本文選題：雪雀屬 + 地雀屬　； 參考：《陜西師范大學》2016年博士論文

【摘要】：雪雀屬(Montifingilla)和地雀屬(Pyrgilauda)鳥類,隸屬于鳥綱(Aves)、雀形目(Passeriformes)、雀科(Passeridae),古北界鳥類。目前世界已報道8種,我國分布有7種,另外阿富汗分布1種。其中5種為青藏高原特有種,主要分布于青藏高原及其鄰近的地區(qū)。對于雪雀類鳥類,學術界有3種觀點:一種觀點認為8種雪雀類鳥類以一個獨立的屬存在;另一種觀點是將該屬劃分為兩個屬,即雪雀屬和地雀屬;第3種觀點將其分為雪雀屬、地雀屬和高原雀屬(Onychostruthus)。線粒體基因組被廣泛地應用于分類與進化研究中,在解決亞科、屬以及種間的系統(tǒng)發(fā)生關系等方面有良好的分辨力。同時,動物線粒體基因組編碼與能量代謝相關的關鍵酶,被廣泛應用于不同類群動物高原適應性研究中。因此利用線粒體基因組研究雪雀屬和地雀屬適應高原環(huán)境的特征,了解其起源、演化與系統(tǒng)發(fā)育關系,對了解青藏高原鳥類區(qū)系的形成與演化具有重要的意義。本文基于長距PCR擴增及保守引物步移法測定了雪雀屬和地雀屬6種鳥類的線粒體全基因組序列,并對序列進行了注釋和分析。結合GenBank中公布的46種雀形目鳥類的線粒體全基因組序列,分析雀形目鳥類線粒體基因組及13個蛋白質編碼基因的特征。并以不同的基因聯(lián)合數(shù)據(jù)集,利用不同方法構建雀形目鳥類的系統(tǒng)發(fā)生樹,分析其進化壓力和分歧時間,獲得以下主要研究結果:1.白斑翅雪雀(Montifringilla nivalis)全線粒體基因長度16923bp;褐翅雪雀(Montifringila adamsi)全線粒體基因長度 16912bp;棕背雪雀(Pyrgilaudda blanfordi)全線粒體基因長度16913bp;棕頸雪雀(Pyrgilauda ruficollis)全線粒體基因長度16909bp;白腰雪雀(Onychostruthus taczanowskii)全線粒體基因長度16917bp;黑喉雪雀(Pyrgilauda davidiana)全線粒體基因長度16912bp。6種雪雀均包括37個編碼基因和一個非編碼的控制區(qū)(CR)。編碼基因為13個蛋白質編碼基因、22個轉運RNA基因(tRNAs)以及2個核糖體RNA基因(rRNAs)。其中由重鏈(H鏈)編碼的有28個基因,由輕鏈(L鏈)編碼的有蛋白編碼基因ND6和8個 tRN A 基因(tRNAAsn、tRNAGln、tRNAAla、tRNACys、tRNASer(UCN)、tRNATry、tRNAGlu、tRNAThr)。線粒體全基因組(mtDNA)的排列順序與雀形目鳥類其他物種的排列順序相似,沒有基因的缺失、插入以及倒位現(xiàn)象。2.6種雪雀類鳥類線粒體全基因組堿基百分含量為CATG,PCGs、rRNAs、tRNAs及控制區(qū)堿基含量A+T大于G+C。其中tRNA重鏈(H鏈)基因A+T含量最高,蛋白編碼基因密碼子第一位點A+T含量最低。各基因堿基A+T含量中雪雀屬低于地雀屬,尤其是在ATP6和ATP8基因中差距達到10%。AT偏斜(A-T/A+T)除密碼子第二位、由輕鏈編碼的tRNA外,都為A偏斜;GC偏斜(G-C/G+C)中由輕鏈(L)編碼的tRNA偏向G,其余均偏向C。蛋白質編碼基因COⅢAT偏斜雪雀屬為T偏斜,地雀屬為A偏斜,其余一致。兩個屬間蛋白質編碼基因和控制區(qū)的核酸變化率(NVR)較高,在ATP8、ATP6、ND1、ND 基因中NVR值相對高,COⅠ、Cytb、COⅡ基因中NVR值較小。在AAVR值中,ATP8基因最高,第二為ND3基因;COⅠ、COⅢ、Cytb基因中AAVR值較小。3.預測了 6種雪雀類鳥類的線粒體基因組控制區(qū),得到六種鳥類的控制區(qū)與已報道鳥類的一樣,包含DomianⅠ、DomianⅡ、DdomianⅢ三個結構域(圖5)。其中Domain Ⅰ包括A和B兩個區(qū),A區(qū)又包括ETAS 1和ETAS 2兩個保守區(qū),及中間由2-5個"T"隔斷的poly(C)序列,相似與雪雁的"goosehairpin"保守框;B區(qū)中分布CSB 1-like序列。Domain Ⅱ為中央保守區(qū),分布有Bird similarity-boxB、C-box、D-box、E-box、F-box四個保守序列區(qū)。Domain Ⅲ有翻譯的雙向啟動子(LSP和HSP),沒有發(fā)現(xiàn)與哺乳動物重鏈復制起始位點相似的poly(C)序列。4.研究結果表明線粒體基因組的A+T%含量和蛋白質編碼區(qū)各基因的A+T%含量的差異,主要由蛋白質編碼基因第3位點GC變化引起的;密碼子第1、2位點面臨的選擇壓力較大,而密碼子第3位點所受的選擇壓力較小;密碼子第2位受到的凈化選擇的壓力遠大于密碼子第1、3位點;12個蛋白質編碼基因密碼子第3位的堿基G始終保持在比較低的水平(小于10%);在51種雀形目鳥類線粒體基因組12個蛋白質編碼基因密碼子第3位點堿基C的含量平均為40%以上,堿基T的含量隨著C的升高而降低。5.雀形目46種鳥類的線粒體13個蛋白質編碼基因和PCGs數(shù)據(jù)集分析dN/dS值都小于1,表明它們都處于與進化選擇的正選擇中,在進化過程中受到了自然選擇的壓力。但在所有研究鳥類中線粒體ATP8基因和ND6基因的dN/dS值相對其它基因都表現(xiàn)出較高的值,而COⅠ基因dN/dS至最低,這種現(xiàn)象在其他研究中也有發(fā)現(xiàn)。本文以海拔、食性、留候鳥和不同分布區(qū)域的劃分,進行51種雀形目鳥類進化速率的分析,揭示鳥類經歷了不同的選擇壓力和不同的進化速度,生活在高海拔地區(qū)的鳥類、候鳥、植食性鳥類和生活在非洲的鳥類積累了比其他類群鳥類更多的非同義替換。6.本文構建的系統(tǒng)樹結果均支持雀形目兩個亞目的劃分,支持鳴禽亞目分為鴉小目和雀小目,支持雀小目中瀇總科、鶯總科和雀總科的劃分,結果與Sibley和Ahlqulst以及Howard和Moore觀點一致。系統(tǒng)樹支持將長尾山雀單列成科并且歸入鶯總科下的觀點,并且長尾山雀和燕科親緣關系較近。支持將雪雀屬劃分為兩個單系性亞屬的觀點,即白斑翅雪雀和褐翅雪雀為雪雀亞屬,棕頸雪雀、白腰雪雀、棕背雪雀、黑喉雪雀為地雀亞屬。7.雀形目分歧和演化時間與地質事件相一致,揭示雀形目鳥類祖先在原始的同一古陸上進化傳衍;在中生代的晚期,隨著原始古陸的分裂漂移,原始鳥類也隨之分裂解散,被帶到各地;新生代,進一步分化,形成目前分布狀況;雪雀作為青藏高原的特有物種,其分歧事件的發(fā)生、輻射演化和種形成過程與青藏高原的構造事件和氣候的轉型相一致。
[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.
【學位授予單位】：陜西師范大學
【學位級別】：博士
【學位授予年份】：2016
【分類號】：Q953

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