Origin and dispersal history of Tibetan peach in the Third Pole

doi:10.17520/biods.2026152

Abstract

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 Xizang, Yunnan, and Sichuan, covering the entire species range. Whole plastid 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 suggested that there was no clear genetic structure in the nrDNA dataset, whereas the plastome recognized three distinct clades (Clade A, Clade B, and Clade C) within P. mira populations, indicating that P. mira comprised three distinct maternal lineages. Notably, geographical distribution patterns showed that Clade C exhibited a narrow distribution, mainly concentrated in the western Sichuan. While Clade A and Clade B had a similar geographic range in the northwestern Yunnan and southeastern Xizang. Divergence time estimates indicated that the P. mira originated around 8.69 Ma, with its three clades diverged in the middle Pliocene (3.64–4.56 Ma), which might 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 exhibited high and unique nrDNA diversity, and together maintained relatively stable potential distributions across multiple historical periods, supported their role as independent refugia during the last glacial period. Population demographic analysis further showed that Clade A and Clade C experienced significant population expansion approximately 1,500 and 600 years ago, respectively, which was consistent with the rise and fall of the Tea Horse Road in the region. Collectively, these findings suggested that P. mira originated in northwestern Yunnan and western Sichuan, and subsequently expanded westward to southeastern Xizang 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 Xizang 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: Third Pole, Prunus mira, plastid genome, maternal origin, phylogeography, ecological niche modelling

Xing Kong, Xiangqian Sun, Benqin Zhao, Xun Gong, Jie Cai, Jie Liu. Origin and dispersal history of Tibetan peach in the Third Pole[J]. Biodiv Sci, 2026, 34(6): 26152.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2026152

https://www.biodiversity-science.net/EN/Y2026/V34/I6/26152

Figures/Tables 6

Fig. 1 Sample sites and occurrence points of Prunus mira. Occurrence data were obtained from the Plant Photo Bank of China (PPBC, http://ppbc.iplant.cn/), Chinese Virtual Herbarium (CVH, http://www.cvh.ac.cn/), Global Biodiversity Information Facility (GBIF, https://www.gbif.org/), and relevant literature.

Fig. 2 Phylogenetic relationships and population structure of Prunus mira as revealed by plastid genome data, different colors represent three clades (green represents Clade A; orange represents Clade B; red represents Clade C). (a) Haplotype network generated using the Templeton Crandall Singh (TCS) approach. Circle sizes reflect the relative frequencies of haplotypes, and the numbers of mutational steps between pairs of haplotypes are indicated along the connecting lines. (b) Maximum likelihood (ML) and Bayesian Inference (BI) phylogenetic tree. Branches of the three major clades are color-coded, with bootstrap values (BS > 95%) and posterior probabilities (PP > 0.95) shown at the corresponding nodes. (c) Principal component analysis (PCA) plot of haplotypes, illustrating genetic differentiation among the three clades. (d) Bayesian population assignment results from STRUCTURE at K = 2-4, where each individual is represented as a vertical bar partitioned into K colored segments representing membership coefficients. Outgroups: P. ferganensis, Prunus ferganensis; P. persica, Prunus persica; P. kansuensis, Prunus kansuensis; P. davidiana, Prunus davidiana; P. dulcis, Prunus dulcis; R. cymosa, Rosa cymosa.

Fig. 3 Geographical distribution of haplotypes of Prunus mira based on plastid genome data. The figure illustrates the spatial distribution patterns of haplotypes across species (a) and different clades, including Clade A (b), Clade B (c) and Clade C (d). Different colors within each pie chart represent distinct haplotype types, and the area of each pie chart is proportional to the sample size of the corresponding haplotype. The bars adjacent to each pie chart indicate the types and numbers of private haplotypes present in each population. Blue lines represent rivers. The map marks mountain ranges that act as a barrier according to Liu et al. (2022).

Fig. 4 Spatial interpolation of genetic diversity of Prunus mira using the inverse distance weighting (IDW) method based on different datasets. (a) and (b) present the haplotype diversity (Hd) and nucleotide diversity (π) of each population based on plastid genome data, respectively. (c) and (d) show the spatial distribution of Hd and π based on nuclear ribosomal DNA (nrDNA) sequences, respectively. Diversity values are represented by a color ramp ranging from blue (low) to red (high).

Fig. 5 Population demography and divergence times of different clades of Prunus mira based on plastid genome data. (a) Bayesian skyline plots for different clades. Solid lines represent the median estimates of effective population sizes, with light-shaded areas indicating the 95% highest posterior density intervals (HPD). The horizontal axis represents time, and the vertical axis represents the effective population size at different periods. Different colors denote distinct clades (green represents Clade A; orange represents Clade B; red represents Clade C). (b) Divergence time tree based on haplotypes. Numbers above nodes indicate divergence times (Ma), and blue bars at nodes and values in brackets represent the 95% HPD. The gray shaded areas represent the outgroups used, including species of Prunus (P.) and Rosa cymose (R. cymose), Rubus pedunculosus (R. pedunculosus), Dryas octopetala (D. octopetala), Boehmeria umbrosa (B. umbrosa), Ficus racemosa (F. racemosa), Malus pumila (M. pumila), Pyrus ussuriensis (P. ussuriensis), and Crataegus hupehensis (C. hupehensis). Black circles with numbers denote fossil calibration points. Pli, Pliocene; Ple, Pleistocene.

Fig. 6 Potential distribution areas of different clades of Prunus mira under different climatic periods. Each column represents a clade (Clade A, B, and C), and each row represents a climatic period (LGM, Contemporary, and Future). The color ramp from dark to light represents habitat suitability from high to low. LGM, Last Glacial Maximum; Contemporary, Contemporary (1970‒2000) climate scenarios; Future, Future (2081-2100) RCP8.5 high-emission scenario.

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