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 2–T 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 2–T 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).