Genome-Wide SNP Data and Species Distribution Modeling Reveal Population Structure and Conservation Implications of...

Integrating population genetics with species distribution models provides powerful insights into species' evolutionary trajectories under climatic and geological contexts, and informs evidence-based conservation strategies for endangered species. In this study, we characterized the population genetic structure of Primula wilsonii, a plant species with extremely small populations (PSESP) endemic to the mountains of Southwest China, to provide insights for the conservation of alpine endangered plants. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) generated 18,313 neutral and unlinked single-nucleotide polymorphisms (SNPs) from 30 individuals across seven populations. Population genetic analysis revealed that these populations formed two major clusters. All populations exhibited low levels of genetic diversity (He = 0.00184-0.00271; π = 0.00176-0.00292), with one population (MG1) showing high genetic differentiation (F _ST > 0.7) from the other populations, possibly reflecting long-term geographic isolation resulting in a small effective population size (Ne). Demographic history analysis indicated an expansion around 0.88 Ma, followed by sustained contraction since approximately 45 ka with low Ne levels maintained. Species distribution models further suggested range contraction from the Last Glacial Maximum to the mid-Holocene and persistence of suitable refugia in the Hengduan Mountains under future warming scenarios. In conclusion, our results indicated that complex topography and Quaternary climatic oscillations have shaped a hierarchical genetic structure with deeply isolated lineages. We therefore recommend delineating at least three independent management units, consistent with patterns of genetic structure, differentiation, and demographic history. These findings highlight the importance of integrating genetic and environmental evidence in the conservation of P. wilsonii and other PSESPs.