<i>In situ</i> diversification and adaptive introgression in Taiwanese <i>Scutellaria</i>

Island habitats provide unique opportunities to study speciation. Recent work indicates that both ex situ origination and in situ speciation contribute to island species diversity. However, clear evidence of local adaptation of endemic plant species on islands requires in-depth studies, which are scarce. This study underscores the importance of local adaptation in maintaining species boundaries by examining how adaptive introgression, hybridization, and local adaptation contribute to genetic variation in island species. Multilocus genome scanning of 51 nuclear genes was used to investigate the evolutionary relationships of the Scutellaria species complex on Taiwan Island and assess the role of in situ diversification in generating high endemism and genetic diversity. Interspecies introgressions were detected by phylogenetic networks and ABBA-BABA-based analysis, suggesting ongoing or recent speciation processes. Coalescent-based simulation identified hybrid speciation in Scutellaria taiwanensis and Scutellaria hsiehii, with evidence of hybridization between more than two parental species. Genotype-environment association studies revealed that the influence of climate, particularly precipitation- and temperature-related factors, contributed to adaptive genetic divergence between species. Additionally, adaptive introgression related to environmental pressures that may have facilitated the colonization of new island habitats were identified. This research illustrates how hybridization, introgression, and adaptation shaped the evolutionary histories and divergence of this island-endemic plant species complex and sheds light on the multifaceted mechanisms of speciation on semi-isolated islands.