雉科鸟类（Phasianidae）是我国富有特色的鸟类类群之一，种类多，分布广，特有化程度高，与人类关系密切。因为多数种类分布在森林之中，其数量的高低可反映森林生态系统的健康状况。由于自然环境的变化和人类活动的影响，该类群中的许多种类出现分布区缩小，种群数量下降的趋势，其生存受到了威胁，一些种类甚至濒临灭绝。加强我国特有濒危雉科鸟类的研究，从宏观和微观两个方面对种群现状进行评估，可为濒危物种的保护和恢复重建奠定基础。本论文采用分子生物学的技术方法，从微观角度对我国四种特有受胁雉科鸟类（海南孔雀雉Polyplectron katsumatae、海南山鹧鸪Arborophila ardens、白冠长尾雉Syrmaticus reevesii和褐马鸡Crossoptilon mantchuricum）的保护遗传学进行了较为深入的研究，以期为这些珍稀濒危物种的保护提供科学依据。本论文的研究内容和所取得的主要成果如下：1. 生活在我国海南岛的雉科鸟类基本上都拥有一些近缘物种分布在我国的西南或华南地区、中南半岛或东南亚的其他岛屿上。迄今，利用分子系统发育的方法探讨海南岛雉科鸟类起源和进化的工作尚属空白。本研究利用线粒体多基因和核基因相结合的分析方法，探讨了海南岛上现存的两种雉科鸟类海南孔雀雉和海南山鹧鸪的分子系统发育及系统地理学模式。线粒体多基因序列与部分核基因的序列分析结果如下：（1）多基因综合分析表明：海南孔雀雉在分子水平上被证明是具有独立物种地位的分类单元，并得到了形态学证据的支持；结合孔雀雉属其他鸟类相应序列，发现改属的起源进化模式与以前研究的结论有所不同，即孔雀雉属的起源祖先更可能是在东南亚的南部岛屿上起源，进而分布扩展到中南半岛，最后分别到达我国海南岛和西南部分地区，适应不同的生态条件而产生物种分化。与同属其他物种相比，海南孔雀雉不仅不是我国大陆的西南分布的灰孔雀雉的亚种，甚至和灰孔雀雉的亲缘关系也不是最近，而是和中南半岛的孔雀雉更为接近。种群历史动态研究显示，该物种在全新世中期曾经历过种群扩张事件，推测是当时环境的急剧暖化促成的结果；（2）分子系统发育研究表明，与孔雀雉属相比，海南山鹧鸪所在属的起源进化可能属于更古老的进化事件，进化历程既有不同，又有相似之处。和海南孔雀雉结论相似的是，与海南山鹧鸪亲缘最近的物种也并非来自我国大陆的华南或西南地区，而是来自中南半岛。种群历史动态分析显示，海南山鹧鸪也经历过全新世中期的扩张事件。综合海南岛两种雉科鸟类的研究表明，除了存在着“海南-华南-西南”生物通道之外，历史上还可能由于第四纪冰期古气候的急剧变冷，导致隔离岛屿之间的海水大幅下降，存在直接连接我国海南岛与中南半岛的生物廊道，可以促成生物拓殖。本研究认为海南的动物类群，特别是具有古老进化历史的物种，可以更多地考虑东南亚诸岛物种与其之间的进化关系。2. 青藏高原隆起及邻近地区阶段性的持续事件，伴随着的第四纪气候变化，在历史上曾对我国的气候、环境和大多数生物类群产出了巨大影响。本论文选取曾广泛分布于我国中部大部分地区的特有物种白冠长尾雉，利用线粒体高变序列片段和多态性微卫星DNA分子标记，利用多种统计软件，对该物种的种群历史动态和种群关键参数进行了研究。结果表明：（1）白冠长尾雉在与该属其他物种产生分化之后，其种群内部也在一段相当长的历史时期一直处于分化状态，其中西南地理种群和其他中、东部地理种群在第四纪早期就有明显分化；在第四纪大部分时期，该物种都保持着较大的、相对稳定的种群数量；对地理种群基因交流的检验显示，白冠长尾雉中东部地理种群在历史上的基因交流较频繁；近期的基因交流检测显示，白冠长尾雉现生中部种群和东种种群间基因交流大幅减少，因此建议确立不同的保护单元，交流廊道值得关注；（2）对现存地理种群进行的种群动态分析显示，白冠长尾雉的地理种群曾经历过大幅衰减事件，时间显示为人类开始频繁活动时段。由于白冠长尾雉的现今种群数量较少且明显片段化，因此保护工作显得十分紧迫。3. 一般认为，我国北方地区分布的物种在第四纪冰期时种群曾出现过严重衰减, 这种现象在遗传多样性方面应该有所反映。本论文利用线粒体多基因（Mitochondria Control Region (CR), Cytochrome B (cyt b) gene, NADH dehydrogenase 2 gene (ND2), Cytochrome oxidase I (COI) gene）序列和大量取样的方法，对现今分布区处于我国华北地区的褐马鸡种群进行了分子系统地理学研究。结果发现：（1）褐马鸡遗传现状十分堪忧（多个基因没有多态性，仅 CR检测到3个单倍型，π= 0.0003），遗传分化较小(Fst=0.001)，推测在第四纪冰期影响之外，历史人类活动造成的负面影响也是该物种主要濒危原因之一。此外，对该物种主要组织相容性复合体（MHC）BLB2基因的深入研究表明，由于各地理种群间存在不同MHC BLB2单倍型及单倍型组，因此认为在将该物种的所有地理种群作为一个保护单元整体考虑的同时，应该给于不同地理种群更多关注；（2）进一步对其功能性抗病基因MHC BLB2的多态性和自然选择规律进行研究，发现褐马鸡该基因存在双拷贝情况，单倍型较多，但分为6个单倍型组；检测不到重组事件；检测到了正选择位点，推测正选择使得基因存在多样性且可能在该物种应对环境变异的适应性生存中起重要作用；在与鸡形目其他鸟类的MHC BLB2做系统发育比较时，发现褐马鸡该基因的6个单倍型组没有单独聚在一个支，有个别支与其他物种的序列聚类一起，显示褐马鸡MHC BLB2基因具有古老进化历史，存在跨种进化的现象，证明多样性由平衡选择来维持。

To conserve the Galliformes resourse in China, conservation gentics works should be taken in advance. My dissertation focused on using molecular techniques to improve our understanding and conservation management of four endangered pheasants Polyplectron katsumatae, Arborophila ardens, Syrmaticus reevesii and Crossoptilon mantchuricum. In my dissertation, I used both the neutral and the adaptive variation in natural population to address conservation genetics of four endangered pheasants native to China. The results are described as follows:1. Gaining a better understanding of the systematic status of threatened taxa will ensure them receive public concerns and conservation efforts, and therefore may avoid them from the blink of extinction. In birds, the majority of extinct taxa have been island endemics. Consequently, the systematic status of threatened taxa on islands deserves more attentions from conservation biologists. I provide the molecular evidence that Hainan peacock pheasant should be a full species by mtDNA CR, cyt b，CO1 and nuclear segment OVOG. I suggest that both geographical isolation and suitable habitat discontinuity during glacial periods would have been important factors in shaping genetic distinctness and created opportunities for deeper population isolation between these two peacock pheasants.In addition, I provide the molecular phylogenetic relationship among Arborophila ardens which is endemic to hainan island and species which are located near or around it in genus Arborophila. Arborophila ardens is belonged to a genus which has a widespread distribution including most of areas in southern of China and southeast asia island. The pattern could be interpreted by the fluctuation of sea level and the booming between these areas which recognized as barries for speciation during late-Pliocene and Pleistocene.2. The climatic oscillations of Pleistocene period have traditionally been considered to have had profound effects on the evolutionary process of most extant species. I used partly highly variable mtDNA control region sequences and 11 high polymorphism microsatellite sites to explore the phylogeographic pattern and demographic history of Syrmaticus reevesii. The results indicated: the genetic differentiation between the southwest populations and the other populations of Syrmaticus reevesii was large and the timing of differentiation was about 1-2 million years ago. The large historical demography of this speices indicated these populations once sailed through the Pleistocene ice ages. But the contemporary effective populaiton size (Ne) was just 1% of historical Ne indicated the populations experienced population collapse and the time was classified no more than 1000 years before present. Combined with the facts that current gene flow detected among popualtions was limited, the different management units should be recognized for conservation.3. It is generally accepted that the Pleistocene glacial periods have played important roles in shaping the phylogeographic patterns of species distributed in north of China. The phylogeographic pattern of Crossoptilon mantchuricum using multiple genes was firstly explored in this dissertation. The extremely low mtDNA variation and lacking of genetic differentiation indicated that current populations should be conserved as one management unit and thereby promoted the further research of adaptive variation of MHC of this pheasant. No more than four alleles in each individuals were detected at the BLB2 gene, suggesting duplication was identified which similar to that of the chicken. Six major haplotype groups of this gene were detected using network analysis. Phylogenetic reconstruction of the gene haplotypes with those from other species showed that the six haplotype groups had not clustered into one clade together,but shared with other species. Some haplotype groups were shared by closely related species in the same family, suggesting trans-species pattern while some other haplotype groups were shared by more distantly related species in different family, explaining by the convergent evolution as a results of common adaptive to similar environmental pressures. Balancing selection could contribute to the generation and maintenance of genetic polymorphism of the gene as positive selection sites were found. Results from this study provided the evidence of evolutionary potential of the pheasant.