Genetic diversity, population structure, and demographic history of Fritillaria thunbergii (Liliaceae) based on RAD markers: Implications for conservation and germplasm management

Fritillaria thunbergii (Liliaceae) is an economically and medicinally important species, widely used in traditional Chinese medicine. However, its genetic diversity, population structure, and evolutionary history remain insufficiently understood, limiting its effective conservation and breeding efforts. Here, we generated a genome-wide SNP dataset for F. thunbergii using ddRAD-seq, yielding 18,029 high-quality SNPs. Population genetic analyses revealed substantial variation in genetic diversity across populations, and identified four well-supported genetic groups but with weak geographic structure. Demographic inference based on approximate Bayesian computation (ABC) indicated that lineage divergence occurred during the late Pleistocene (∼177.9, 99.7, and 30.0 ka under a five-year generation time assumption), broadly overlapping with interglacial periods and suggesting a potential role of climatic warming in promoting habitat fragmentation and refugial isolation. Consistent with patterns reported in other cold-adapted species, species distribution modeling showed range expansion during glacial periods and contraction during interglacials, supporting a “glacial expansion–interglacial contraction” model. Future climate change may reduce and fragment suitable habitats, particularly under high-emission scenarios. Long-term cultivation and recurrent germplasm exchange may have increased admixture among geographically separated populations, partially obscuring natural geographic genetic structure. A core germplasm collection capturing 97.75% of allelic diversity was also established, providing a valuable resource for conservation, breeding, and functional studies. Overall, our findings suggest that both historical climatic fluctuations and long-term human activities have contributed to the present genetic patterns of F. thunbergii , and provide important guidance for its conservation and sustainable utilization.