The Evolutionary History And Taxonomy Of Rosa Brunonii Complex

The genus Rosa L.belongs to Rosaceae,and most species of this genus are of great economic and ecological importance.Over-lapped morphological variation,frequent hybridization and introgression are common in Rosa,especially for those complex species（such as Rosa brunonii complex）that differentiation recently,which makes it difficult for the taxonomy.Multiple evidences were used to study the evolutionary history and relations between species of Rosa brunonii complex.Firstly,whole-genome resequencing data at the population level were used to product phylogenetic tree construction,principal component analysis,structure analysis and genetic diversity parameters calculation to evaluate the population genetic structure of the Rosa brunonii complex and the genetic diversity of each lineage;then we simulated the niche and the differentiation of environmental factors in the distribution area of each lineage to compare the geographical distribution and environmental differentiation among lineages;and analyzed the changes in effective population size,combined with the results of niche simulation in the LGM and LIG periods to speculate the mechanisms of speciation and evolution.Besides,species definition of Rosa brunonii complex were evaluated by constructing a phylogenetic tree based on the chloroplast genome,performing morphology cluster analysis and niche analysis.The main conclusions are as following:（1）Population structure and evolutionary history of the Rosa brunonii complex1)The Rosa brunonii complex consists of three obvious genetic components and can be divided into three lineages geographically: the East,the Central and the West,and the heterogeneous habitats might have promoted the differentiation between each lineage.2)The population genetic diversity,niche simulation of the LGM and LIG periods and population historical dynamics all indicated that the Hengduan Mountains and the marginal areas of the Sichuan Basin might be the Quaternary glacial refuges of the complex.The complex species expanded outward from the refuges and gradually formed independent evolutionary units after the LGM.（2）The interspecific relationships and integrative taxonomy suggestions of the Rosa brunonii complex1)The 17 complete chloroplast genomes of the Rosa brunonii complex were obtained through assembly and annotation,and these chloroplast genomes were conserved in size and structure.Phylogenetic relationships based on the 17 chloroplast genomes is consistent with the population genetic structure,and it showed that the same species distributed in different regions may have diverged due to geographical isolation and adaptive evolution.Sympatric or parapatric species exchange genes more frequently and exhibit closer genetic relationships.2)Morphological clustering of the Rosa brunonii complex showed that the morphological characteristics of the same species are similar,and the morphological characteristics of the different species have been differentiated to different degrees,but the phenomena of intraspecific morphological variation and interspecific morphological crossover and continuity were common in the Rosa brunonii complex.In addition,the morphological variation within the complex is mainly concentrated in the reproductive organs,instead of the vegetative organs.3)Based on molecular,morphological,and ecological evidence,the phylogenetic relationships among species in the Rosa brunonii complex are chaotic and difficult to distinguish.The distribution range of R.brunonii,R.helenae and R.filipes is wide and have frequent genetic exchange with other species,but various evidences still support that they are independent species.There is gene exchange between R.shangchengensis and sympatric R.helenae.,but the distribution range of R.shangchengensis is relatively independent,and the morphological characteristics is easily differentiated,therefore we treat the R.shangchengensis as an independent species.The distribution ranges of R.ludingensis and R.weisiensis are narrow and have no independent niche,they have small genetic distances and frequent gene exchanges with the sympatric or parapatric species,as well as the differentiation in some morphology characteristics are slight and not stable,therefore,we believe that these two narrow-range species are the variants of similar species,which may be in the process of differentiation and are not an independent species.This study inferred the evolution history and species delimitation of the Rosa brunonii complex based on multiple evidence,verified the influence of climate shock in the Quaternary glacial period on the complex population,and redefined the species in the complex population,which provided evidence for understanding the boundary of close species in Rosa and the taxonomic revision of this genus,the protect and utilizing of germplasm resources,even for taxonomic and evolutionary research of such species complex.