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.