Population genomic analysis based on geographically large-scale samples provides insights into the evolutionary history of the wood oil plant Lindera glauca in East Asia

Lindera glauca is a dioecious tree widely distributed in East Asia, possessing significant economic and ecological value. Despite its importance, large-scale population genomic studies on this species have been lacking. This study aims to address this gap by conducting an in-depth analysis of population genetic structure, genetic diversity, demographic history and adaptive evolution using genome-wide single nucleotide polymorphism (SNP) markers. Utilizing RAD-seq to genotype 116 individuals from 15 populations spanning the mainland and Taiwan China, Japan, and Korea, four genetic groups were identified: two in mainland China, one in Taiwan, and one in Japan-Korea. The Taiwan group showed the highest genetic differentiation with other groups, indicating prolonged isolation, while Japanese and Korean groups exhibited minimal differentiation, suggesting a shared history or gene flow. Two groups in mainland China shows some degree of admixture, reflecting the complex evolutionary history. A rooted phylogenetic analysis and demographic inference both traced the origin of L. glauca to the mainland China, followed by dispersal and differentiation into Japan-Korea and Taiwan at around 14,000 and 4700 years ago. All the groups showed a gradually decrease in N e except a historical bottleneck in mainland Chinese populations likely caused by climate changes. Selective sweep analysis highlighted population-specific adaptations, particularly in photosynthesis and energy metabolism genes, with strong selection in Japanese and Korean groups. These findings enhance our understanding of L. glauca ’s genetic diversity and provide valuable insights into its evolutionary history and the role of geographic isolation, gene flow and selection in shaping current genetic patterns. • Lindera glauca is a tree species in East Asia with significant economic and ecological value, ideal for biofuel production. • This is the first population genomic analysis of L. glauca across East Asia, including China, Japan, and Korea. • Four major genetic groups were identified: two in mainland China with admixture, one in Taiwan, and one in Japan-Korea. • All the groups showed a gradually decrease in N e except a historical bottleneck in mainland China likely due to climate changes. • Selective sweep highlighted population-specific adaptations, particularly in Japanese and Korean groups.