The Evolutionary History Of Hippopha(?) Gyantsensis(Elaeagnaceae)

Hybridization plays an important role in the process of speciation,and allopolyploidization is often considered to be the main form of hybrid speciation for higher plants.With the in-depth research and understanding of hybridization,people gradually realized that homoploid hybridization,which does not involve changes in the number of chromosomes,is also one of the important mechanisms of hybrid species formation.The unique climate,landform types and geological history of the QinghaiTibet Plateau and adjacent areas provide convenience and conditions for the formation of homoploid hybrid species.So far,only four cases of homoploid hybrid species have been reported in this area.Among them,Hippophae gyantsensis,a shrub or small tree distributed in the southeast of the Qinghai-Tibet Plateau,is proposed to have originated from a homoploid hybrid cross between H.neurocarpa and H.rhamnoides ssp.yunnanensis.The morphological traits of H.gyantsensis are stable,and most of the traits are shared with one of its two parents.In addition,H.gyantsensis and its parents have complete ecological and spatial isolation.However,the conclusions of previous research are mainly based on the discordance between the phyloginies constructed by a small number of nuclear and chloroplast markers.The limited genetic polymorphisms exhibited by a small number of molecular markers still cannot rule out other potential "hybridization signals",such as incomplete lineage sorting and secondary gene flow,etc.In order to further examine and clarify the evolutionary history and speciation patterns of H.gyantsensis,the approach of restriction-site-associated DNA sequencing(RAD-seq)was performed on 153 individuals from 37 populations representing the putative hybrid and its parents.By screening SNP and INEDL markers in the whole genome,we analyzed the genetic diversity,population genetic structure,and interspecific gene flow patterns of the three species.Finally,we performed coalescent simulation using Approximate Bayesian Computation(ABC)to simulate the evolutionary history and hybrid speciation patterns of H.gyantsensis.The main findings are as follows:1.In this study,a total of 2,952,637 SNPs and 108,495 INDELs were collected.After filtering,20297 SNP loci and 2622 INDEL loci were retained,and the genetic diversity of H.gyantsensis and its two parents,H.neurocarpa and H.rhamnoides ssp.yunnanensis were analyzed.The results showed that H.gyantsensis has the highest genetic diversity(Na = 1.891,Ne = 1.335,Ho = 0.133,and He = 0.213),followed by H.neurocarpa(Na = 1.737,Ne = 1.331,Ho = 0.089,He = 0.207)and H.rhamnoides ssp.yunnanensis(Na = 1.698,Ne = 1.330,Ho = 0.103,He = 0.205).The higher degree of genetic variation compared to the two parents indicates that H.gyantsensis has experienced more complex population dynamics during its long-term evolutionary process,which may be caused by the more complex geological history and climate fluctuations on the Qinghai-Tibet Plateau platform.2.Based on SNPs data,the phylogenetic relationships of the three species was reconstructed.The results showed that,except for a few individuals,most samples of the three species were clustered into three large branches,respectively.H.gyantsensis and H.neurocarpa are more closely related,and sister to each other.ADMIXTURE cluster analysis and principal coordinate analysis(PCo A)based on the pairwise Fst values supported this result and further revealed the intraspecific differentiation within H.gyantsensis.AMOVA analysis shows that 47% of genetic differences were distributed among the three species.The results of gene flow analysis showed that there was a limited gene flow among the three species.The above results showed that there was a relatively obvious genetic divergence and reproductive isolation between H.gyantsensis and its two parents,and further confirmed the independent species status of H.gyantsensis.3.The simulation based on the ABC method was performed to clarify the hybrid origin of H.gyantsensis.The simulation results excluded the other models that may generate hybridization signals,such as incomplete lineage sorting,hybrid swarm,and secondary gene flow.The scenario with a hybrid origin of H.gyantsensis was determined to be the best model,with a posterior possibility value of 0.6252.This result further clarified the homoploid hybrid origin of this species.4.Based on the Extended Bayesian skyline method(EBSP),the ancestral simulation of the effective population size of H.gyantsensis,H.rhamnoides ssp.yunnanensis and H.neurocarpa changes over time.The EBSP results analyzed by Beast showed that the three populations all showed a trend of population expansion,and the effective population of H.gyantsensis became larger.After 0.06 million years(Mya),the effective population began to increase rapidly at the end of the Quaternary glacial period,indicating the fourth The glacial refuge plays an important role in the effective population size of H.gyantsensis.In summary,this study used RAD-seq data and various approaches includingcoalescent simulations to examine the evolutionary history and speciation pattern ofH.gyantsensis.The results of the study verified and identified the origin of H.gyantsensis through homoploid hybridization.The findings will improve ourunderstanding of the mechanism of homoploid hybrid speciation.Additionally,thisstudy also provided a case for the application of RAD-seq in non-model organismswithout reference genomes to determine their evolutionary histories and speciationpatterns.