Integrating Phylogeography And Landscape Genetics Reveals Formation Mechanism Of Genetic Variation And Its Spatial Distribution Pattern For Stipa Breviflora

Genetic diversity,the foundation of biodiversity,is a result of long-term survival,evolution and adaptation of species,and has great importance to the biodiversity protection.Contemporary genetic diversity and genetic structure are the result of the combined effects of historical and modern microevolutionary process.Stipa breviflora Griseb.?Poaceae?,a perennial herb,is one of the dominant species distributed in the desert steppe region.Study on phylogeography and landscape genetic of S.breviflora is conducive to infer the influence of historical environment evolution on lineage divergence,elucidate the current spatial distribution of genetic variation on regional scale,and explain the effect of human activities on genetic diversity and structure of S.breviflora.Here,we focus on phylogeographic structure,genetic diversity and genetic structure of 27 populations of S.breviflora distributed on regional scale by integrating cpDNA and EST-SSR.And explore the genetic diversity and genetic differentiation of 52 populations of S.breviflora distributed on local scale using EST-SSR.By integrating the analysis methods of phylogeography and landscape genetics to reveal the formation mechanism of genetic variation and its spatial distribution pattern for S.breviflora.The main results are shown as below:?1?Based on the transcriptome data of S.breviflora,21 polymorphic EST-SSRs were developed for the first time.And these SSRs primers had good universality in the other 6 related species of S.breviflora.?2?A total of 13 cpDNA haplotypes were identified among 27 populations of S.breviflora,of which H1 was a widely distributed haplotype.At species level,the haplotype diversity was estimated to be 0.494,and the nucleotide diversity was 1.02*10-3.The spatial distribution pattern of genetic variation showed a decreasing trend from east to west.The divergence time and ancestral range reconstruction demonstrated that S.breviflora originated in the northeast QTP and Helan Mountain in the Late Miocene?7.66Ma?,and then dispersed along two separate routes,namely from northeast QTP to Xinjiang through the southern foot of Qilian Mountains,and from northeast QTP and Helan Mountain to Hexi Corridor,southwest QTP and Mongolia Plateau.Neutrality tests and mismatch distribution analysis indicated that S.breviflora experienced a spatial expansion process from Early Pleistocene?1.5 Ma?to Middle Pleistocene?0.5 Ma?.Therefore,it was inferred that rapid uplift of the QTP and formation of Asian monsoon led to the differentiation of S.breviflora,loess deposition accelerated the radiation of S.breviflora,climate fluctuation of Pliocene and Pleistocene promoted the evolution of haplotype of S.breviflora.?3?On regional scale,the genetic diversity of S.breviflora belongs to the medium low level.The general trend of genetic diversity distribution pattern of S.breviflora was decrease from the center to the edge with increase genetic differentiation of its geographic range,which conformed to the center-periphery hypothesis?CPH?.STRUCTURE divided the populations into three clusters,namely the east,central and west subpopulations,and continuous gene flow was discovered between the east and west subpopulations.sPCA discriminated populations distributed in the east part of study area?Mongolia Plateau,Loess Plateau,Hexi Corridor and northeast QTP?from those in the west?southwest QTP and Xinjiang?.The east and central subpopulations of STRUCTURE was corresponding to the east part of sPCA.On regional scale,genetic differentiation of S.breviflora was mainly caused by IBD,while the Kunlun Mountains,Tianshan Mountains and extreme arid desert terrain had formed geographical barriers to gene flow.Differential expression gene?DEGs?analysis between east and west group based on sPCA documented the west group enhanced its adaption by upregulating the FPKM of stress resistance gene and regulating the metabolic pathways.Compared with the east group populations,the west group was more adaptable to the environmental pressure of drought,low oxygen and high UV radiation.?4?On local scale,human activities could promote the functional connectivity of S.breviflora populations inhabited in fragmented habitats,and improve the genetic diversity.Mantel test demonstrated that the genetic differentiation was mainly caused by environment dissimilarity.And dbRDA analysis showed the Mean Diurnal Range?bio 2?and Mean Temperature of Wettest Quarter?bio₈?were the dominant factors.The current landscape configuration and geographic distance had no significant influence on microevolution process of S.breviflora.In conclusion,S.breviflora was characterized by moderately lower genetic diversity and genetic differentiation at the species level,and there was no obvious phylogeographic structure.In Late Miocene/Pliocene,rapid uplift of QTP,formation of Asian monsoon and loess deposition caused by monsoon accelerated the differentiation of S.breviflora.The general trend of genetic diversity distribution pattern of S.breviflora was decrease from the center to the edge of its geographic range,which was line with the center-periphery hypothesis?CPH?.On regional scale,genetic differentiation was mainly shaped by IBD.While on local scale,the IBE was the main factor.Furthermore,it was found that human activities were contributed to the improvement of genetic diversity of S.breviflora.Conclusively,this research revealed the formation mechanism of genetic variation and its spatial distribution pattern for S.breviflora on different temporal and spatial scales,which not only provided a case study for the combination of phylogeography with landscape genetics,but facilitated to biodiversity protection of Stipa steppe under the effects of climate changes and human activities in the future.