Phylogenetic Position And Population Biogeography Of Cerasus Dielsiana(Rosaceae)

Cerasus dielsiana belongs to the subgenus Cerasus of the family Rosaceae.It is a typical deciduous wild ornamental tree endemic from subtropical China and its natural populations are widely distributed and geographically diverse.Thus,this species has broad development and utilization prospects.However,according to years of field investigations,its germplasm resources are mainly in a wild state.Meanwhile,it is also facing the risk of population decline caused by human disturbance and habitat fragmentation.Therefore,in this study,the natural population of C.dielsiana from its major distribution area was taken as the research object.Based on extensive specimen records and field sampling surveys,we carried out in-depth research on this species by integrating morphological maker,molecular phylogeny and biogeography,as well as landscape genetic methods.The main content and obtained results were listed as follows:?1?Phylogenetic analysis and taxonomic treatmentBased on a fragment of the chloroplast DNA non-coding region,the phylogenetic reconstruction of C.dielsiana was initially carried out in order to clarify the genetic relationship and classification status of this species and its relatives.The results showed that:1)There were a total of 15 polymorphism sites in the 774 valid sites of the atpB-rbcL sequence matrix,accounting for 1.94%.Total nine haplotypes were detected,with average haplotype diversity?H_d=0.8805±0.026?and average nucleotide diversity??=0.007 11±0.000 54?,respectively.Except for C.dielsiana?Hap5?Hap7?,the remaining species had their own unique haplotype,which indicates abundant genetic diversity.2)After integrating with the results of the MJ network,reconstruction of the phylogenetic tree as well as the output of a quantitative analysis of RNA secondary structure prediction by bioinformatics,we speculated that C.dielsiana was a sister branch to C.dielsiana var.longistyla,also together constituted an independent evolutionary unit.Even though the system location of C.pananensis has not been confirmed,it is speculated that this species is most closely related to C.schneideriana and may have originated from multiple hybridizations from ancient to modern times.It is also likely to have been recently affected by the dual gene introgression from C.schneideriana and C.serrulata.3)Based on the above molecular evidence combined with morphological description,we support the publication of the new variety of C.dielsiana--C.dielsiana var.longistyla.Meanwhile,we designated NO.5812?GH-00032047?as the lectotype for C.dielsiana,according to the spirit of the International Code of Nomenclature for algae,fungi,and plants?ICN?.?2?Leaf phenotypic variation and ecological response of the natural populationWe analyzed eleven leaf phenotypic traits from five provinces of China in eight natural populations of C.dielsiana by using multiple comparisons,nested analysis of variance,correlation analysis,principal component analysis?PCA?,principal coordinate analysis?PCoA?and unweighted pair-group method with arithmetic mean?UPGMA?cluster analysis.Results showed that:1)Rich leaf phenotypic variation existed among and within populations,and the average coefficient of variation?CV?was 22.44%,the maximum and the minimum were leaf area?CV=50.83%?and primary lateral veins?CV=7.96%?,respectively.The mean differentiation coefficient?Vst?for all traits was 30.78%,and the variation within populations?51.55%?was higher than that among populations?22.55%?.2)The principal component analysis showed that the cumulative contribution rate of the first three main components of variation from leaf phenotypic traits of C.dielsiana made a major contribution reached to 92.400%,and can be comprehensively summarized and sorted as“size traits”?73.242%?and“shape traits”?19.158%?.3)Leaf width?r=-0.641?,leaf area?r=-0.658?and primary lateral veins?r=0.659?showed a significant negative or positive correlation with longitude,and the temperature seasonality and precipitation of wettest quarter were showed more influence on leaf phenotype variation.4)The eight natural populations of C.dielsiana could be divided into four groups according to principal coordinate analysis?PCA?and UPGMA cluster analysis.?3?Molecular phylogeographyWe detected 203 individuals from 25 populations of C.dielsiana across its natural distribution area by using the nrDNA marker?ITS?of the transcription compartment of ribosome inherited from both parents.1)A total of 18 unique ribotypes?R1–R18?were derived among all the individuals surveyed,High level of ribotypes and nuclear diversity?H_d=0.879±0.012,p<3.56±0.16?were detected at the species level.Spatial analysis of molecular variation?SAMOVA?,Median-joining network and phylogenetic Neighbor-Joining tree assigned the populations into four genetically distinct groups:West Group+North Group+Group+Central&South Group+East Group.Phylogenetic reconstruction based on Neighbor-joining?NJ?showed that the northern formation was a non-monogenetic group,namely,the remaining three geographic groups were embedded in it,indicating the existence of Incomplete lineage sorting?Incomplete lineage sorting,ILS?in populations.The analysis of molecular variance?AMOVA?revealed a high genetic differentiation variation with 78.27%of the total variability residing among populations while 21.73%of the rest within populations,implying the presence of significant phylogeographic patterns(N_st=0.837>G_st=0.585;P<0.05).2)BEAST software was used to estimate the molecular clock divergence time by combining seven secondary calibration points as outgroups.It showed that the time to the most recent common ancestor?TMRCA?of C.dielsiana occurred from 6.28 Mya?95%HDP:3.64?8.83Mya?,namely,from the late Miocene to the early Pliocene.The time of the Crown group of the eastern group was around the Pleistocene?about 1.97 Mya?,which was consistent with the period of the Last Glacial Maximum?LGM?.3)Combined with the SDM-based Maximum entropy?MaxEnt?model,we compared the potential distribution areas in the LGM period and the current climate conditions,multiple glacial refugia were inferred from China's subtropical region.4)The application of the statistical dispersal-vicariance analysis?S-DIVA?in the reconstruct ancestral state in phylogenies?RASP?software analysis further speculated events of the time-geographic expansion route for C.dielsiana.Results showed that the origin of its ancestor group might occur from the north geographic group of Qinling and Daba Mountains,then successively experienced two southward diffusion events.There were two secondary differentiation centers between the eastern and northern geographic groups and the eastern and western geographic ancestors,and then they expanded to the west,south,west and east directions,respectively,gradually forming a modern distribution pattern.?4?Landscape genetics analysisBased on a variety of algorithms,the effects of habitat landscape characteristics on the genetic structure formation of population of C.dielsiana were quantitatively analyzed:1)It reflects that the genetic diversity of the population of this species has uneven spatial distribution and an east-west geographical distribution pattern along with longitude.2)Result of the Mantel test based on geographic distance and genetic distance show a weak negative correlation?r=-0.345,R²=0.1193?between has been revealed,which was consistent with the hypothesis of isolation by environment?IBE?.3)According to the pairwise gene flow,Nanling-Luoxiao,Wushan-Wuling Mts.had been detected by forming geographical isolation among populations.Especially the east-west trending Nanling Mts.range was the most significant natural physical barrier of C.dielsiana,which hindered gene flow between the geographical groups of the four lineages,thus promoting the exotic differentiation among different lineages.Besides,the gene flow of the Ali Mts.population?ALS?has not affected by the geographical isolation of the Taiwan Strait between Fujian and Taiwan,which was probably closely related to the formation of"Dongshan land bridge"in Pleistocene ice age.?5?Suitability modeling and ecological characteristicsTo quantitatively evaluate the contemporary diversity distribution pattern of C.dielsiana and its ecological adaptability,the BIOCLIM model-based DIVA-GIS software was used for analysis.Results include:1)The current distribution of C.dielsiana occupied a relatively wide range but exhibited an uneven pattern eastward in general,and the core distribution zone of its population were projected to concentrate in the Wushan&Wuling Mountain ranges of western China.2)Hydrothermic variables,particularly the Temperature Seasonality?bio4?,were screened out quantitatively to be the most influential factor that has shaped the current geographical patterns of C.dielsiana.3)By comparison with other sympatric families,the climatic niche pattern within cherry species of Rosaceae supported the hypothesis of water-energy dynamic and phylogenetic niche conservatism?PNC?at a regional scale,and 4)The results of pearson correlation analysis and canonical correspondence analysis?CCA?show that the effect of habitat filtering from altitude was more significant than those of longitude and latitude.?6?Conservation policy formationUnderstanding genetic diversity and distribution patterns provide scientific decisions for species conservation or core germplasm bank construction.Hence,the four independent-unit in situ conservation from conservation genetics on a broad scale should be suggested.Meanwhile,the natural populations from the North geographic group of Group II,mainly in the Dabashan-Wushan Mts.and Wuling Mts.are most likely the ancestral and current genetic diversity centers for C.dielsiana,should gain protection to some degree.Under the condition of limited funds,populations ZJJ,FJS,NL and HPS with the most genetic diversity deserve particular attention as prime in situ conservation targets in high priority.Besides,in the process of utilizing the resources of C.dielsiana?e.g.,selected as a material or core gene pool for the genetic breeding industry?,plans of reasonable ex situ protection,seed introducing and reproduction,or artificial hybrid across different geographical can serve as essential supplements.In general,under a series of historical-ecological combinations including geological events,natural selection,geographical isolation,environmental scale,and other factors,C.dielsiana has gradually formed the current biogeographic pattern by expanding the diffusion-isolation-differentiation event.The above research results provide a new case for the diversified origin and evolution model of subtropical forest species in China,as well as provide a reference for the future protection and development of wild cherry germplasm resources.