雪雀类鸟类的比较、进化及谱系线粒体基因组学研究

发布时间：2018-07-09 11:26

本文选题：雪雀属 + 地雀属　；参考：《陕西师范大学》2016年博士论文

【摘要】：雪雀属(Montifingilla)和地雀属(Pyrgilauda)鸟类,隶属于鸟纲(Aves)、雀形目(Passeriformes)、雀科(Passeridae),古北界鸟类。目前世界已报道8种,我国分布有7种,另外阿富汗分布1种。其中5种为青藏高原特有种,主要分布于青藏高原及其邻近的地区。对于雪雀类鸟类,学术界有3种观点:一种观点认为8种雪雀类鸟类以一个独立的属存在;另一种观点是将该属划分为两个属,即雪雀属和地雀属;第3种观点将其分为雪雀属、地雀属和高原雀属(Onychostruthus)。线粒体基因组被广泛地应用于分类与进化研究中,在解决亚科、属以及种间的系统发生关系等方面有良好的分辨力。同时,动物线粒体基因组编码与能量代谢相关的关键酶,被广泛应用于不同类群动物高原适应性研究中。因此利用线粒体基因组研究雪雀属和地雀属适应高原环境的特征,了解其起源、演化与系统发育关系,对了解青藏高原鸟类区系的形成与演化具有重要的意义。本文基于长距PCR扩增及保守引物步移法测定了雪雀属和地雀属6种鸟类的线粒体全基因组序列,并对序列进行了注释和分析。结合GenBank中公布的46种雀形目鸟类的线粒体全基因组序列,分析雀形目鸟类线粒体基因组及13个蛋白质编码基因的特征。并以不同的基因联合数据集,利用不同方法构建雀形目鸟类的系统发生树,分析其进化压力和分歧时间,获得以下主要研究结果:1.白斑翅雪雀(Montifringilla nivalis)全线粒体基因长度16923bp;褐翅雪雀(Montifringila adamsi)全线粒体基因长度 16912bp;棕背雪雀(Pyrgilaudda blanfordi)全线粒体基因长度16913bp;棕颈雪雀(Pyrgilauda ruficollis)全线粒体基因长度16909bp;白腰雪雀(Onychostruthus taczanowskii)全线粒体基因长度16917bp;黑喉雪雀(Pyrgilauda davidiana)全线粒体基因长度16912bp。6种雪雀均包括37个编码基因和一个非编码的控制区(CR)。编码基因为13个蛋白质编码基因、22个转运RNA基因(tRNAs)以及2个核糖体RNA基因(rRNAs)。其中由重链(H链)编码的有28个基因,由轻链(L链)编码的有蛋白编码基因ND6和8个 tRN A 基因(tRNAAsn、tRNAGln、tRNAAla、tRNACys、tRNASer(UCN)、tRNATry、tRNAGlu、tRNAThr)。线粒体全基因组(mtDNA)的排列顺序与雀形目鸟类其他物种的排列顺序相似,没有基因的缺失、插入以及倒位现象。2.6种雪雀类鸟类线粒体全基因组碱基百分含量为CATG,PCGs、rRNAs、tRNAs及控制区碱基含量A+T大于G+C。其中tRNA重链(H链)基因A+T含量最高,蛋白编码基因密码子第一位点A+T含量最低。各基因碱基A+T含量中雪雀属低于地雀属,尤其是在ATP6和ATP8基因中差距达到10%。AT偏斜(A-T/A+T)除密码子第二位、由轻链编码的tRNA外,都为A偏斜;GC偏斜(G-C/G+C)中由轻链(L)编码的tRNA偏向G,其余均偏向C。蛋白质编码基因COⅢAT偏斜雪雀属为T偏斜,地雀属为A偏斜,其余一致。两个属间蛋白质编码基因和控制区的核酸变化率(NVR)较高,在ATP8、ATP6、ND1、ND 基因中NVR值相对高,COⅠ、Cytb、COⅡ基因中NVR值较小。在AAVR值中,ATP8基因最高,第二为ND3基因;COⅠ、COⅢ、Cytb基因中AAVR值较小。3.预测了 6种雪雀类鸟类的线粒体基因组控制区,得到六种鸟类的控制区与已报道鸟类的一样,包含DomianⅠ、DomianⅡ、DdomianⅢ三个结构域(图5)。其中Domain Ⅰ包括A和B两个区,A区又包括ETAS 1和ETAS 2两个保守区,及中间由2-5个"T"隔断的poly(C)序列,相似与雪雁的"goosehairpin"保守框;B区中分布CSB 1-like序列。Domain Ⅱ为中央保守区,分布有Bird similarity-boxB、C-box、D-box、E-box、F-box四个保守序列区。Domain Ⅲ有翻译的双向启动子(LSP和HSP),没有发现与哺乳动物重链复制起始位点相似的poly(C)序列。4.研究结果表明线粒体基因组的A+T%含量和蛋白质编码区各基因的A+T%含量的差异,主要由蛋白质编码基因第3位点GC变化引起的;密码子第1、2位点面临的选择压力较大,而密码子第3位点所受的选择压力较小;密码子第2位受到的净化选择的压力远大于密码子第1、3位点;12个蛋白质编码基因密码子第3位的碱基G始终保持在比较低的水平(小于10%);在51种雀形目鸟类线粒体基因组12个蛋白质编码基因密码子第3位点碱基C的含量平均为40%以上,碱基T的含量随着C的升高而降低。5.雀形目46种鸟类的线粒体13个蛋白质编码基因和PCGs数据集分析dN/dS值都小于1,表明它们都处于与进化选择的正选择中,在进化过程中受到了自然选择的压力。但在所有研究鸟类中线粒体ATP8基因和ND6基因的dN/dS值相对其它基因都表现出较高的值,而COⅠ基因dN/dS至最低,这种现象在其他研究中也有发现。本文以海拔、食性、留候鸟和不同分布区域的划分,进行51种雀形目鸟类进化速率的分析,揭示鸟类经历了不同的选择压力和不同的进化速度,生活在高海拔地区的鸟类、候鸟、植食性鸟类和生活在非洲的鸟类积累了比其他类群鸟类更多的非同义替换。6.本文构建的系统树结果均支持雀形目两个亚目的划分,支持鸣禽亚目分为鸦小目和雀小目,支持雀小目中瀇总科、莺总科和雀总科的划分,结果与Sibley和Ahlqulst以及Howard和Moore观点一致。系统树支持将长尾山雀单列成科并且归入莺总科下的观点,并且长尾山雀和燕科亲缘关系较近。支持将雪雀属划分为两个单系性亚属的观点,即白斑翅雪雀和褐翅雪雀为雪雀亚属,棕颈雪雀、白腰雪雀、棕背雪雀、黑喉雪雀为地雀亚属。7.雀形目分歧和演化时间与地质事件相一致,揭示雀形目鸟类祖先在原始的同一古陆上进化传衍;在中生代的晚期,随着原始古陆的分裂漂移,原始鸟类也随之分裂解散,被带到各地;新生代,进一步分化,形成目前分布状况;雪雀作为青藏高原的特有物种,其分歧事件的发生、辐射演化和种形成过程与青藏高原的构造事件和气候的转型相一致。
[Abstract]:Montifingilla and Pyrgilauda, belonging to the bird class (Aves), the passerine (Passeriformes), the fafins (Passeridae) and the Palaearctic bird. Currently, 8 species are reported in the world. There are 7 species in our country and 1 species in Afghanistan. Among them, the special species of the Qinghai Tibet Plateau are mainly distributed in the Qinghai Tibet Plateau and its adjacent areas. There are 3 points of view in the academic circle: one view that 8 species of finch species exist in one independent genus; the other is to divide the genus to two genera, namely, the genus Finch and the genus finch; the third points are divided into the genus Finch, the genus Finch and Onychostruthus. The mitochondrial genome is widely used in classification and in the classification. In evolutionary studies, there is a good resolution in solving the relationship between subfamilies, genera and interspecific systems. At the same time, the key enzymes related to the coding of the mitochondrial genome and energy metabolism are widely used in the study of the adaptability of different groups of animals. Therefore, the use of the grain genome to study the high adaptation of the genus Finch and the genus Finch The characteristics of the original environment, understanding its origin, evolution and phylogenetic relationship, is of great significance for understanding the formation and evolution of the avian fauna of the Qinghai Tibet Plateau. Based on the long distance PCR amplification and conservative primer step method, the sequence of the mitochondrial whole gene group of 6 species of birds of the genus Finch and the genus finch were determined, and the sequences were annotated and analyzed. The mitochondrial genome sequence of 46 species of passerine birds published in GenBank, analyzed the characteristics of the mitochondrial genome and the 13 protein encoding genes of the passerine birds, and constructed the phylogenetic tree of the passerine birds by different combinations of genes. The whole mitochondrial gene length of 1. white winged finch (Montifringilla nivalis) is 16923bp; the whole mitochondrial gene length of Montifringila AdamsI (Montifringila AdamsI) is 16912bp; the whole mitochondrial gene length of the brown back snow finch (Pyrgilaudda blanfordi) is 16913bp; the length 16909bp of the whole mitochondrial gene of the brown cervix (Pyrgilauda ruficollis); white waist snow The whole mitochondrial gene length of the Onychostruthus taczanowskii is 16917bp, and the whole mitochondrial gene length of the Pyrgilauda davidiana of the black larynx (Pyrgilauda davidiana) consists of 37 encoding genes and one non coded control area (CR). The encoding gene is the 13 protein encoding gene, 22 transshipment RNA (tRNAs) and 2 ribosome RNA genes ( RRNAs. There are 28 genes encoded by the heavy chain (H chain), which are encoded by the light chain (L chain), the protein encoding gene ND6 and the 8 tRN A genes (tRNAAsn, tRNAGln, tRNAAla, tRNACys, tRNASer (UCN)). The sequence of the whole mitochondrial genome is similar to the order of other species of the passerine birds, and there is no gene. The total genomic DNA content of the mitochondrial genome of.2.6 species of finch species was CATG, PCGs, rRNAs, tRNAs and A+T greater than G+C., and the tRNA heavy chain (H chain) gene A+T content was the highest, and the first loci of the protein coding gene was the lowest. In ATP6 and ATP8 genes, especially in the ATP6 and ATP8 genes, the gap (A-T/A+T) is second bits except for the codon, and from the light chain encoded tRNA to A deviation; the GC skew (G-C/G+C) is biased toward G by the tRNA of the light chain (L), and the rest are biased toward the C. protein encoding gene, and the genus finch is a deviation, and the rest is the same. Two The nucleic acid change rate (NVR) of the Intergenera protein encoding gene and the control region is higher, and the NVR value is relatively high in the ATP8, ATP6, ND1, and ND genes. The NVR values of CO I, Cytb, and CO II genes are smaller. In AAVR, the ATP8 gene is the highest and the second is the gene. The control area of the six species is the same as that of the reported birds, including the three domains of Domian I, Domian II, and Ddomian III (Figure 5). Among them, the Domain I includes two regions of A and B, and the A zone includes two conservative regions of ETAS 1 and ETAS 2, and a poly (C) sequence separated by 2-5 "T", similar to the conservative box of snow goose. The distributed CSB 1-like sequence.Domain II is a central conservative region, and there are four conservative sequences of Bird similarity-boxB, C-box, D-box, E-box, and F-box (LSP and HSP), which have not been found to be similar to the starting sites of heavy chain replication in mammals. The difference in the A+T% content of each gene in the coding region of the quantity and protein is mainly caused by the change of the third locus GC of the protein encoding gene; the selection pressure of the codon 1,2 site is larger and the selection pressure of the codon third loci is smaller; the codon second positions are much more pressure than the codon 1,3 site; 12 eggs. The base G of the third bits of the white matter coded gene codon remains at a relatively low level (less than 10%), and the average content of the 12 protein coded gene codon third loci of the 51 passerine birds is more than 40%. The content of the base T decreases with the increase of C, which reduces the 13 protein of the mitochondria of the 46 birds of the.5. passerine. The dN/dS values of the qualitative coding gene and the PCGs dataset were both less than 1, indicating that they were all in the positive selection of the evolutionary selection and were under the pressure of natural selection during the evolutionary process. But the dN/dS value of the mitochondrial ATP8 gene and the ND6 gene in all the study birds showed a higher value compared to the other genes, while the CO I gene dN/dS was the lowest. This phenomenon is also found in other studies. In this paper, the evolution rate of 51 species of passerine birds was analyzed by the division of altitude, food, migratory birds and different distribution regions, which revealed that birds experienced different selection pressures and different evolutionary speeds, birds, migratory birds, phytophagous birds, and living in Africa at high altitudes. Birds have accumulated more unsynonymous substitutions than other groups of birds. The results of the system tree constructed in this paper all support the division of two suborders of the passerine, supporting the suborders of songbirds to be divided into ravine and Que Xiaomu, supporting the Taxus, warbler and Pasco, and the results are in accordance with the views of Sibley and Ahlqulst, as well as Howard and Moore. The system tree supports the view that the long tailed tits are classified into single family and under the view of warbler, and the relationship between the long tailed tits and the Yanke is close. It supports the view that the genus canary is divided into two monophyletic subgenera, that is, the white winged Finch and the brown finch are of the genus snow finch, the brown necking Finch, the white waist Finch, the brown back snow finch, the black larynx as the subgenus.7.. The differences and evolution time of the passerine are consistent with the geological events, revealing the evolution of the ancestor of the passerine birds in the original same ancient land; in the late Mesozoic era, with the split and drift of the original paleo land, the original birds also split and dissolve and were brought to various places; the new generation, with a step of differentiation, formed the current distribution situation; the snow finches as Qingzang. The occurrence of the divergent events, the evolution of radiation and the process of species formation are consistent with the tectonic events and climatic transformation of the Qinghai Tibet Plateau.
【学位授予单位】：陕西师范大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q953

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