Understanding the population genetic structure and demographic history helps in the management and restoration of endangered species. Cycas panzhihuaensis (Panzihihua sago palm) is narrowly distributed in the eastern Sichuan Basin of China. The only extant population is in the Panzhihua Cycad Nature Reserve (PCNR), which is close to Panzhihua City, and is threatened by the mining industry and slash-and-burn agriculture. To protect this rare species, the local government implemented an ex situ conservation project. In this study, amplified fragment length polymorphism (AFLP) was used to explore the genetic diversity of wild and cultivated populations. Two evolutionarily significant units (ESUs) in PCNR were determined based on significant differences in genetic diversity and demographic histories. The western ESU has low genetic diversity and shares common genotypes with a part of the eastern ESU. The founder effect is suggested as the best-fit scenario to explain the current genetic distribution among the eastern and western ESUs. Small carrying capacity limits both census and effective population sizes, and the gene surfing hypothesis explains the high frequency of fixed alleles without private alleles in multiple loci in the western subpopulation. Every cultivated population, established for either conservation or horticultural purposes, has only genotypes from a single ESU. Supplementary collection for ex situ conservation is suggested to preserve the genetic features of C. panzhihuaensis.
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