海南山鹧鸪（Arborophila ardens）是我国海南岛的特有鸟类和国家I级重点保护动物，已被列入世界濒危鸟类红皮书。近年来，栖息地破坏和人类活动的干扰造成其种群数量不断下降。本研究以线粒体DNA的细胞色素b和控制区序列作为分子标记，对海南山鹧鸪的种群遗传多样性状况做出了评价。海南孔雀雉（Polyplectron katsumatae）也是我国海南岛的特有鸟类，野外数量已十分稀少。然而，它是否为一个独立的物种尚存在争议。本文通过线粒体DNA细胞色素b序列、细胞核卵类粘蛋白基因内含子G序列以及体长、翅长等宏观形状对海南孔雀雉的分类地位进行了分析，并运用线粒体控制区序列检验了其遗传多样性水平。最后，本文通过构建鸡形目雉科的系统进化树，探讨了山鹧鸪属和孔雀雉属系统进化地位。主要研究结果如下：1 海南山鹧鸪的遗传多样性分析在47条线粒体控制区序列（443bp）中，发现多态位点40个、单倍型14个，单倍型多样性指数（h）和核苷酸多样性指数（π）分别为0.786和0.01828；在43条线粒体细胞色素b序列（702bp）中，共发现多态位点37个，单倍型11个，h值和π值分别为0.511和0.01357。显示出了较高的遗传多样性。两个取样种群之间控制区序列共享单倍型为3个，细胞色素b序列共享单倍型为4个。单倍型系统进化分支结构和单倍型网络分布图均没有体现出两种群的分化。核苷酸位点差异分布和Tajima’ D检验显示，历史上海南山鹧鸪的种群结构稳定，没有经历过种群快速扩张。2 海南孔雀雉的分类地位和遗传多样性 海南孔雀雉9条线粒体细胞色素b序列（1143bp）中发现多态位点13个，细胞核卵类粘蛋白基因内含子G序列（446bp）中发现多态位点3个。与灰孔雀雉（Polyplectron bicalcaratum）6条序列一起进行比对后发现细胞色素b多态位点54个，卵类粘蛋白基因内含子G多态位点53个，且有插入缺失突变。系统进化树分析表明海南孔雀雉与灰孔雀雉为独立的进化分支，它们之间的遗传距离达到0.028，应当认为是两个独立的种。利用分子钟推算它们的分化时间大约为1.4±0.3百万年前。另外，现有海南孔雀雉样品的体长、翅长等也明显小于灰孔雀雉，但尚需进一步取样进行统计分析。海南孔雀雉遗传多样性水平较低，单倍型多样性指数（h）和核苷酸多样性指数（π）分别为0.714和0.00395。3 山鹧鸪属和孔雀雉属系统进化地位 在所有构建的系统进化树中，山鹧鸪属都形成了一个独立于雉类和鹑类的分支，并且在贝叶斯树中以很高的支持率出现在了雉类和鹑类共同的基部，证明山鹧鸪属是雉科鸟类中一个较原始的类群，推算其分化时间大约在54.9±6.2百万年前。在由4个线粒体基因和7个细胞核基因拼接序列（8816bp）所构建的贝叶斯系统树中，孔雀雉属显示出与鹑类聚为一支的趋势，说明孔雀雉是比雉类原始的类群。但是系统树在孔雀雉属周围的支持率有限，推测孔雀雉属可能是在雉科鸟类的快速辐射进化事件（rapid diversification）中所形成的类群。

The Hainan Hill Partridge (Arborophila ardens) is endemic to the Hainan Island, China and regarded as ‘vulnerable’ in the IUCN Red List of Threatened species. Recent years, its population size continues to decline because of the habitat destruction and the human industrial activities. In this study, we used the mitochondrial cytochrome b sequence and the control region sequence as molecular markers to evaluate the genetic diversity of the Hainan Hill partridge. The Hainan Peacock Pheasant (Polyplectron katsumatae) is another endemic species to the Hainan Island and its wild population size has became considerably small. However, whether the Hainan Peacock Pheasant is a full species or not is still in the dispute. By using the mitochondrial cytochrome b sequence, the intron G of the nuclear ovomucoid gene and some morphological characters such as body-length, wing-length etc., we re-evaluated the species status of the Hainan Peacock Pheasant. By using the mitochondrial control region sequence, we evalued its genetic diversity. Finally, by constructing the phylogenetic trees of Phasianidae, we explored the phylogenetic positions of the Peacock Pheasants (genus Polyplectron) and the Hill Partridges (genus Arborophila). Key findings are as follows: 1. The genetic diversity of the Hainan Hill Partridge By analyzing 47 mitochondrial control region sequences (443 bp), we found 40 variable sites, 14 haplotypes. The haplotype diversity (h) and nucleotide diversity (π) were 0.786 and 0.01828. By analyzing 43 mitochondrial cytochrome b sequences (702 bp), we found 37 variable sites, 11 haplotypes. The haplotype diversity (h) and nucleotide diversity (π) were 0.511 and 0.01357. The two sampling populations shared three cytochrome b haplotypes and four control region haplotypes. Haplotype phylogenetic relationships and haplotype network distribution indicated no genetic differentiation between these two populations. Mismatch distribution test and Tajima 'D test revealed that the historical population structure of the Hainan Hill Partridge was stable, and had not experienced a rapid population expansion. 2. The species status of the Hainan Peacock Pheasant We found 13 variable sites among the cytochrome b sequences (1143 bp) of Hainan Peacock Pheasant and 3 variable sites among the intron G of the nuclear ovomucoid gene sequences (446 bp). By analyzing the data of the Gray Peacock Pheasant (Polyplectron bicalcaratum) sequences and the Hainan Peacock Pheasant sequences, we found there were 54 variable sites to cytochrome b gene and 53 variable sites to the intron G of the nuclear ovomucoid gene. Phylogenetic trees showed that the Hainan peacock pheasants and grey peacock pheasant were in independent branch of evolution, the genetic distance between them reached 0.028, indicating that they should be regarded as two separate species. By using molecular clock, we infered the two peacock pheasant became divergent about 1.4 ± 0.3 million years ago. In addition, morphological data showed that the Hainan Peacock Pheasant were smaller than the grey peacock pheasants. The haplotype diversity (h) and nucleotide diversity (π) of the Hainan Peacock Pheasant were 0.714 and 0.00395.3. The phylogenetic status of the Peacock Pheasants and the Hill Partridges In all constructed phylogenetic trees, the Hill Partridges formed as an evolutionary branch independent from the pheasants and the partridges. The Bayesian trees showed that the Hill Partridges was basal to the pheasants and partridges with a high support, indicating that the Hill partridges is a primitive group. We inferred its divergence time was about 54.9 ± 6.2 million years ago. In the Bayesian phylogenetic tree which constructed by combined data of the mitochondrial DNA (4 genes) and the nucleus (7 genes), there showed the Peacock pheasants tend to be close to the partridges, this at least meant that the Peacock pheasants was more primitive than the pheasants. However, the support values around the Peacock pheasants were limited, indicating that the Peacock pheasants were very possible to formed in the rapid diversification of the Phasianidae.