Inference of population demography
Regarding divergence patterns among the six species/ecotypes (species P, species G, and ecotype S in the Chichijima Islands; and ecotypes ST, SG, and SD in the Hahajima Islands), at step (a), among the three species divergence models in the Chichijima Islands, model a2 was the best model (Fig. S2a; Table S2). At step (b), among the four-ecotype divergence models in the Chichijima and Hahajima Islands, model b1 was the best model (Fig. S2b; Table S3). Similarly, at steps (c) and (d), among the three- and four-ecotype divergence models in the Hahajima Islands and in the Chichijima and Hahajima Islands, models c2 and d2 were the best models (Fig. S2c and d; Tables S4 and S5). Among six-ecotype divergence models in the Chichijima and Hahajima Islands, built considering steps (a)–(d), model e1 was the best model (Fig. S2e; Table S6). In this model, most ecotypes, except for S and SD, exhibited significant recent population expansion at 70.2 kya (95% CI could not be estimated; refer to Table S7), whereas S and SD did not show significant population size change (Fig. 4; Tables S7 and S8). Divergence timesT 2T 5 showed a narrow range of 72.9–76.9 kya. However, the divergence time between ST and the other ecotypes was 170.7 (95% CI: 162.2–183.4) kya (more than twofold that of T 2T 5).
Regarding the divergence patterns of the five ecotypes in the Chichijima, Hahajima, and Mukojima Islands, at step (f), among the three-ecotype divergence models in these islands, model f1 was the best model (Fig. S2f; Table S9). At step (g), among the five-ecotype divergence models in the Chichijima, Hahajima, and Mukojima Islands, model g2 was the best model (Figure S2g; Table S10). In this model, ecotype S and the two ecotypes in Mukojima Islands (Sm and STm) showed significant recent population reduction at 37.1 (95% CI: 33.9–40.5) kya, whereas the two ecotypes in the Hahajima Islands (SG and ST) exhibited significant recent population expansion (Fig. 4b; Tables S8 and S11). Divergence times T 2 andT 3 were 81.4 (72.7–86.4) and 82.3 (75.0–88.2) kya, respectively, and were very close. However, the divergence time between the two ancestral lineages was 168.8 (95% CI: 160.6–179.1) kya (more twofold that of T 2 andT 3).
Migrant numbers per generation estimated in the best models e1 and g2 were 0.020–0.511 and all significantly lower than 1.0 (Tables S7 and S11). These two best models indicated that, although the timings of recent population size change and the onset of migration differed between models, the timings of divergence between ecotypes were very similar (approximately 80 and 170 kya; Fig. 4; Tables S7 and S11), i.e., most ecotypes underwent recent divergence (approximately 73–77 kya), whereas ST experienced ancient divergence (around 170 kya).