Genetic Diversity,Phylogeography And Ecological Adaptation Of Phragmites Australis

Common reed(Phragmites australis)is a cosmopolitan wetland plant with a high variation in ploidy level,genetics and phenotype.Common reed could spread over a along distance by seed dispersal,and colonize in a short distance by vegetative propagation.Common reed is widely distributed in diverse wetland habitats.Under the background of global changes,natural populations of P.australis will face a high risk of both invasion and retreat,which threatens functions and services of wetland ecosystems where P.australis inhabits.Therefore,the study on genetic diversity,phylogeography and ecological adaptation of P.australis has attracted broad attention.Both phylogenetic divergence and local adaptation contribute to the acclimations of P.australis to various ecological factorsIn this study,the P.australis samples were collected from field survey,common garden and other manipulated experiments.Several plant functional traits were measured,such as aboveground biomass per shoot,shoot height,specific leaf area and leaf length.The haplotype was determined by two chloroplast DNA fragments(trnT-trnL and rbcL-psaI),and the genetic variation was detected by microsatellites(SSR)and AFLP markers.The epigenetic variation(DNA methylation pattern)was detected by MS-AFLP markers.The genetic diversity of P.australis was estimated in different scales,regions and conditions,and the phylogenetic structure of P.australis in China was demonstrated by haplotype and SSR.Combined with geographical occurrence records and manipulated experiments,I analyzed the niche divergence and ecological adaptation of Chinses lineages of P.australis,and explored the adaptation mechanisms of P.australis at phenotypic,genetic and epigenetic levels in the view of phylogenetic divergence and local adaptation.The main results are as follows:(1)The significant differences in morphology and phenology were observed among the natural populations of P.australis in the Yellow River Delta,Nansi Lakes and Ningxia Plain,and the P.australis population in new wetlands of the Yellow River Delta might come from both the upstream of the Yellow River and the surrounding wetland.The phenotypic variation of P.australis in natural populations was mostly influenced by environment.Nansi Lakes are the freshwater wetlands in east China,therefore the habitat there is very suitable for P.australis and the morphological features(e.g.shoot height,leaf length and leaf width)were largest among three regions(ANOVA,P<0.001).Ningxia Plain is in northwest China with relative low precipitation,and the phenology(e.g.flowering time)of P.australis there was earlier.The Yellow River Delta was geographically close to Naisi Lakes,and linked to Ningxia Plain by the Yellow River,which may explain the complexity of genetic lineages in the Yellow River Delta.Common reed in the Yellow River Delta could be genetically divided into two groups,similar with Nansi Lakes and Ningxia Plain,respectively.The genetic structure of P.australis in the Yellow River Delta was very weak(AFLP,?st=0.072;SSR,?st<0.165).Mantel tests and multiple matrix regression analyses with randomization(MMRR)revealed that the isolation by geographical distance was an important factor for genetic and epigenetic structure of P.australis at individual level for each region.The epigenetic variation was significantly affected by genetic variation,but the effects of genetic and epigenetic variation on phenotypic variation might depend on the environmental context in P.australis.(2)A total of fifteen haplotypes of P.australis were found in China by this survey,including nine reported haplotypes(O,P,M,L,U,I,AT,AS and BA)and six new haplotypes(BF,BG,BH,BI,BJ and BK).Combined other reported haplotypes(K,Q,AY,AZ,BB,BC and BD),so far 22 haplotypes of P.australis were found in China.The two major lineages of P.australis in China were delimited by chloroplast haplotype and nuclear microsatellites,and they were named lineage O and lineage P.Lineage O is dominated by haplotype O with a relatively low ploidy level(e.g.tetraploid)across northern China,and lineage P is dominated by haplotype P with a high ploidy level(e.g.octoploid)in eastern China.The geographical distributions of the two lineages are partly overlapped,which provides the potential of the introgression between two lineages.Haplotype M in China was not a monophyletic clade in nuclear phylogeny.Haplotype M in east China tended to be lineage P,while haplotype M in west China was more similar to lineage O.The genetic differentiation between the two lineages in the east was more significant than that in the west,and the introgression level from lineage O into P was higher than backward.The introgression was influenced by ploidy levels,phylogenetic history and future global changes,which might cover the effect of local lineage abundance.(3)Ecological niche model analysis was performed for delimiting P.australis lineages and their sister species P.japonicas.The MaxEnt model analysis revealed that there was a niche divergence between two haplotypes(haplotype 0 and M)in the lower-ploidy lineage(i.e.lineage O)(niche overlap index,Schoener's D=0.73),which suggested that the fate of nascent polyploids could not be predicted without accounting for phylogenetic relatedness.Relative to lineage O,the higher-ploidy lineage(i.e lineage P)displayed a niche shift and constriction[Schoener's D=0.48,0.26;haplotype M(B1=0.40;B2=0.95)>haplotype O(B1=0.30;B2=0.93)>haplotype P(B1=0.19;B2=0.91)],and a close niche similarity with P.japonicas(Schoener's D=0.42).The rapid changes of the suitable areas in east China were not found under the simulated paleoclimatic conditions,and thus cannot provide available evidence for the phylogeographical history of P.australis lineages.The model predicted that all lineages would expand northwards and westwards in the future climate changes(4)AFLP and MS-AFLP were used to analyze the genetic and epigenetic variation for the introduced P.australis in North America,the native in North America and the origin in Europe.The results showed a significant positive correlation between genetic and epigenetic variation(Pearson correlation:r=0.75,P<0.001),suggesting that the epigenetic variation was mostly controlled or regulated by genetic variation.In the Great Lakes region,the introduced group(INT)exhibited a high level of both genetic and epigenetic diversity(genetic,uHe=0.255;epigenetic,uHe=0.330),which was higher than the native group(NAT)(genetic,uHe=0.178;epigenetic,uHe=0.240)but lower than original groups(EU)(genetic,uHe=0.344;epigenetic,uHe=0.375).In the Gulf Coast region,the native group(LAND)had a much higher level of genetic diversity than the introduced group(DELTA)(DELTA,uHe=0.296;LAND,uHe=0.340)but a lower level of epigenetic diversity(DELTA,uHe=0.344;LAND,uHe=0.339).When the invasive populations could not obtain enough genetic diversity via hybridization among multiple introductions,the complementary effect of epigenetic diversity will emerge.However,the result did not showed any rapid convergence of epigenetic variation between invasive and native populations.The results suggested the role of genetic diversity in biological invasion and ecological adaptation of P.australis cannot be ignored.(5)The ecological adaptation of major lineage of P.australis in eastern China was analyzed based on salt pot and pond experiments at the individual and population levels.The results showed a better performance of lineage P than lineage O in the low-salinity condition(ANOVA,P<0.01).The differences in biomass and phenotype between two lineages under the salt stress were much smaller than those in the control,which might explain why lineage O could dispread in partial coastal wetlands(e.g.the Yellow River Delta)in eastern China.The phenotypes of P.australis were plastic,mostly dependent on environment,and were also affected by genetic and epigenetic variation(the correlation indices R in Mantel tests were 0.39,0.39 and 0.15 for environmental,genetic and epigenetic variation,respectively;P<0.001).Epigenetic variation could influence the phenotype independently from genetic variation(partial Mantel test,R=0.14,P<0.01).Epigenetic variation generally depended on genetic variation,and was also directly influenced by environment(MMRR correlation indices were 23.39 and 1.71 for genetic and environmental variation,respectively;P<0.001).Drought and salinity decreased the genetic diversity(ANOVA,P<0.05).Under the heterogeneity in salt and water,the genetic diversity of P.australis was shaped by environmental filtering rather than competitive exclusion in a short term,but environmental filtering could not lead to a monoclonal community of P.australis.In conclusion,natural populations of P.australis have a high level of genetic diversity,which provides a significant basis for phenotypic variation and ecological adaptation.The epigenetic variation represented by DNA methylation is significantly correlated with genetic variation,and could play an important role in stress response and biological invasion of P.australis.In temperate China,common reed could be genetically separated into two major lineages with significant differences in geographical distribution,ploidy level,hydrothermal niche and habitat adaptation.Migration,hybridization and introgression between lineages would deeply affect the wetland ecosystem of P.australis under the future global change conditions,which deserve more attention in the further study.The study lays the foundation for the further exploration in evolutionary history,adaptation traits and molecular mechanisms of P.australis.The study provides a theoretical basis for the protection and breeding of reed germplasm,the monitoring and restoration of reed population,and the development and utilization of reed resources.Firstly,natural wetlands dominated by common reed should be protected from various pollutions to avoid die-back.Secondly,the native wetlands should be well retained or designed in new parks or botanical gardens to save the genetic resource of common reed.Thirdly,the native seeds of common reed were recommended in wetland revegetation engineering,which could increase genetic diversity and reduce the cryptic invasion.Lastly,genetic resource of common reed could be efficiently utilized by breeding specific varieties.