AbstractPolyploidization plays an important role in plant speciation and adaptation. To address the role of polyploidization in grass diversification, we studied Phragmites australis, an invasive species with intraspecific variation in chromosome numbers ranging from 2n = 36 to 144. We utilized a combined analysis of ploidy estimation, phylogeny, population genetics and model simulations to investigate the evolution of P.

摘要多倍体化在植物物种形成和适应中起着重要作用。为了解决多倍体化在草地多样化中的作用，我们研究了芦苇（Phragmites australis），这是一种入侵物种，染色体数量的种内变异范围为2n=36至144。。

australis. Using restriction site-associated DNA sequencing (RAD-seq), we conducted a genome-wide analysis of 88 individuals sourced from diverse populations worldwide, revealing the presence of six distinct intraspecific lineages with extensive genetic admixture. Each lineage was characterized by a specific ploidy level, predominantly tetraploid or octoploid, indicative of multiple independent polyploidization events.

澳大利亚。使用限制性位点相关DNA测序（RAD-seq），我们对来自全球不同人群的88个个体进行了全基因组分析，揭示了存在六个不同的种内谱系，具有广泛的遗传混合物。每个谱系的特征在于特定的倍性水平，主要是四倍体或八倍体，表明存在多个独立的多倍体化事件。

The population size of each lineage has declined moderately in history while remaining large, except for the North American native and the US Land types, which experienced constant population size contraction throughout their history. Our investigation did not identify direct association between polyploidization events and grass invasions.

每个血统的人口规模在历史上都有所下降，但仍然很大，除了北美原住民和美国土地类型，它们在整个历史上都经历了不断的人口规模收缩。我们的调查没有发现多倍体事件与草入侵之间的直接关联。

Nonetheless, we observed octoploid and hexaploid lineages at contact zones in Romania, Hungary, and South Africa, suggestively due to genomic conflicts arising from allotetraploid parental lineages..

尽管如此，我们在罗马尼亚，匈牙利和南非的接触区观察到了八倍体和六倍体谱系，这可能是由于异源四倍体亲本谱系引起的基因组冲突。。

IntroductionPolyploidization in the form of allopolyploidization, autopolyploidization, or segmental polyploidization, has been associated with speciation and shaping genetic diversity in the plant kingdom1,2,3. Polyploids have been suggested to outperform their diploid progenitors in highly stressed abiotic environments4, and hence have an access to a wider range of habitats.

引言异源多倍体化，自多倍体化或节段多倍体化形式的多倍体化与植物王国的物种形成和遗传多样性形成有关1,2,3。已经提出多倍体在高度胁迫的非生物环境中优于其二倍体祖细胞4，因此可以获得更广泛的栖息地。

Successful polyploids may be more disposed towards evolving into invasive species5 and drive diploid ancestors to extinction by recurrent hybridization followed by genomic recombination and duplications, as seen in the well-known Spartina species6. However, several empirical studies have challenged this view7, and in contrast Martin and Husband8 suggested that differing ploidy levels might facilitate the coexistence of diploid and tetraploid congeners.

成功的多倍体可能更倾向于进化成入侵物种5，并通过反复杂交，然后进行基因组重组和重复，使二倍体祖先灭绝，如众所周知的米草属物种6所示。然而，一些实证研究对这一观点提出了挑战7，相反，Martin和Husband8认为不同的倍性水平可能有助于二倍体和四倍体同源物的共存。

After the founding polyploid event (or Whole Genome Duplication, WGD), genomic redundancy is reduced through major genomic arrangements including shuffling and deletion of chromosome segments in a process known as “diploidization”. This allows the newly formed genome to function cohesively in the new species9,10.

在建立多倍体事件（或全基因组复制，WGD）后，通过主要的基因组安排（包括在称为“二倍体化”的过程中改组和删除染色体片段）减少了基因组冗余。这使得新形成的基因组在新物种中具有凝聚力9,10。

WGD events are particularly common among grasses11. For example, all cereals have undergone rho, sigma and tau WGD events. The grass family (Poaceae), which includes more than 10,000 species today, originated from a common ancestor with five chromosomes12. A series of genome duplication and subsequent genome fractionation events, involving chromosomal structural rearrangements and loss of redundancy, led to a common ancestral genome with 12 chromosomes in cereals.

WGD事件在草地中特别常见11。例如，所有谷物都经历了rho，sigma和tau WGD事件。禾本科（禾本科）今天包括10000多种，起源于具有五个染色体的共同祖先12。。

This genome structure is shared across the early diverging grass subfamilies Anomochlooideae, Pharoideae, and Puelioideae12,13. Hence, all extant Poaceae species are paleopolyploi.

这种基因组结构在早期分化的草亚科Anomochlooideae，Pharoideae和Puelioideae12,13中共享。因此，所有现存的禾本科物种都是古水龙骨科。

For RAD-seq data, a histogram of the proportion of reads supporting the alternative allele revealed modes at around 0.5 for flow cytometry-confirmed tetraploids, at 0.35 and 0.65 for hexaploids, and between 0.35 and 0.65 for octoploids (Fig. 4). These proportions indicate that the RAD-seq loci were unique to the two subgenomes of the allotetraploid common reed.

对于RAD-seq数据，支持替代等位基因的读数比例的直方图显示，流式细胞术证实的四倍体模式约为0.5，六倍体为0.35和0.65，八倍体为0.35和0.65（图4）。这些比例表明RAD-seq基因座对于异源四倍体普通芦苇的两个亚基因组是独特的。

Out of the 88 individuals, the ploidy levels of 64 were quantified using flow cytometry. Only three samples (Y24, E3, Y37) showed discrepancies between the flow cytometry and our read-based prediction method, which may be attributed to mislabeling of samples or potential aneuploidy. Therefore, the prediction accuracy is at least 95.3% (Table 1), demonstrating that the prediction of ploidy levels from RAD-seq data can be done accurately.Fig.

在88名个体中，使用流式细胞术定量了64倍性水平。只有三个样品（Y24，E3，Y37）显示流式细胞术与我们基于读数的预测方法之间存在差异，这可能归因于样品的错误标记或潜在的非整倍性。因此，预测精度至少为95.3%（表1），表明可以准确地从RAD-seq数据预测倍性水平。图。

4: The alternative allele frequency histograms from aligning the RAD-seq reads to the reference genome.Solid line shows frequency distribution of alternative alleles in individuals where the result was confirmed with flow cytometry. Dashed line shows frequency distribution of alternative alleles in individuals with missing or differing flow cytometry measurement.

4： 将RAD-seq读数与参考基因组对齐的替代等位基因频率直方图。实线显示了用流式细胞术证实结果的个体中替代等位基因的频率分布。虚线显示缺失或不同流式细胞术测量的个体中替代等位基因的频率分布。

Turquoise, red, and blue color represented tetraploid, hexaploidy, and octoploid respectively. Pattern of alternative allele frequency in population tetraploids (a), USnat (b), hexaploids (c), and octoploids (d).Full size imageWe predicted the ploidy levels for the remaining 24 individuals using the in silico method.

绿松石色，红色和蓝色分别代表四倍体，六倍体和八倍体。群体四倍体（a），USnat（b），六倍体（c）和八倍体（d）中替代等位基因频率的模式。全尺寸图像我们使用计算机方法预测了其余24个人的倍性水平。

Most individuals from North America, Northern China, Mediterranean regions, and Europe (representing the USnat, CN, Med, EU lineages; see Fig. 4) were predicted to be allotetraploid, with a unimodal distribution peaking at 0.5 (Table 1; Fig. 4a, b). All representatives from the Gulf Coast (USland lineage).

来自北美，华北，地中海地区和欧洲（代表USnat，CN，Med，EU谱系；见图4）的大多数个体被预测为异源四倍体，单峰分布峰值为0.5（表1；图4a，b）。所有来自墨西哥湾海岸（USland血统）的代表。

Based on our phylogenetic analyses, the USnat lineage diverged early from the main Laurasian population. Consequently, genetic divergence between USnat and other lineages was high (Fst > 0.27, Fig. 2c), especially with USland, see refs. 27,47. The USland lineage showed high divergence from CN (Fst = 0.40) and showed moderate divergence with EU and Med (0.28 < Fst < 0.29).

。因此，USnat与其他谱系之间的遗传差异很高（Fst＞0.27，图2c），尤其是USland，参见参考文献。27,47。USland血统与CN（Fst=0.40）表现出高度差异，与EU和Med（0.28 <Fst<0.29）表现出中度差异。

The lowest Fst values were observed between EU and Med, as well as between EU and CN lineages (0.213), suggesting more recent divergence and gene flow (Fig. 2c). We therefore analyzed gene flow using formal tests of introgression.To trace the origin of higher ploidy levels, we conducted f3 tests to investigate whether octoploids and hexaploids were sourced from hybridization among different populations within the same species.

在EU和Med之间以及EU和CN谱系之间观察到最低的Fst值（0.213），表明最近的分歧和基因流（图2c）。因此，我们使用基因渗入的正式测试分析了基因流。为了追踪更高倍性水平的起源，我们进行了f3测试，以调查八倍体和六倍体是否来自同一物种内不同种群之间的杂交。

In an f3 test, a negative value for f3(Pop1; Pop2, Pop3) indicates that Pop1 is admixed between populations related to Pop2 and Pop3. We tested all combinations of the six populations and found that none of the f3 tests yielded negative values, providing no evidence of hybridization (Supplementary Table S2; Supplementary Fig.

在f3测试中，f3的负值（Pop1；Pop2，Pop3）表明Pop1在与Pop2和Pop3相关的种群之间混合。我们测试了六个种群的所有组合，发现f3测试均未产生负值，未提供杂交证据（补充表S2；补充图）。

S4). Population migrations estimated with Treemix were consistent with the topology of the maximum likelihood phylogenetic tree. A model incorporating two migration events received the highest support from the data (Supplementary Fig. S5). This model suggests one migration event from an ancestral lineage genetically related to the USnat lineage into the USland lineage, alongside a more pronounced migration from the ancestral population of the EU lineage into the USnat lineage (Fig.

S4）。用Treemix估计的种群迁移与最大似然系统发育树的拓扑结构一致。包含两个迁移事件的模型得到了数据的最高支持（补充图S5）。该模型表明，从与USnat谱系遗传相关的祖先谱系向USland谱系的一次迁移事件，以及从欧盟谱系的祖先种群向USnat谱系的更明显迁移（图）。

6a). This suggests that one of the ancestors of the hexaploid USland lineage may be a ghost lineage not sampled in our study. In fact, the USland lineage, habituated in the Gulf C.

6a）。这表明六倍体USland血统的祖先之一可能是我们研究中未采样的幽灵血统。事实上，USland血统习惯于海湾C。

Data Availability

数据可用性

The data underlying this article are available in NCBI SRA database and can be accessed with the BioProject ID PRJNA753984.

本文的基础数据可在NCBI SRA数据库中找到，可以使用生物项目ID PRJNA753984进行访问。

Code availability

代码可用性

The scripts used for the reads mapping, SNP calling, as well as population genetic analysis in this article could be found from github https://github.com/smallfishcui/PhragPopGen.

本文中用于读取映射、SNP调用以及种群遗传分析的脚本可以从github找到https://github.com/smallfishcui/PhragPopGen.

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Download referencesAcknowledgementsThis work was supported by International Postdoctoral Exchange Fellowship Program of China Postdoctoral Science Foundation (C.W.), the National Natural Science Foundation of China Grant No. U22A20558 to W.G., Grant No. 31800299 to T. W., and Nanyang Technological University startup grant and Academy of Finland (decisions 318288 and 319947) to J.S.

下载参考文献致谢这项工作得到了中国博士后科学基金会（C.W.）国际博士后交流奖学金计划，中国国家自然科学基金会授予W.G.的U22A20558号拨款，授予T.W.的31800299号拨款，以及南洋理工大学启动拨款和芬兰科学院（决定318288和319947）授予J.S。

We would like to thank Pasi Rastas for providing the script to calculate alternative allele count, and Carla Lambertini for the help of geographic coordinate corrections. Finally, we want to acknowledge CSC–IT Center for Science, Finland, and NTU HPCC, Singapore, for computational resources.Author informationAuthor notesThese authors contributed equally: Jarkko Salojärvi, Weihua Guo.Authors and AffiliationsInstitute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, ChinaCui Wang, Lele Liu, Meiqi Yin & Weihua GuoShandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, ChinaCui Wang, Lele Liu, Meiqi Yin & Weihua GuoOrganismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1, Biocentre 3, Helsinki, FinlandCui Wang & Jarkko SalojärviDepartment of Biology, Aarhus University, Aarhus, DenmarkFranziska Eller & Hans BrixCollege of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, ChinaTong WangSchool of Biological Sciences, Nanyang Technological University, Singapore, SingaporeJarkko SalojärviAuthorsCui WangView author publicationsYou can also search for this author in.

我们要感谢Pasi Rastas提供了计算替代等位基因计数的脚本，感谢Carla Lambertini提供了地理坐标校正的帮助。最后，我们要感谢芬兰CSC-IT科学中心和新加坡NTU HPCC的计算资源。作者信息作者注意到这些作者做出了同样的贡献：Jarkko Salojärvi，Weihua Guo。作者和单位山东大学生命科学学院生态与生物多样性研究所，青岛，中国崔王，刘乐乐，尹美琪和郭卫华山东省植物生态工程技术研究中心，山东大学，青岛，中国崔王，刘乐乐，尹美琪和郭卫华生物与进化生物学研究计划，赫尔辛基大学生物与环境科学学院，维金卡里1号，生物中心3号，赫尔辛基，芬兰德崔王和Jarkko SalojärviDepartment of Biology，奥胡斯大学，奥胡斯，DenmarkFranziska Eller&Hans BrixCollege of Landscape和林业，青岛农业大学，青岛，中国通旺生物科学学院，南洋理工大学，新加坡，新加坡Jarkko SalojärviAuthorsCui WangView作者出版物您也可以在中搜索这位作者。

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PubMed Google ScholarWeihua GuoView author publicationsYou can also search for this author in

PubMed谷歌学者Weihua GuoView作者出版物您也可以在

PubMed Google ScholarContributionsC.W., J.S., and W.G. conceived the study; H.B., L.L., F.E., and T.W. maintained and collected the samples as well as provided sampling information; C.W., L.L., and M.Y. performed DNA extraction; C.W. and J.S. led the data analysis; C.W. and J.S.

PubMed谷歌学术贡献中心。W、 ，J.S.和W.G.构思了这项研究；H、 B.，L.L.，F.E。和T.W.维护和收集样本以及提供的采样信息；C、 W.，L.L。和M.Y.进行了DNA提取；C、 W.和J.S.领导了数据分析；C、 W.和J.S。

wrote the paper with input from W.G., L.L., F.E., H.B., T.W., and M.Y.Corresponding authorsCorrespondence to.

根据W.G.，L.L.，F.E.，H.B.，T.W.和M.Y.通讯作者的意见撰写了这篇论文。

Jarkko Salojärvi or Weihua Guo.Ethics declarations

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Reprints and permissionsAbout this articleCite this articleWang, C., Liu, L., Yin, M. et al. Genome-wide analysis tracks the emergence of intraspecific polyploids in Phragmites australis.

转载和许可本文引用本文Wang，C.，Liu，L.，Yin，M。等人。全基因组分析追踪了芦苇种内多倍体的出现。

npj biodivers 3, 29 (2024). https://doi.org/10.1038/s44185-024-00060-8Download citationReceived: 28 February 2024Accepted: 29 August 2024Published: 01 October 2024DOI: https://doi.org/10.1038/s44185-024-00060-8Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

npj生物潜水员3,29（2024）。https://doi.org/10.1038/s44185-024-00060-8Download引文接收日期：2024年2月28日接受日期：2024年8月29日发布日期：2024年10月1日OI：https://doi.org/10.1038/s44185-024-00060-8Share本文与您共享以下链接的任何人都可以阅读此内容：获取可共享链接对不起，本文目前没有可共享的链接。复制到剪贴板。

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