Genetic evidence of adaptative variation
To identify adaptive genetic variants, we used multivariate approaches, which perform better than univariate procedures while maintaining a low false-positive rate (Forester et al., 2018; Sang et al., 2022). However, we observed significant overlap between the climate and demographic factors, indicating high multicollinearity (Capblancq et al., 2023). To balance potentially missing weak-effect sites and minimize false-positive rates, we adopted a strategy in which sites detected by more than two approaches were considered outliers (Ahrens et al., 2018; Forester et al., 2018). We deliberately avoided relying solely on sites detected by all methods simultaneously. This approach was chosen to increase the true-positive rate while circumventing limitations inherent in the least potent methods.
Chiang, Huang, and Liao (2012) proposed repeated dispersal and vicariance within the current geographic distribution but did not address how local adaptation contributes to species divergence. The detection of adaptive SNPs points to local adaptation within these species. Notably, partial RDA revealed 15.2% overlap in variation between climate factors and genetic structure, indicating that climate adaptation has played a crucial role in maintaining species divergence. Among the genes implicated in climate-related adaptation, CBF2and PHYB function in the response and acclimation to cold inArabidopsis thaliana (Jiang et al., 2020; Zhao et al., 2016).ABA1 and HSA32 play essential roles in responding to heat and temperature stimuli in plants (Charng et al., 2006; Suzuki et al., 2016), and YUC6 and CRY2 have been linked to drought recovery in Arabidopsis thaliana (Cha et al., 2015; Mao et al., 2005). PKT3 and MYB4 are associated with UV-B and high-light-intensity responses in plants (He et al., 2016; Zhao et al., 2007). The adaptive divergence of these climate-related genes suggests that local climate has been a significant driver of the rapid speciation and maintenance of species divergence in Taiwanese Scutellariaspecies.
Moreover, previous studies have highlighted the importance of positive selection in the diversification of Taiwanese Scutellaria . For example, Huang et al. (2015) identified interspecific differences in the expression of growth and environmental regulation genes, specificallyR2R3-MYB , suggesting that these genes are associated with positive selection and functional gene divergence in TaiwaneseScutellaria species. Positive selection of the anthocyanin biosynthesis gene UFGT has also been linked to accelerated floral diversity on Taiwan Island (Huang et al., 2016a). Moreover, adaptive subfunctionalization of the anthocyanin gene DFR was instrumental in anthocyanin diversification (Huang et al., 2016b), which is ecologically relevant in terms of attracting pollinators, repelling herbivores and parasites, and providing abiotic stress resistance (e.g., UV resistance) (Lev-Yadun & Gould, 2009).
In summary, the genetic variations of Taiwanese Scutellariaspecies have been shaped by a combination of factors. Hybridization and ghost introgression provide greater genetic variation by increasing standing genetic variation, and further local adaptation driven by climate-related genes and adaptive introgression has likely contributed to the ability of these species to thrive in specific environments. Furthermore, the positive selection of functional genes has played a crucial role in driving their diversification and ecological characteristics. These findings shed light on the intricate mechanisms that shaped the evolutionary history of Scutellaria on Taiwan Island in response to ecological selection pressures.