Abstract:

Aims: Tibetan peach (Prunus mira) is an endemic wild relative of cultivated peach distributed in the Third Pole, primarily within the Himalaya and Hengduan Mountains biodiversity hotspots. It possesses unique ecological adaptability and significant economic value. This study aims to investigate the population structure and genetic diversity of P. mira, reconstruct its origin and dispersal history, and identify glacial refugia, thereby providing a scientific basis for the conservation and sustainable utilization of this wild peach germplasm resource. 

Methods: We analyzed 746 individuals of P. mira from Tibet, Yunnan, and Sichuan Province, covering the entire species range. Whole chloroplast genome and nuclear ribosomal DNA sequences were used to investigate genetic diversity and phylogeographic structure, estimate divergence times, and infer population demographic history. Additionally, we conducted species distribution modeling to assess stable potential distribution areas of P. mira from the past to the future. 

Results: Population structure analyses suggest that there is no clear genetic structure in the nrDNA dataset, whereas the plastome recognizes three distinct clades (Clade A, Clade B, and Clade C) within P. mira populations, indicating that P. mira comprises three distinct maternal lineages. Notably, geographical distribution patterns show that Clade C exhibits a narrow distribution, mainly concentrated in the western Sichuan. While Clade A and Clade B have a similar geographic range in the northwestern Yunnan and southeastern Tibet. Divergence time estimates indicate that the P. mira originated around 8.69 Ma, with its three clades diverged in the middle Pliocene (3.64–4.56 Ma), which may be related to the uplift of the Tibetan Plateau and the intensification of the Asian Summer Monsoon. Genetic diversity analysis identified northwestern Yunnan as the genetic diversity core and private haplotype hotspot for Clade A and Clade B, and western Sichuan as the diversity center for Clade C. Moreover, the observation that these two regions exhibit high and unique nrDNA diversity, and together maintain relatively stable potential distributions of P. mira across multiple historical periods, supports their role as independent refugia during the last glacial period. Population dynamics analysis further shows that Clade A and Clade C experienced significant population expansion approximately 1,500 and 600 years ago, respectively, which is consistent with the rise and fall of the Tea Horse Road in the region. Collectively, these findings suggest that P. mira originated in northwestern Yunnan and western Sichuan, and subsequently expanded westward to southeastern Tibet and the Himalaya, likely along the ancient Tea Horse Road. 

Conclusion: By combining molecular phylogeography with species distribution modeling, this study provides a coherent framework for understanding the complex evolutionary history of P. mira. The results reveal three distinct maternal lineages within the species, identify two independent glacial refugia (northwestern Yunnan and western Sichuan), and suggest that the ancient Tea Horse Road may have served as a dispersal corridor facilitating the westward expansion of P. mira into southeastern Tibet and the Himalaya. Together, this study not only provides new insights into the evolutionary history of P. mira and a scientific basis for the conservation and sustainable utilization of its genetic resources, but also establishes a new research paradigm for using phylogeographic approaches to explore biological distribution shifts driven by the synergistic effects of natural processes and human activities.

Key words: Ecological niche modelling, Maternal origin, Prunus mira, Plastid genome, Phylogeography, Third Pole