Phylogenetic relationships and divergence patterns
We investigated the phylogenetic relationships of various genetic
groups, considering the presence and absence of the hybrid ecotype ofC. subpubescens (SH; Figs. 2 and 3). When a hybrid ecotype arises
between two distantly related parent ecotypes, the parent ecotype is
expected to be located closer to the hybrid ecotype compared with its
original position on the phylogenetic tree. In the Central American
genus Aphelandra , the inclusion of hybrids between distantly
related species in phylogenetic analyses caused a breakdown in cladistic
structure and significant topological changes (McDade, 1992). Thus, we
concluded that the phylogenetic tree lacking hybrid ecotype SH (Fig. 3b)
represents the true phylogenetic relationships, and ecotype SG is
considered to have originated from ecotype S in the Chichijima Islands,
subsequently colonizing the Hahajima Islands as ecotype SG.
Based on the phylogenetic tree lacking the hybrid ecotype (Fig. 3b) and
the population demography model (Model e1 in Fig. S2e), we determined
that the ancestral ecotype ST in the Hahajima Islands is the most
ancient. Subsequently, ecotype SD in the Hahajima Islands underwent
divergence. This was followed by species P and G in the Chichijima
Islands, as well as ecotype S. Finally, ecotype SG in the Hahajima
Islands emerged from ecotype S in the Chichijima Islands. Population
demography analysis revealed that ecotype ST diverged from the ancestral
species approximately 170 kya, whereas the other species and ecotypes
underwent nearly simultaneous divergence around 73–77 kya (Table S6).
Given that 73–77 kya, corresponds to the time when Marine Isotope Stage
(MIS) 5 (interglacial period) changed to MIS 4 (glacial period)
(Martinson et al., 1987), estimated to have been a period of rapid
cooling, cold weather may have triggered the simultaneous divergence of
this taxon. Kadereit and Abbott (2021) reviewed studies examining
divergence times from phylogenetic trees from all continents and major
climatic zones, finding that many plant speciation events occurred in
the Quaternary and suggesting that climate change during this period was
the cause.
However, it should be noted that estimated divergence times are highly
dependent on the generation time used, as these times are calculated by
multiplying generation time by approximate generation time. Cultivation
experiments involving ecotypes SD and SG confirmed that flowering
occurred within 1–2 years of sowing (Setsuko S., personal observation).
We consider a 5-year generation time to be suitable for estimating
divergence time; however, to validate our findings, it is essential that
comparative analyses are conducted using alternative methods, such as
BEAST (Drummond A, 2007), which employs fossil data for a more precise
age calibration.
In this study, species and ecotypes adapted to a dry environment
(species P and ecotype SD) and forest understory and forest edge
environments (species G and ecotypes S and SG) diverged at the same time
from ecotype ST that constitutes the canopy of tall mesic forests.
Although speciation timing may lack precision due to methodological
challenges regarding glacial or interglacial periods, it is evident that
simultaneous diversification occurred concurrently. Considering the
characteristics of the divergent species/ecotypes, the timing of
speciation likely aligns with the onset of aridification on the islands.
Initially, species/ecotypes adapted to the forest understory and forest
edge environment may seem unrelated to aridification. However, species G
inhabits forests that are not tall (dry scrub) (Toyoda, 2014), ecotype S
inhabits the edges of mesic forests, and ecotype SG does not flower in
overly dark forests (Setsuko S., personal observation). Therefore, they
are all considered maladaptive to taller forests where ecotype ST grows.
This suggests that the environment has changed from a forest with high
tree height to a forest with reduced tree height and increased forest
edges (Olson et al., 2018), potentially caused by the aridification of
the island. Examples of organisms rapidly altering their phenotypes upon
aridification have been reported in animals, such as Darwin’s finches
(Grant & Grant, 2006), and in plants, such as Mimulus andBrassica (Dickman et al., 2019; Johnson et al., 2022). Selection
has also been observed on the HMGA2 gene, causing beak size
variation during drought in Darwin’s finches (Lamichhaney et al., 2016),
and multiple genes associated with drought response traits evolving
during drought in Brassica (Franks et al., 2016; Johnson et al.,
2023). In the Callicarpa genus in the Bonin Islands, rapid
adaptation to aridification may have led to speciation. Therefore,
future research will involve identifying genes associated with drought
adaptation.
Surprisingly, we revealed that the differentiation timing of the five
species/ecotypes, occurring 73–77 kya, and the migration of ecotypes Sm
and STm in the Mukojima Islands from ecotypes S in the Chichijima
Islands and ST in the Hahajima Islands, respectively, took place during
approximately the same period, around 81–82 kya (Fig. 4; Table S6 and
S10). Aridification usually hinders the successful fruit reproduction of
previously abundant plants (Abobatta, 2021), leading to food shortages
across the entire island; therefore, it is plausible that avian seed
dispersers may have moved to new islands in search of food (Boyle &
Conway, 2007).
Population size changes, exhibiting large increases of more than two
orders, were observed for species/ecotypes P, G, and SG in model e1
(Fig. 4a; Tables S6 and S8). Dry scrub, the habitat of species P and G,
may have increased due to aridification during the glacial period.
Ecotype SG currently inhabits the understory of mesic forests throughout
the Hahajima Islands and has the largest population of any ecotype in
the Hahajima Islands (Setsuko et al. 2023). Compared with the Chichijima
Islands, the area of mesic forests is larger in the Hahajima Islands
(Shimizu, 1999), and the substantial increase in population size of
ecotype SG may be due to successful adaptation to the mesic forest
environment through migration from the Chichijima Islands to the
Hahajima Islands. However, large decreases of more than two orders were
observed in ecotype Sm and STm in model g2 (Fig. 4b; Tables S8 and S10).
This may be due to the limited number of individuals that migrated from
the original island populations to the Mukojima Islands (i.e., the
founder effect).