中文题名: | 岷江景天属(Ohbaea)及其近缘类群的系统发生关系研究 |
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保密级别: | 公开 |
论文语种: | chi |
学科代码: | 071300 |
学科专业: | |
学生类型: | 硕士 |
学位: | 理学硕士 |
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学位年度: | 2023 |
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研究方向: | 演化生物学 |
第一导师姓名: | |
第一导师单位: | |
提交日期: | 2023-06-14 |
答辩日期: | 2023-05-23 |
外文题名: | Phylogenetic relationships of Ohbaea (Crassulaceae) with its genealogical allies |
中文关键词: | |
外文关键词: | Phylogeny ; Sedum ; Ohbaea balfourii ; Hyb-Seq ; Plastid genome |
中文摘要: |
岷江景天属(Ohbaea V. V. Byalt & I. V. Sokolova)隶属景天科(Crassulaceae),为 一单种属,仅包含岷江景天 [Ohbaea balfourii (Raym.-Hamet) V.V. Byalt & I.V. Sokolova]一 个物种,主要分布于我国横断山区的干热河谷。由于该属的形态特征与景天属(Sedum)、 红景天属(Rhodiola)和瓦莲属(Rosularia)等都既有联系又有区别,其系统位置或分类 地位长期不定,不同学者将其处理为不同的分类等级或置于不同的属:岷江景天作为新 种发表时被置于景天属;而后随着红景天属从景天属中独立出来,岷江景天因其看似根 状茎的结构以及从根部伸出的“花枝”而被归入红景天属;上世纪 80 年代的《中国植物 志》接受其为景天属的成员,但作为该属中特征较为独特(具有莲座状基生叶)的一个 独立的组——岷江景天组(S. Sect. Balfouria);而最新的 Flora of China(中国植物志英文 版)则将其提升为一个单种属。 我国横断山区是新生代物种辐射演化和多样性的摇篮,也是世界景天科植物的多样 性中心之一,岷江景天与近缘类群复杂的亲缘关系和颇具争议的系统位置显然与该地区 物种的快速适应性分化有关。以往基于形态性状的分类研究由于可能的适应性趋同特征 而无法准确判断类群的真实演化历史;此外,由于过去 20‒30 年分子标记技术的局限,少 数质体和细胞核 DNA 片段也无法解析快速分化类群间的系统发生关系。近年来随着高通 量测序技术的发展,我们有可能获得所研究类群更丰富的遗传信息,从而更可靠的重建 它们的系统发生关系。 本研究对中国横断山区及周边地区的景天科植物进行了广泛的采样,共选取 9 属 86 个物种的标本和 DNA 材料,利用杂交捕获技术(Hyb-Seq)结合二代测序获取了该类群 的 623 个直系同源基因位点;同时,利用基因组浅层测序技术(Genome skimming)对 72 个物种的完整质体基因组进行了测序。利用所获得的核、质两套序列数据,分别进行了 系统发生重建,探讨了岷江景天的系统位置;进而依据鉴定到的单拷贝核基因对岷江景 天及其近缘类群的关系进行了基因树与物种树冲突的评估及拓扑分析,并检测了近缘类 群间潜在的基因流和杂交事件,最后通过分化时间估算,对岷江景天的演化历史、与近 缘类群的演化关系等进行了深入解析。研究结果如下: (1)基于 623 个单拷贝核基因和 72 个质体基因组的分析都支持东亚景天科植物分化 为三个单系支,即 Hylptelephium 支、Rhodiola 支和 Acre,其中 Hylptelephium 支包括八宝 属(Hylotelephium)、瓦松属(Orostachys)、石莲属(Sinocrassula);Rhodiola 支仅包 含红景天属;而 Acer 支的成员除了岷江景天属之外,都是景天属的种类。在以伽蓝菜属 (Kanlanchoe)为外类群的核基因树上,八宝属为基部类群,Rhodiola支与 Acre支更近, II 互为姊妹类群;在质体基因树上,Rhodiola 支却与 Hylptelephium 支为姊妹类群,两者组 成的单系群再与 Acer 支互为姊妹类群。尽管核、质基因树在大分支式样上存在一定的冲 突,但岷江景天的位置在两个树上是一致的,即都嵌套在景天属的内部分支中,与分类 学上的山景天组(Sect. Oreades)的物种有十分密切的关系,因此本研究结果支持岷江景 天属于景天属,但不支持其独立成组,更不支持将其分类地位上升成属。 (2)中国的景天属植物主要分布在横断山区和我国东南地区。东南地区的物种大多 位于景天属的基部分支,而横断山区的种类则属于景天属中较为晚期分化的分支,且分 类群间系统发生关系较为复杂,暗示该地区物种的快速辐射演化和谱系间频繁的基因流 或杂交。Phylonet 结果支持这个推测,表明岷江景天近缘物种中的高原景天( S. przewalskii)、小景天(S. fischeri)、铲瓣景天(S. trullipetalum)和藓茎景天(S. dugueyi) 可能是杂交起源的,但不支持岷江景天可能为杂交起源的假说。 (3)利用核基因数据的拓扑结构分析表明,岷江景天与横断山区的其他景天属物种 具有更为紧密的演化关系,它们组成了景天属的冠群。四重频率检验的结果表明,岷江 景天所处的这个冠群中物种可能是同一时期快速分化出来的,因此可能伴随着比较严重 的不完全谱系分选,导致了其系统发育关系的不稳定。 (4)分子钟推算表明,中国景天属物种在渐新世-中新世过渡期(25~22Mya)经历 了一次较为快速的辐射演化。最大分支可信树的拓扑结构表明,岷江景天及其姊妹种柔 毛景天(S. giajae)可能是横断山地区的景天属植物中较为原始者,这两个物种于 9.8 Mya 分化。 (5)景天属植物的质体基因组具有典型的四分体结构,包括两个单拷贝区域(LSC 和 SSC)和两个反向重复区域(IRA 和 IRB)。然而,不同物种的质体基因组长度变异较 大,本研究所测物种的质体总长度在 136335 bp 到 151540 bp 之间,其中最短者为藓茎景 天(S. dugueyi)的,最长者为火焰草(S. stellariifolium)的。长度变异主要是基因丢失事 件导致的,基因丢失主要集中于横断山区的景天属物种;丢失的基因主要为 NAD(P)H 脱 氢酶相关基因,丢失这些基因的物种大多还伴随有质体 IR 区一定程度的扩张。 综上所述,本研究通过对中国横断山区及周边地区景天科植物的广泛采样,利用大量 单拷贝核基因和质体基因组的遗传信息,对岷江景天及其近缘类群的系统发生关系、基 因流和杂交事件以及分歧时间进行了评估和分析,结果显示岷江景天与景天属的横断山 区物种有最近的共祖关系,不足以在分类学上独立成属。 |
外文摘要: |
Ohbaea V. V. Byalt & I. V. Sokolova is a monospecific genus belonging to the family Crassulaceae, which includes only one species, Ohbaea balfourii (Raym.-Hamet) V.V. Byalt & I.V. Sokolova. It is mainly distributed in the dry and hot river valleys of the Hengduan Mountains in China. Due to the morphological similarities and differences between Ohbaea and other genera, such as Sedum, Rhodiola, and Rosularia, its phylogenetic position has long been uncertain. Different taxonomists have placed it at different taxonomic ranks or in different genera. When Ohbaea balfourii was first described as a new species, it was placed in the genus Sedum. Later, after Rhodiola was separated from Sedum, Ohbaea balfourii was classified into Rhodiola due to its tuberous root structure and "flowering branches" extending from the roots. In the 1980s, the Flora of China (Chinese edition) merged Ohbaea balfourii back into Sedum, but it was treated as an independent section, S. Section. Ohbaea due to its unique characteristics (lotus-like basal leaf). The latest version of the Flora of China (English edition) elevates it to an independent genus. The Hengduan Mountains in China are considered a cradle of species radiation and plants diversity, as well as one of the centers of diversity for the Crassulaceae family. The complex phylogeny relationships of Ohbaea balfourii and with its close relatives are likely related to the rapid adaptive divergence of species in this region. Previous studies based on morphology were unable to accurately determine the true evolutionary history of these groups due to possible convergent adaptive traits. Additionally, due to limitations in molecular marker technology over the past 20-30 years, a few plastid and nuclear fragments were insufficient to resolve the phylogenetic relationships among rapidly diverging groups. However, recent advances in nextgeneration sequencing technology provide the possibility of obtaining more reliable genetic information of these groups, allowing for a more accurate reconstruction of their phylogenetic relationships. This study conducted extensive sampling of plants of the Crassulaceae family in the Hengduan Mountains and surrounding areas of China. A total of 86 species from 9 genera were sampled for both specimens and DNA material. Using a combination of hybrid capture technology (Hyb-Seq) and next-generation sequencing technology, 623 orthologous loci were obtained for this study. IV Additionally, genome skimming was used to obtain complete plastid genomes of 72 species. Based on the obtained nuclear and plastid genome data, phylogenetic reconstructions were performed to explore the phylogeny position of Ohbaea. Furthermore, the conflict between gene tree and species tree, potential gene flow and hybridization events of Ohbaea and its close relatives were evaluated. Finally, the divergence time of Ohbaea and its related taxa was estimated. The study results are as follows: (1) Based on the analysis of 623 single-copy nuclear genes and 72 plastid genomes, East Asian Crassulaceae species consisted of three monophyletic clades: the Hylptelephium clade, the Rhodiola clade, and the Acre clade. The Hylotelephium clade includes Hylotelephium, Orostachys, and Sinocrassula, while the Rhodiola clade consists only of Rhodiola, and the Acre clade comprises all Sedum species and Ohbaea balfourii. Using the Kalanchoe as the outgroup, the nuclear gene tree places the Hylptelephium clade at the base. The nuclear gene tree shows the Rhodiola and Acre clades as sister groups, whereas the plastid gene tree places the Rhodiola clade as sister to the Hylotelephium clade. Despite some conflicts between the topologies of the nuclear and plastid gene trees, the position of Ohbaea balfourii is consistently nested within the internal branches of the Sedum clade, indicating a close relationship to species in the S. Sect. Oreades. These results do not support the classification of Ohbaea balfourii as an independent section in Sedum, nor do they support elevating its taxonomic status to the level of a genus. (2) The Chinese Crassulaceae plants, especially in the Sedum, are mainly distributed in the Hengduan Mountains and southeastern China. Species in southeastern China mostly belong to the basal branches of the Sedum, while those in the Hengduan Mountains are located within the internal branches of the phylogenetic tree, and their relationships are complex. This suggests that the species in this region have undergone rapid radiation and frequent gene flow or hybridization among lineages. Phylogenetic network analysis supports this hypothesis, indicating that S. przewalskii, S. fischeri, S. trullipetalum, and S. dugueyi, which are closely related to Ohbaea balfourii, may have originated through hybridization. However, the hypothesis that Ohbaea balfourii itself may have originated through hybridization is not supported by the present results. (3) Comparative analysis of the topology of nuclear gene data shows that Ohbaea balfourii is more closely related to Sedum species located in the Hengduan Mountains. Results from the quartet frequencies test indicate that Ohbaea balfourii and its closely related species in the crown group of Sedum may have rapidly evolved at the same time, potentially accompanied by severe incomplete lineage sorting, leading to the instability of its phylogenetic relationship. (4) Divergence time analyse suggest that the Chinese Sedum species underwent a relatively rapid radiation evolution at the oligocene-miocene transition periods (25~22Mya), leading to the V formation of the species we see today. The topology of the maximum likelihood tree suggests that Ohbaea balfourii and Sedum giajae may represent a more primitive group of Sedum species in the Hengduan Mountains. These two species diverged around 9.8 million years ago. (5) The plastid genome of Sedum species has a typical quadripartite structure, consisting of two single-copy regions and two inverted repeat regions. However, the length of the plastid genome varies greatly among different species, with a total length ranging from 136,335 bp to 151,540 bp in the sampled Sedum species. The shortest plastid genome belongs to Sedum dugueyi, while the longest belongs to Sedum stellariifolium. These variations are mainly caused by gene loss events, which are concentrated in the Sedum species from the Hengduan Mountains region. The lost genes are mainly NAD(P)H dehydrogenase-related genes. For the species with gene loss, the IR regions have also expanded to some extent. In sum, based on analyses of sequences of hundreds of nuclear single/low copy genes and plastid gonomes, the present study clarifies the phylogentic position of Ohbaea balfourii actually within the genus Sedum, and proposes that the generic name Ohbaea should be denied and the name S. balfourii should be recovered. |
参考文献总数: | 115 |
馆藏号: | 硕071300/23018 |
开放日期: | 2024-06-14 |