abstract

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.

Keywords: Lamiaceae; Ogasawara Islands; ddRAD‐Seq; oceanic islands; quaternary.

FIGURE 1

Results of ADMIXTURE analysis performed on 89 individuals from 14 populations of the Bonin Islands using denovo dataset. The cross‐validation (CV) error values for each run (a) and bar plots depicting the genetic admixture proportions for K = 2–8 (b). Vertical columns represent individuals; heights of bar plots are proportional to the posterior means of the estimated admixture proportions.

FIGURE 2

Neighbor‐net network tree reconstructed using 89 individuals from 14 populations (a) and 82 individuals from 13 populations (excluding ecotype SH, b) of the Bonin Islands and two outgroup individuals using the referenced dataset. Phylogenetic clade colors correspond to those used in Figures 1 and 3.

FIGURE 3

The phylogenetic tree inferred from RAxML‐NG utilizes SNPs with a genotyping rate of 80% from a referenced dataset comprising a total of 16 individuals (excluding ecotype SH) from eight genetic groups in the Bonin Islands, and two individuals of the outgroup (Out_Cmol, Out_Cjap). Phylogenetic clade colors correspond to those used in Figures 1 and 2.

FIGURE 4

Best six‐species/ecotype divergence model (a), and best five‐ecotype divergence model (b). These correspond to models e1 and g2 in Figure S2, respectively. Period shown in dashed lines assumes migration between ecotypes. Direction of migration shows the movements of individuals (i.e., forward‐in‐time). Ecotype colors correspond to those used in Figures 1, 2, 3.

FIGURE 5

Distributions of the first and third principal components (pc1 and pc3) for 11 leaf morphological traits of nine species/ecotypes (a), and those of the second and third principal components (pc2 and pc3) for ecotypes of 11 leaf morphological traits of seven species/ecotypes (ecotypes P and SD are masked) (b).