Cerasus conradinae is an important germplasm resource of wild cherry in China. In this work, sampling was expanded and genetic evidence was added for further study. The current and future potential populations were predicted by niche model. Based on three cpDNA sequences and one nrDNA sequence, and combined with the phylogeographic evolution of 12 populations of 244 individuals in Cerasus conradinae, The temporal and spatial patterns of genetic variation in Cerasus conradinae were investigated, and the effects of genetic drift and differentiation as well as natural environmental factors on the genetic variation and evolutionary distribution of Cerasus conradinae were elucidated. Finally, morphological evidence combined with molecular evidence was used to discuss the species definition of population variation and differentiation. The results showed that Central China, East China and Southwest China were the core regions for the conservation and utilization of germplasm resources of Cerasus conradinae. Support for variant Cerasus conradinae var. ruburm is established. The genetic diversity of Cerasus conradinae was high (Hd = 0.830; Rd = 0.798). There was genetic variation among populations of Cerasus conradinae, and genealogical geographic structure existed among the populations and three geographical groups, but the genetic differentiation coefficient at each level was low. The gene exchange was obvious in Southwest China, and the differentiation was obvious in Central China. Two distinct lineages (three geographic groups) were identified from the population of Cerasus conradinae: Central China+ East China lineage and East China+ (Central China+Southwest China) lineage, two lineages of 4.38Mya occurred in the early Pliocene based on geographical isolation. One lineage is Central China + East China geographic group, Central China and East China completed the lineage differentiation in 3.32Mya Pliocene. In 2.82mya, the population of Cerasus conradinae in Central China (Dawei Mountain, Gexian Mountain, etc.) expanded to the southeast (Wuyi Mountain, Qingliangfeng Mountain, etc.), and then expanded to Dabie Mountain in Anhui Province in the northwest from the southeast. Another lineage, East China+ (Central China+Southwest China), differentiated at about 2.17Mya in the early Pleistocene. During the Pleistocene 1.10Mya, about the interglacial period of the Quaternary glacial period, Cerasus conradinae spread from Central and Eastern China to Southwest China (Heifeng Valley and Mount Emei). The distribution center and overall pattern of Cerasus conradinae were formed during the Pliocene to Pleistocene transition. The population and three geographic groups do not reject the expectation of expansion model. The southeastern part of Eastern China near Mount Wuyi was the most likely refuge for Cerasus conradinae; Southwestern of Central China is another refuge for Cerasus conradinae. This study reveals the distribution prediction, phenotypic variation, classification and phylogeography of potential suitable areas of Cerasus conradinae. The results provided a theoretical basis for the classification and identification of Cerasus conradinae and the protection and utilization of germplasm resources.
