Evolutionary history of genetic admixture in S.
taiwanensis and S. hsiehii
The results of fastsimcoal2 analysis indicated that the Recentghost and
Hybrid models best explained the evolution of S. taiwanensis andS. hsiehii , respectively (Fig. 4). For the first set,
TAI-IND-PLA, the AIC and bootstrapping likelihood comparison of all
models revealed that recent introgression from S. playfairii andS. indica to S. taiwanensis was the optimal model (Fig.
S7; Fig. 4A). This model also had the highest congruence with the
observed SFS (Figs. S8-S10). The best-fitting model suggested that a
ghost lineage diverged from the common ancestor at approximately 700
kya. This divergence was followed by more recent independent
introgression events with S. indica and S. playfairii at
7.62 kya and 4.77 kya, respectively, with ~60% of the
genetic component inherited from introgression (Fig. 4A; Fig. S11; Table
S7). The time of divergence from the ghost lineage (700 kya) aligns with
the coalescent time estimated in the Stairway plot (Fig. S12;
Supplemental Materials and Methods), whereas the introgression time
corresponds to the onset time of population decline (Fig. S12). Our
approach supports that TAI originated from multiple introgressions of
more than one Scutellaria species.
For the second set, HSI-AUS-IND, we again constructed and compared three
speciation scenarios to investigate the evolutionary history of S.
hsiehii . Although the AIC values did not informatively distinguish
between hybrid speciation (Hybrid model) and divergence from S.
austrotaiwanensis (AUSdiv model) (Fig. 4B), the bootstrapping
likelihoods strongly supported the model corresponding to hybridization
between S. austrotaiwanensis and S. indica (Fig. S13-16;
Table S8). However, the genetic components provided by each species in
the estimated hybridization model differed (Fig. S4C; Table S8): more
than 90% of the genetic components in S. hsiehii were inherited
from S. austrotaiwanensis approximately 9.07 kya according to the
results of STRUCTURE, indicating another substantial but potential
hybrid speciation event in the studied species.