Supplementary data of "The origin and evolution of Clematis sect. Fruticella/铁线莲属灌木铁线莲组的起源与演化"
Creators: name: He, Jian
Publisher: name: Zenodo
Year: 2022
Subjects: 旱生适应性,基因组系统学,灌木习性,趋同演化,同倍体杂交/xerophytic adaptation, phylogenomic, shrubby habit, convergent evolution, homoploid hybridization

description: 旱区拥有着地球上最为独特的生态系统,其自然环境非常严酷,却孕育了极为丰富的生物多样性。旱生植物的起源一直是研究者们非常关心的问题。铁线莲属 (<em>Clematis</em> L.) 为毛茛科世界广布的大属,多数种类为藤本植物。该属中有一群植物 (广义灌木铁线莲组<em>C.</em> sect. <em>Fruticella s.l.</em>,约8–9种) 具有灌木习性、小而退化的叶片等旱生适应性特征,广泛分布于亚洲中部的旱区内。铁线莲属中的这一特殊类群是何时、何地、通过何种方式产生,地质历史与古气候变化对其起源演化与扩散有何影响,都是值得关注的问题。因此,本研究利用Genome skimming、转录组等数据结合多学科手段,在铁线莲属系统发育背景下结合古地质、古气候历史事件,对该属灌木习性与旱生适应性类群的起源与演化进行了详细的探讨。 首先,利用Genome skimming数据,我们获得了56个铁线莲属物种 (其中包括8个广义灌木铁线莲组物种) 的叶绿体全基因组序列以及其核核糖体DNA (nrDNA) 序列,并构建了该属系统发育框架。研究结果表明,广义灌木铁线莲组不是单系类群,其物种内嵌于三个大分枝中。通过分子钟分析和祖先分布区及形态性状重建,发现铁线莲属三个灌木谱系均起源于其他藤本类群。三个谱系的起源时间虽不同,但均在中新世 (Miocene) 末期之后。推测中新世末期以来亚洲中部地区气候的干旱化可能是导致这些类群发生趋同演化的主要原因。另外,铁线莲属尤其是一些灌木种类的系统发育存在明显的核质冲突现象,暗示了一些灌木种类可能为杂交起源并通过杂交获得了干旱环境的适应性。 为了验证以上假说,本研究获得28个居群的广义灌木铁线莲组和38个铁线莲属其他物种样品的转录组数据。经聚类并筛选得到了8,147个单拷贝直系同源核基因,构建了高分辨率的物种树。通过多物种溯祖模型分析表明,古杂交是其核质冲突的主要原因。因此,本研究进一步结合多种方法对杂交事件进行了详细的检测,并结合细胞学和生态学等多学科数据。最终验证了铁线莲属灌木习性趋同演化假说,并揭示了同倍体杂交事件在各个灌木演化分支的起源演化过程中同样起到了重要作用。明确了中新世以来亚洲内陆地区干冷化以及第四纪冰川波动可能是中亚旱地广义灌木铁线莲组起源和多样化的驱动力。本研究还明确了杂交事件在植物新适应性获得方面的重要作用。杂交为铁线莲属的演化提供更多的遗传组合与进化潜能,使得一些类群面对环境干旱化,可以快速适应与其亲本不同的生态环境并形成新的物种,并最终扩散到广大的亚洲干旱生态环境。 此外,我们还在方法学上进行了一些尝试,证实了使用硅胶干燥材料完全满足转录组系统学研究的需求,以及开发了一套快速检测大规模系统发育关系中杂交事件的流程。综上,本研究结果一方面为旱区植物起源与进化研究提供了重要证据,另一方面也可为其他研究者提供相关的方法学参考。 The drylands have the most special ecosystems on earth. Its natural environment is drastic, but hosts a surprisingly rich biodiversity. Xerophytes are one of the most important parts of dryland ecosystems, and how these taxa originated has always been of great interest to researchers. <em>Clematis</em> is one of the cosmopolitan genera of the buttercup family (Ranunculaceae), and is well known for its climbing habit. However, there are also several erect shrubby species (<em>C</em>. sect. <em>Fruticella</em> <em>s.l.</em>, with about 8–9 species) widely distributed in the Central Asian dryland ecosystems and adjacent dry areas. These species not only have well-branched woody stems, but also have simple or rarely very reduced compound leaves, which are specialized adaptations that minimize water loss. How, when and where the shrubby habit and xerophytes of <em>Clematis</em> originated, and its relationship with geological history and past environmental changes are issues worthy of attention. Therefore, in this study, we try to explore the origin and evolution of those taxa with a combined multidisciplinary approach. Firstly, we used genome skimming data to assemble the whole chloroplast genome and nrDNA sequences of 56 <em>Clematis</em> species (including 8 species of <em>C</em>. sect <em>Fruticella s.l.</em>). The phylogenetic relationships were generated. The taxa of shrubby species of<em> Clematis</em> are not monophyletic, and are embedded in three major clades. Then, the molecular dating, historical range reconstruction, and character optimization analyses were conducted. The results clearly showed that the three lineages originated from vine plants independently and have different ancestral distribution areas. All of three lineages diverged from its sister after the late Miocene. The drought in Central Asia since the late Miocene may be the major driver for the convergence of these taxa. In addition, the strong cyto–nuclear discordance of the phylogenetic relationships within <em>C.</em> sect. <em>Fruticella</em> <em>s.l</em>. were observed, and it implies some hybridization events in those taxa. To test the above hypothesis, all species of <em>C.</em> sect. <em>Fruticella</em> <em>s.l.</em> (covering 28 populations) and its related taxa (covering 34 species) were sampled in the field. After transcriptome sequencing and filtering, we obtained a total of 8147 single-copy orthologs. Using this data, we reconstructed a high-resolution phylogenetic relationship. The multi-species coalescent model simulation was conducted and it showed that the cyto–nuclear discordance of these taxa is mainly caused by interspecific hybridization events. Therefore, we used a variety of methods to perform detailed detection of hybridization events, and combined with multi-disciplinary data such as cytology and ecology. The hypothesis of convergent evolution of <em>C.</em> sect. <em>Fruticella s.l.</em> was verified. And it was revealed that the homoploid hybridization also played an important role in the origin of some lineages of shrubby species of <em>Clematis</em>. The aridity of Central Asian after the Late Miocene and glacial period fluctuation in the Pleistocene may be the driving forces for the origin and diversification of the shrubby <em>Clematis</em>. This study also clarifies an important mechanism for the hybridization events in the evolution of new adaptations. The hybridization between ancestral lineages can provide more genetic variation and evolutionary potential to adapt new niche and fuel high diversification rates and it led the shrubby species of <em>Clematis</em> adapted to the extremely vast and diverse dryland environment in Central Asia. In addition, we also made several attempts at methodology. At first, we verified that silica gel-dried plant tissues can be used for phylotranscriptomic studies. Then we developed a pipeline for rapid detection of hybridization in large-scale phylogenetic relationships. In summary, this study not only can provides important evidence for the origin and evolution of species in drylands, but also can be used as a methodology reference for other studies.