灰胸薮鹛（Liocichla omeiensis）是我国特有的一种森林鸟类，隶属于雀形目（Passeriformes）噪鹛科（Leiothrichidae）薮鹛属（Liocichla），仅分布于我国西南地区的四川和云南的局部地区。由于栖息地特化、种间竞争剧烈加上人类活动的干扰，导致灰胸薮鹛的栖息地持续破碎化、野生种群繁殖成功率较低、种群数量不断下降，因此被IUCN受胁物种红色名录列为全球“易危”物种。尽管对该物种的繁殖生态和栖息地选择等已经开展了一些研究，但迄今尚无有关其遗传多样性、种群遗传结构和有效种群历史动态方面的报导。为此，本论文利用微卫星DNA、线粒体DNA和单核苷酸多态性位点三种分子标记，并借助高通量基因组测序技术，对灰胸薮鹛的遗传多样性、种群遗传结构以及种群历史动态等开展了研究，以便为今后科学有效地对灰胸薮鹛开展保护和管理提供依据。本论文获得的主要结果如下： 1. 灰胸薮鹛的遗传多样性 本研究通过简化基因组测序的方法，成功开发了24个针对灰胸薮鹛的微卫星DNA位点，利用这些微卫星位点对64只个体进行了遗传多样性的检测。结果发现，灰胸薮鹛等位基因数目的平均值为6.25；观察杂合度的平均值是0.657；期望杂合度的平均值为0.706，多态信息含量的平均值为0.657。经过Bonferroni校正，四个微卫星DNA座位（LO299、LO313、LO514和LO55）偏离哈迪—温伯格平衡。选用细胞色素b（Cyt b）和NADH脱氢酶亚单位2（ND2）这两个线粒体DNA分子标记，基于64只灰胸薮鹛野生个体的Cyt b+ND2的联合序列，共检测到52个变异位点（segregating sites），定义了24个单倍型（haplotype number），单倍型多样性（haplotype diversity, Hd）是0.922。基于微卫星DNA和线粒体DNA的研究结果，并与其他物种的有关数据进行比较，显示灰胸薮鹛野生种群的遗传多样性处于一个中等偏上的水平。 2. 灰胸薮鹛的种群遗传结构 通过对微卫星DNA的数据分析发现，灰胸薮鹛种群内的遗传距离为0.019；而经过贝叶斯聚类分析、主坐标分析及个体与种群间系统发育关系的构建，结果表明不同地理种群之间不存在分化的遗传背景。通过线粒体DNA数据计算的遗传距离为0.048，由63只个体构建的中央联接网状图和系统发育树的结果一致，均显示灰胸薮鹛种群可能只有一个母系起源，并未发生遗传分化。应用微卫星DNA和线粒体DNA的数据对6个地理种群进行Mantel Test分析，结果显示其种群间并不符合IBD（Isolation by Distance）模型，说明在灰胸薮鹛的种群内并不存在明显的种群遗传结构。 3. 灰胸薮鹛的种群历史动态 本研究采用微卫星DNA位点、线粒体DNA位点联合单核苷酸多态性位点的方法，构建了灰胸薮鹛从远期到近期的较为完整的种群历史动态。首先应用单核苷酸多态性位点构建的PSMC模型结果显示，灰胸薮鹛种群在约200万年前开始了扩张，约30万年前开始了下降，这次下降持续到大约6万年前，而后又出现了一个较小的种群上升，SNP数据估算的历史上有效种群大小约为22万只。另外，线粒体DNA分子标记的中性检验结果显示，其Tajima’s D和Fu’s Fs呈现负值，表明灰胸薮鹛种群可能经历过扩张。贝叶斯天际线模型结果显示，在约7万年以来灰胸薮鹛的种群经历了一次持续的扩张，直到近期才又发生了一次种群衰退。最后，应用微卫星DNA数据对灰胸薮鹛进行了种群瓶颈检测，结果显示其种群在700-1350年之间可能并未经历过瓶颈；而MSVAR模型模拟的结果显示，大约130年前灰胸薮鹛种群经历了一次严重的种群下降；经过计算获得其现阶段的有效种群数量大约是339只个体。综合来看，灰胸薮鹛种群在远期与气候波动存在一定的一致性，近期的瓶颈可能与人类活动产生的影响关系更为密切。 以上结果显示，在未来的保护工作中，可以把灰胸薮鹛作为一个保护管理单元。根据其有效种群数量及其栖息地现状，我们建议应尽快采取有效保护措施，尤为重要的是应降低人类活动干扰对其野生种群的影响，以期灰胸薮鹛的种群能够健康持续地存活。

Liocichla omeiensis is a passerine bird of the Liocichla genus, Leiothrichidae family, which only distributed locally in Sichuan, Yunnan in southwestern China. Recently, due to the specialization of habitat, the intense competition between species and the disturbance from human activities, the habitat of Liocichla omeiensis have been fragmented, the breeding success of wild breeding populations drops down, which result in the population keeps decreasing. Therefore, this species had been classified as “vulnerable” in the IUCN Red List. Although some research had focused on the breeding ecology and habitat selection of this species, no reports on its genetic diversity, population genetic structure and historical dynamics of effective populations. In order to protect this endemic species, this study aims at evaluating the genetic diversity, analyzing population structure and reconstructing population demographic of Liocichla omeiensis by microsatellite, mitochondrial markers and single nucleotide polymorphisms. This study provided a powerful theoretical basis for the scientific protection and management of this bird. The main results are shown below: 1. The evaluation of genetic diversity levels In this study, we applied restriction site-associated DNA sequencing (RAD-Seq) for identification of 24 novel microsatellite markers of the Liocichla omeiensis. The average number of alleles in 64 individuals was 6.25; mean value of observed heterozygosity and expected heterozygosity was 0.657 and 0.706 respectively; and mean value of the polymorphic information content was 0.657. After Bonferroni correction, LO299, LO313, LO514 and LO55 deviated from Hardy Weinberg equilibrium. Besides, there were two mitochondrial markers developed, which were cytochrome b and NADH dehydrogenase subunit 2. Based on the combined sequence of Cytb+ND2 of 64 individuals, 52 segregating sites were detected, defining 24 haplotype numbers, with haplotype diversity of 0.922. Based on the comparison with other birds, it showed that both microsatellite data and mitochondrial data presented the genetic diversity of Liocichla omeiensis was little higher than the medium level. 2. Population structure analysis Based on the microsatellite data, the genetic distance of whole Liocichla omeiensis population was 0.019. After Bayesian cluster analysis, principal coordinate analysis and phylogenetic construction, it was indicated that samples from different populations did not show differentiation on genetic background. While the calculation of mitochondrial data showed the genetic distance of whole population was 0.048. Meanwhile, the median joining network and the phylogenetic tree of 63 individuals were consistent, indicating that the whole population might originated from one maternal group, without differentiation. The Mantel Test results of six sampled populations indicated that the populations does not conform to the Isolation by Distance model. In general, there was no obvious population genetic structure in Liocichla omeiensis. 3. Historical population demographic reconstruction In this study, microsatellite loci, mitochondrial loci and single nucleotide polymorphism loci were used to reconstruct a relatively complete population history of Liocichla omeiensis from short term to long term. First, the PSMC model using single nucleotide polymorphism(SNP) sites showed that the Liocichla omeiensis population had expanded about 2 million years ago, and began to decline 200,000 years ago, and lasted till 60,000 years ago, and then there was a slight population increase. The historical effective population size estimated by SNP data was about 220,000. In addition, the neutrality test of mitochondrial molecular markers indicated that the Liocichla omeiensis population might have experienced expansion, as Tajima's D and Fu's Fs showed negative value. The Bayesian skyline plot results show that the population of Liocichla omeiensis experienced a sustained expansion within about 70,000 years until recent. Finally, microsatellite data were used for the population bottleneck detection, and the results showed that the Liocichla omeiensis population might have not experienced bottlenecks in recent 700 to 1350 years. While the results of the MSVAR model showed there was a severe bottleneck of Liocichla omeiensis about 100 years ago, which resulted in the effective population at current stage was about 340 individuals. In summary, the demographic of Liocichla omeiensis has a certain consistency with climate fluctuations in the long-term, while the recent bottleneck closely related to the impact of human activities. Our results demonstrate that, for the protection of Liocichla omeiensis, we may consider the whole population as one protection unit, and the current tiny effective population of the Liocichla omeiensis and its habitat status requires that we should take action as soon as possible to protect it. Reducing the impact of human activities is the most important to guarantee the sustained survival of Liocichla omeiensis populations.