Large-scale population genomics reveals genetic diversity and evolutionary history of Saxifraga stolonifera

Saxifraga stolonifera is widely distributed across the subtropical monsoon regions of China and has been extensively utilized for its medicinal and horticultural importance. A comprehensive assessment of its genetic variation can clarify both the extent and spatial patterns of diversity within available germplasm, thus supporting the identification of representative and diverse materials for future utilization. Here, we analyzed genetic diversity and population structure in S. stolonifera by examining 49 populations sampled throughout China, based on single nucleotide polymorphism (SNP) markers. Phylogenetic inference combined with population structure analysis indicated relatively low levels of genetic diversity but pronounced genetic differentiation, allowing the samples to be classified into five distinct genetic groups (π = 0.00,394–0.00,959; F ST = 0.221–0.513). Estimates from molecular dating together with ancestral range reconstruction suggest that Chinese populations of S. stolonifera likely originated in eastern China during the late Miocene, followed by a westward expansion and diversification. In addition, we detected pronounced patterns of both geographic and environmental isolation in S. stolonifera , as well as limited interspecific gene flow with species in S. sect. Irregulares , and only limited gene exchange was observed among populations of S. stolonifera . These findings enhance our understanding of the diversity patterns of S. stolonifera and offer important perspectives on its evolutionary trajectory and clarify how geographic isolation and gene flow have contributed to the formation of its present genetic structure.