S. indica and S. playfairii as sources of hybridization of S. taiwanensis
The fastsimcoal2 simulation indicated that S. taiwanensis arose from hybridizations of a ghost lineage with S. indica andS. playfairii approximately 7.62 and 4.77 kya,respectively, suggesting multiple origins of extant S. taiwanensis . Older specimens of S. taiwanensis are often mistaken morphologically for S. indica , and the habitat ofS. taiwanensis on shady slopes is similar to that of S. playfairii (Hsieh & Huang, 1995). Despite this multiple-source hybridization, S. taiwanensis is considered a single species since the two hybrid lineages (TAI1 and TAI2) are monophyletic in multispecies coalescent (ASTRAL) inferences. Hybridization events may displace certain gene trees, leading to gene tree incongruence or topological inconsistencies between multispecies coalescent and concatenated analyses (Degnan & Rosenberg, 2009), as supported by the low F ST with other indica group members (Fig. S3A). Approximately 60% of the genetic components of S. taiwanensis are from indica group members.
S. taiwanensis is scattered in the shallow mountains of southern Taiwan and partially overlaps with S. playfairii , enabling hybridization between the ancestor of S. taiwanensis (ghost lineage) and S. playfairii . Surprisingly, S. taiwanensishybridized with S. indica , a species that has no distributional overlap with S. taiwanensis and is distributed in north-central Taiwan. In addition to long-distance dispersal, we cannot exclude the possibility that an ancestor or close relative of S. indicaspread to the south (Chiang, Huang, & Liao, 2012) and hybridized withS. taiwanensis after the glacial climate began. Although the middle and low altitudes of Taiwan Island did not experience glacial coverage, the arid and cold glacial climate forced many organisms to hide in multiple relict refugia during the Pleistocene glacials. In Taiwan, glacial refugia are commonly found in mountainous areas in the south or southeast (Huang, Hwang, & Lin, 2002; Lee et al., 2006; Wu et al., 2006) and Mount Sylvia (Xue-shan) in the northeast (Cheng, Hwang, & Lin, 2005; Huang, Hwang, & Lin, 2002; Lee et al., 2006; Wu et al., 2006). The warm and humid southern mountains of Taiwan served as a glacial refugium for numerous species, including Castanopsis carlesii (Cheng, Hwang, & Lin, 2005), Quercus glauca (Huang, Hwang, & Lin, 2002; Lee et al., 2006), Cinnamomum kanehirae(Liao et al., 2010), and Machilus kusanoi (Wu et al., 2006), resulting in high genetic diversity.
During the refuge period, hybridization between closely related species may have occurred. A previous study showed that the Pleistocene glacial oscillations accelerated Scutellaria species interbreeding in southern Taiwan and that current environmental heterogeneity is responsible for shaping the genetic structure of Scutellariapopulations (Huang et al., 2017). Due to this genetic legacy, glacial refugia in southern Taiwan contributed to genetic diversity in extant populations. Genetic mixing in refugia in the south may have been delayed until the postglacial period (ca. 7-4 kya from ABC). This inference is supported by the fact that demography explains more than half of the adaptive genetic variation, whereas the current climate explains only a small share. This result suggests that demographic history, such as changes in population size and gene flow, was crucial in shaping the genetic structure of the current population/species.
The spread of beneficial genes may broaden the ecological niche or enable hybridized species to colonize novel habitats (Suarez-Gonzalez et al., 2018). We identified two adaptive genes involved in the introgression between S. taiwanensis and each of the potential hybridized species: PHYB (between S. taiwanensis andS. indica ) and OPCL1 (between S. taiwanensis andS. playfairii ). PHYB was associated with the mean diurnal range (BIO2), and S. indica was present within a broad range of BIO2, suggesting that this species can acclimate to a diverse distribution of habitats and tolerate large temperature variations within a year. PHYB has been shown to promote plant adaptation to cold environments (Jiang et al., 2020; Zhao et al., 2016). The introgression of PHYB between S. indica and S. taiwanensis may have enabled S. taiwanensis to colonize and thrive in southern Taiwan. OPCL1 was associated with several temperature and precipitation-related factors, including the mean diurnal range (BIO2), temperature seasonality (BIO4), maximum temperature of the warmest month (BIO5), minimum temperature of the coldest month (BIO6), temperature annual range (BIO17), and precipitation of the warmest quarter (BIO18). Among these environmental variables, variations in BIO5 were larger in the habitats of S. playfairii than in the habitats of S. taiwanensis . The transmission of alleles of OPCL1 may further increase the adaptability of S. taiwanensis to lower temperatures in warm seasons compared to most Scutellaria species in Taiwan except forS. hsiehii . However, the niches of S. taiwanensis differed from those of either potential hybridized species and were characterized by lower BIO4, higher BIO6, and higher BIO18, indicating a shift toward temperature- and precipitation-related traits associated with tropical climates in southern Taiwan. Alternatively, these differences could indicate relics of ancestral traits of ghost lineages that are not related to the hybridization events. Overall, we infer that climate drivers of the introgression of adaptive alleles combined with demographic history associated with climate oscillation generated the unique genetic components and high genetic diversity of S. taiwanensis .