Phylogeography Of Prunus Discoidea Yü Et Li

Prunus discoidea belongs to the subg.Cerasus of the Prunoideae subfamily of the Rosaceae family,is known for its flowing branches,early-flowering pink flowers,and leaves appearing after the flowers.Which is a unique cherry blossom germplasm resource native to China.P.discoidea has a wide distribution in several Chinese provinces such as Anhui,Zhejiang,Jiangxi,Jiangsu,and Henan.It usually grows in valley forests or streamside shrublands at altitudes of200-1100m,exhibiting significant variability due to its broad distribution.This study aims to explore the changes in distribution areas and phylogeography of P.discoidea.We will use suitable area simulations and sequence marking techniques to investigate the dynamics of its distribution areas and the historical and geographical patterns of its genetic diversity.These findings will provide a theoretical foundation for future strategies related to the conservation and utilization of P.discoidea resources.（1）Simulation of the suitable area of Prunus discoideaAccording to the Chinese Virtual Herbarium（CVH）and related paper materials,a total of113 effective geographical distribution data points of P.discoidea were obtained.Combined with the data of 13 sampling points from field investigation,comprehensive climate data and topography and other factors,the key climatic factors and topographic factors affecting the distribution of P.discoidea were discussed through analysis such as distribution map drawing,contribution rate,knife cut test,and response curve of environmental and topographic factors.Using the Max Ent model and Arc-GIS software to predict the potential suitable habitats for P.discoidea in China under current and future climate change scenarios.Our analysis shows that under current environmental conditions,the potential suitable areas for P.discoidea are mainly located in the middle and lower reaches of the Yangtze River.These suitable areas account for approximately 8.07%of the national land area,with highly suitable areas comprising about 1.56%of the country’s land area.These highly suitable areas are primarily found in southeastern Hubei,central Hunan,northwestern Jiangxi,central and southern Anhui,northern Zhejiang,and southwestern Jiangsu.The growth range of P.discoidea is relatively narrow,with a high concentration in the Dabie mountain area at the junction of Hubei and Anhui,and the junction of Jiangxi,Hubei,and Zhejiang.The key climatic factor affecting the distribution of P.discoidea is the precipitation in the driest season.Under future climate conditions,the area of suitable habitats for P.discoidea is projected to increase.However,under a low greenhouse gas emission scenario in 2050（RCP2.6）,the total area of suitable habitats is projected to be the smallest,at 96%of the total area of contemporary suitable habitats.Moreover,the change of the total suitable area area is mainly the change of the height and moderate suitable area.Under the medium greenhouse gas emission conditions（RCP4.5）in 2050,the maximum areas of highly suitable and moderately suitable habitats are expected to reach 1.89×10⁵km² and 2.63×10⁵km²,respectively,which are126%and 123.47%of the area of contemporary suitable habitats,respectively.The potential suitable habitats also show a trend of migrating to higher latitudes.（2）Genetic diversity and genetic structure of Prunus discoidea populationThis study analyzed the genetic diversity of P.discoidea using three chloroplast DNA（cp DNA）fragments（rpo B,rps16,and trn D-E）and one nuclear DNA（nr DNA）fragment in 348individuals from 13 populations.The three chloroplast fragments were sequenced and combined to form a joint fragment of 1801 base pairs（bp）in length,from which a total of 17 haplotypes were identified.The analysis revealed a haplotype diversity H_d=0.782,a nucleotide polymorphism P_i=0.00104,and an average nucleotide difference K=2.005.A molecular analysis of variance（AMOVA）indicated that 34.26%of the variation in P.discoidea is between populations,while 65.74%is within populations,suggesting that variation within the population is the main source of genetic diversity in P.discoidea.The genetic differentiation index of the P.discoidea population was calculated as F_st=0.34264(nr DNA F_st=0.57621),which is greater than0.25.This result suggests that there is significant genetic differentiation within the P.discoidea population.Gene flow（N_m）can reflect the genetic information exchange between populations to a certain extent.The gene flow between populations of P.discoidea N_m=0.56,which was less than 1,indicating that the genetic information exchange between populations of P.discoidea was weak,and the populations is moving towards genetic differentiation.Combined with the genetic differentiation index of species N_st=0.40104>G_st=0.30809 and P<0.05,it indicated that there was a lineage structure between the groups of P.discoidea.Based on the separate analysis of the two geographical groups,the genetic differentiation index F_st=0.34409,N_st=0.34413>G_st=0.32690and P<0.05 in the eastern region,F_st=0.34539 in the western region.N_st=0.34538>G_st=0.22369,and P<0.05,both geographical groups detected lineage structure.In conclusion,the genetic diversity and genetic differentiation indices of nr DNA are consistent with those of cp DNA,further substantiating the high degree of genetic differentiation within the P.discoidea species.（3）Genealogical structure and historical dynamics of Prunus discoidea groupThis comprehensive study of the P.discoidea population based on haplotype phylogenetic tree,distribution,and network diagram analysis shows that it can be divided into two distinct lineages.One lineage is primarily located in the central region of Anhui and the western region of Hubei,indicated by the unique haplotypes H6-H11,H16-H17 was mainly distributed in THC（Hubei Huanggang）,YZH（Anhui Jinzhai）and ZJS（Hubei Xianning）.The second lineage is found in the Jiangsu region north of Daming Mountain in the eastern region and the Zhejiang region,characterized by the distinct haplotypes H1,H12-H13 distributed in BMQ（Zhejiang Jiande Bamuqiu）,HS（Anhui Huangshan）,YTS（Jiangsu Lianyungang）and SMS（Ningbo,Zhejiang）.There were no discernible population expansion or contraction events detected within the P.discoidea population in the two geographical groups.However,mismatch analysis based on cp DNA markers showed that the population and geographical grouping curves of the P.discoidea population were unimodal curves,while the SSD value of 0.01938（P=0.18000）and the Herg value of 0.05561（P=0.33000）were not obvious（P>0.05）,combined with AMOVA analysis,it was shown that the population sizeθ₀=5.33203 before the outbreak of P.discoidea broke out,the population sizeθ₁=99999 after the population outbreak,and the change of effective population size was（θ₀-θ₁=5.33203-99999）was very large,so it was believed that the P.discoidea population had recently experienced population expansion events.The phylogenetic tree based on molecular clock data suggests that P.discoidea diverged from P.campanulata around 1.5 million years ago,during the Pleistocene epoch.Haplotype H2,located centrally in the TCS network diagram and having wide distribution,is presumed to be an ancient haplotype.H3 and H4 are considered sub-ancient haplotypes from which other haplotypes have derived.Two specific areas,the Swallow River Grand Canyon and Daming Mountain,are proposed as potential Quaternary glacial refuges for P.discoidea due to the presence and abundance of these three haplotypes,and the high haplotype diversity index.After the glacial period,P.discoidea spread around these refuges,and its diffusion route was roughly Anhui-Henan-Hubei-Jiangxi or Anhui directly spread to Jiangxi;Another diffusion route is Zhejiang-Anhui-Jiangsu or Zhejiang directly to Jiangsu,so that the P.discoidea forms two lineages in the middle and east,forming two lineages and the current distribution pattern.In conclusion,based on the simulation of suitable regions and sequence marker analysis,there is extensive genetic communication among P.discoidea populations,and there is high genetic diversity at the species level.There are obvious genetic differentiation between groups of P.discoidea,and the main source of variation exists within the population.The divergence of P.discoidea and P.campanulata is estimated to have occurred approximately 1.5 million years ago during the early Pleistocene.The changeable climate and the alternation of glacial and interglacial periods led to species extinction and the formation of refuges.The species’distribution in central and eastern China,characterized by flat terrain and a warm climate,facilitated genetic communication between populations,leading to the formation of continuous lineages from west to east and east to north.This study provides a scientific theoretical basis for the conservation and utilization of germplasm resources of P.discoidea.