Phylogenetic relationships
In ADMIXTURE analysis, the minimum CV error occurred at K = 8 (Fig. 1a), revealing that the 14 populations in the Bonin Islands can be divided into eight genetic clusters: species P, species G, and ecotype S in the Chichijima Islands; ecotypes ST, SG, and SD in the Hahajima Islands; and ecotypes STm and Sm in the Mukojima Islands (Fig. 1b). Ecotype SH on Hahajima Island exhibited a mixture of ecotypes ST and SG on these islands. Populations of the same ecotype from different islands within the same island groups shared the same genetic cluster, whereas populations of the same ecotype from different island groups exhibited different genetic clusters.
Neighbor-net network analysis using SplitsTree revealed that the outgroups were positioned at the tips of exceptionally long branches (Fig. S10). Fourteen populations in the Bonin Islands clustered into nine genetic groups (Fig. 2). The additional group relative to the ADMIXTURE analysis was due to ecotype SH forming an independent genetic cluster. Ecotype SH was positioned between ecotypes SG and ST in the Hahajima Islands, forming a reticulate structure. Conversely, in the network diagram without ecotype SH, ecotype SG was located between ecotype S and species P but not between ecotypes S and ST, suggesting that ecotypes SG and ST were not genetically similar (Fig. 2b). Akin to the results from ADMIXTURE analysis, populations of the same ecotype from different islands within the same island groups shared the same genetic groups, whereas populations of the same ecotype from different island groups exhibited different genetic groups.
The phylogenetic tree generated using Mr. Bayes showed that, with ecotype SH, the 14 populations in the Bonin Islands were divided into clade 1 (species P and G) and clade 2 (ecotypes S, SG, SD, SH, and ST) (Fig. 3a). Clade 1 was further divided into two subclades, with species P and G, as monophyletic clades. Clade 2 was divided into subclade 2-1 (ecotypes S and Sm) and subclade 2-2 (ecotypes SG, SD, SH, ST, and STm).
The phylogenetic tree excluding ecotype SH exhibited a different arrangement of species and ecotype positions, splitting into clade 1 (species P and G, and ecotypes S, Sm, and SG) and clade 2 (ecotypes SD, ST, and STm) (Fig. 3b). In this tree, the positions of ecotypes S and SG differed compared with the tree including ecotype SH. Clade 1 was divided into two clades: subclade 1-1 (species P and G) and subclade 1-2 (ecotypes S, Sm, and SG). Clade 2 was divided into two clades: subclade 2-1 (ecotype SD) and subclade 2-2 (ecotypes ST and STm).