兰州大学机构库 >生命科学学院
鹅耳枥属和铁木属系统发育基因组学研究
Alternative TitlePhylogenomics of Carpinus and Ostrya (Betulaceae)
杨勇志
Thesis Advisor刘建全 ; 邱强
2018-05-31
Degree Grantor兰州大学
Place of Conferral兰州
Degree Name博士
Keyword鹅耳枥属 铁木属 DNA 条形码 系统发育基因组学 基因流 群体历史
Abstract

鹅耳枥属 (Carpinus) 和铁木属 (Ostrya) 是桦木科 (Betulaceae) 中的一对姊妹属,是北半球温带森林树种的重要组成部分。两属共包含约58个种,亚洲是它们的分布中心。目前对于两个属的系统发育研究主要基于少量叶绿体片段或ITS片段,涉及的物种数、每个物种的个体数和居群数目少且遗传信息有限,并未能很好地解析两个属的系统发育和种间关系。本研究广泛收集了国内外样品,开展了迄今为止规模最大的鹅耳枥属和铁木属的系统发育学相关研究,分别从形态、居群水平的DNA条形码和基因组水平对两个属属间和属内物种间的进化关系进入了深入分析;基于基因组数据,利用多种手段,检查了物种间可能存在的基因流。研究结果如下:

1) 对鹅耳枥属36个种,铁木属8个种,共计243个居群,1,330棵树的材料进行了DNA条形码序列(trnL-F和ITS)的扩增和测序。系统发育分析发现鹅耳枥属和铁木属的物种可以分成4大稳定的支系,这也和形态学分类一致:(1)为所有的铁木属物种,其果序中的小坚果完全被苞片包裹;(2)为鹅耳枥属内的千金榆组,苞片成半闭合状态,介于铁木和鹅耳枥组之间,基本将小坚果遮盖;(3)和(4)为鹅耳枥属内鹅耳枥组内的两个支系,果序中的小坚果完全裸露,其中(3)支系果序中苞片内侧具有明显的裂片,而(4)直系果序中苞片内侧无裂片或裂片极不明显。尽管如此,属间关系和大部分的种间关系并未得到解决。2) 为了更详细的解读鹅耳枥属和铁木属内物种的系统发育关系,我们首先构建了高质量的天目铁木基因组作为参考序列,再在居群水平的DNA条形码物种鉴定和系统发育研究基础上,挑选了鹅耳枥属的33个种(与涵盖了66%的物种)和铁木属全部8个种共170个个体,代表了每支系的多数物种,进行全基因组重测序分析。我们使用了两种分析方法:联合分析法和基于溯祖理论的系统发育分析。在联合分析法中,我们选用了9种数据集进行建树,包括全基因组SNP集合、叶绿体基因组、编码区、密码子前两位、密码子第三位、四重简并位点、内含子区、基因间区和重复序列。在基于溯祖理论的建树中,我们使用了两种数据集(单拷贝基因编码区和内含子区)和两种软件(ASTRAL和MP-EST)。结果表明鹅耳枥属和铁木属可分成稳定的4大支系,和前面DNA条形码系统发育分析与苞片形态结果一致;每个物种的个体基本聚类在一起组成一个小单系,但其中O. chisosensis内嵌于O. knowltonii,大庸鹅耳枥内嵌于多脉鹅耳枥,峨眉鹅耳枥、软毛鹅耳枥和岩生鹅耳枥相互混杂聚在一起,小叶鹅耳枥、鹅耳枥和川陕鹅耳枥互相混杂在聚一起。每个支系内的物种组成是稳定的,但是支系内部物种的系统发育关系有冲突在不同的数据集和不同的分析方法存在差异。3) 为了解析不同数据集或分析方法构建系统发育关系导致的冲突,我们对有冲突的物种或支系进行了基因流检测以及遗传结构分析。结果表明,相互混杂的物种间具有较强的基因流,存在系统发育关系冲突的物种大多和其相邻的支系具有一定的基因流。因此,杂交渐渗应该是造成不同数据集或分析方法所导致的两个属内物种间系统发育关系存在冲突的主要原因之一。

4) 通过祖先分布区域模拟、分歧时间评估和群体历史模拟,我们推测鹅耳枥属和铁木属的祖先分布在亚洲,并在距今约20个百万年前 (Mya) 开始分化成了两个属。铁木属内物种之间的分化时间比较长,大部分在8 Mya以上,为中新世的残存物种;而鹅耳枥属内大部分物种起源的时间在5 Mya以内,为新近分化形成的年青物种。我们同样观测到所有的物种对于第四纪的气候具有相似的响应,都在在2~3 Mya达到群体大小的峰值;这时期正处于上新世 (Pliocene epoch, 5.3~2.5 Mya),气候开始变干和变冷,温带植被替换了热带植被,这些温带树种占领了更多的分布区域,有效群体发生了扩张。由于鹅耳枥属物种寒冷和干燥气候的适应能力比铁木属要强,前者能在气候变冷、变干的过程中的分化出很多个种,而后者可能因适应能力差而发生一定的灭绝事件,从而使其物种数量相对较少。

Other Abstract

Carpinus Linnaeus and Ostrya Scopoli are two sister genera in the family Betulaceae and trees of two genera comprise the important forest components in the Northern Hemisphere. Two genera include around 58 species with main distributions in Asia. In the previous researches, phylogenetic studies of the two genera are mainly based on few individuals of each species, few species and several chloroplast fragments and/or ITS fragments with the limited information and usually conflicting relationships. The evolutionary relationship of the species within two sister genera are not accurately undstood by using traditional method. In recent years, as the development of the next-generation sequencing technologies, phylogenomics has been prospered, which provides a powerful way to study the complicated phylogenetic relationships. Based on a large number of samples collected from China and abroad, we carried out the phylognenomic study of Carpinus and Ostrya for the first time. We expected to interpret the phylogenetic relationships between and within two genera in three levels: morphology, DNA barcoding and genomics at the population levle. Gene flows between these species were also examined to resolve the phylogenetic conflicts. The results were summarized as follows:

1) A total of 1,330 trees were sampled from 243 populations 44 species of two genera (Carpinus: 36, Ostrya: 8) for DNA barcoding at the population level. Phylogenetic results based on the DNA barcoding data (trnL-F and ITS) indicated that 44 species could be divided into four clusters, largely consistent with the traditional morphological classification. Cluster A includes all eight Ostrya species with the nutlets completely covered by bracts in the infructescence. Cluster B comprises sect. Distegocarpus of the genus Carpinus with the slightly exposed nutlets in the infructescence. Cluster C and Cluster D include species of sect. Carpinus, in which nutlets are totally exposed. Species within Cluster C contain an obvious lobes at the base of inner bracts, different from those in the Cluster D. Howerer, relatinships between four clauses are not well solved.2) To reconstruct a more convincing phylogenetic tree for these species of two genera, a high-quality O. rehderiana genome as the reference for the following whole genome sequencing analysis was assembled firstly. Based on phylogenetic results of DNA barcoding data at the population level, a total of 170 individuals from 33 species, representing most species within each of above four major clusters were sequenced. All different datasets were generated based on the reads mapping file. Two methods were used to reconstruct the phylogenetic trees: the joint analysis and the coalescent-based methods. Nine datasets were used in the joint analysis, including the whole genome SNP set, the whole chloroplast genome, the coding region, the first two codons, the third codon, the four degenerate sites, the intron regions, the intergenic regions and the repeat sequences. Two datasets (single copy gene coding regions and intron regions) and two softwares (ASTRAL and MP-EST) were used to establish phylogenetic trees. Four stable clusters (Cluster A, (Cluster C, Cluster C)) were recovered from all the constructed trees, which are consistent with phylogenetic analyses of two barcoding DNAs and morphological traits. The multiple individuals from each species could be identified as the monophyletic for most species, while those from four groups of species could not be discerned as the species-monophyletic. O. chisosensis nested within O. knowltonii and C. dayongina within C. polyneura.  Individuals of C. mollicoma, C. omeiensis and C. rupestris were mixed together a group without the clear divisions. Similarly, the individuals from C. stipulata, C.turczaninowii and C. fargesiana could not comprise the separate lineages.3) A strong gene flow was detected between major clusters and some species, especially those with the conflicting phylogenetic relationships through multiple methods to detect the hybridization/introgression such as the examinations of genetic structure and gene flow. Multiple lines of evidence suggested that hybridization/introgression contributed mainly to the phylogenetic conflicts found for species within these two genera.4) In the combination of ancestral distribution simulations, divergent time assessments, and demograpghic history simulations, we found that the ancestor of the two genera was distributed in Asia and differentiated approximately 20 million years ago (Mya). Most of the species in Ostrya were divergenced before 8 Mya, while most of the Carpinus species formed after 5 Mya, which suggested most members in the former genus are relic species in the Miocene and most in Carpinus are ‘young’ species. In addition, we also found the consistent population peak for all species in two genera during 2~3Mya. Therefore, the temperate vegetation replaced tropical vegetation in the Pliocene period (5.3-2.5 Mya) and some species have the alternative chances to occupy widespread areas in this age. The Ostrya species prefer to the marmer and wetter climates than the Carpinus species. The climatic changes in this stage probably promoted the origin of numerous species in the Carpinus and probably leaded to the mass extinction in Ostrya.

URL查看原文
Language中文
Document Type学位论文
Identifierhttp://ir.lzu.edu.cn/handle/262010/221504
Collection生命科学学院
生态学创新研究院
Recommended Citation
GB/T 7714
杨勇志. 鹅耳枥属和铁木属系统发育基因组学研究[D]. 兰州. 兰州大学,2018.
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