金线鲃属(Sinocyclocheilus) 隶属于鲤形目(Cypriniformes)鲤科(Cyprinidae)鲃亚科(Barbinae)，是中国的特有类群，仅分布于云南东部、贵州中南部和广西西北部的岩溶地貌发育地区。目前所知几乎属内所有物种都有洞穴生活的习性。一部分典型洞穴物种具有很多适应洞穴环境的特征；另一部分营非典型洞穴生活的物种无明显特化的性状。用形态和分子数据对金线鲃属的系统发育关系进行了研究，还存有争议，特别是洞穴物种之间的关系。因此本研究选择线粒体基因组中的细胞色素b和NADH4（ND4）基因作为分子标记，用多种系统发育重建的方法分析数据，探讨金线鲃属的系统发育关系；并用几种松散分子钟方法估算本属及内部分支的起源时间。同时也研究了视蛋白基因在金线鲃属中的进化，并探讨视蛋白基因不同进化模式的原因。本论文的主要研究结果如下： 1、获得了34种金线鲃属鱼类及一些外类群的细胞色素b和ND4基因序列，分别采用最大似然法、最大简约法和贝叶斯法重建了金线鲃属的系统发育关系，并用松散分子钟方法估算了本属及内部分支的起源时间。结果表明：（1）金线鲃属的单系性得到强烈的支持，本属可分为6个分支。（2）洞穴物种的多系起源假说以及季氏金线鲃（Sinocyclocheilus jii）的基部位置得到支持。（3）松散分子钟的估算表明金线鲃属起源于晚中新世，大约在11百万年前（million years ago, Mya），比以前设想的要古老。（4）金线鲃属的起源及分化可能与东亚夏季风的形成及大气中二氧化碳含量的波动有关。 2、测定了16种金线鲃和一些其它鲤科鱼类的视蛋白基因序列，包括RH1，LWS-1和SWS2。我们用PAML集成的基于密码子的模型分析了视蛋白基因在金线鲃属中的进化。结果显示：（1）RH1编码区没有发生移码突变或无义突变，在金线鲃属中受松散的负向选择，具有显著高于其他鲤科鱼类RH1的ω，可归因于本属鱼类的洞穴习性。金线鲃属洞穴物种和地表物种RH1的ω差异不显著。RH1在缺乏光线的环境下，可能具有未知的功能，或许在生理节律的调节中起作用。（2）金线鲃的LWS-1具有脊椎动物典型的6外显子/5内含子的结构，内含子的剪接信号很保守，均为GT/AG。LWS-1的内含子具有较多的插入缺失，部分序列的编码区具有移码缺失或无义突变。分子进化及关键位点变异的分析表明LWS-1在金线鲃属中受到了正向选择和分歧选择，并发现了分支特异的位点。LWS-1的两个拷贝极可能具有不同的lmax。基因加倍或者洞穴环境或者两者共同作用导致了LWS-1的假基因化。（3）金线鲃的SWS2具有5外显子/4内含子的结构，这与其它脊椎动物SWS2的结构是相同的，内含子具有保守的剪接信号GT/AG和许多插入缺失。金线鲃SWS2的编码区序列没有发生假基因化，受负向选择。位点的分析及PAML的估算表明金线鲃的SWS2可能并没有发生功能上的分化。综合以上的结果，我们认为视蛋白基因在金线鲃属中的进化显得非常有趣而又扑朔迷离。
The cyprinid genus Sinocyclocheilus is endemic to China, and only distributes in karst area of Yun-Gui Plateau, including Guizhou Province, Yunnan Province, and Guangxi Zhuang Autonomous Region. Almost all known Sinocyclocheilus species dwell in or around caves. Some species are troglobites with distinct troglomorphic characters; and some are troglophiles which lack special adaptations to cavelife. Despite considerable studies, the phylogenetic relationships within Sinocyclocheilus remain controversial, especially for the cave species. The cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) gene sequences were analyzed with a variety of phylogenetic methods to reconstruct the phylogenetic relationships of Sinocyclocheilus. Divergence times of the recovered clades were estimated using several relaxed molecular clock methods. The molecular evolution of opsin genes of Sinocyclocheilus was explored, and the causes of different patterns of molecular evolution were discussed. The main conclusions and hypotheses of present study were as follows. 1. We obtained the sequences of cyt b and ND4 of 34 species within Sinocyclocheilus. Phylogenetic trees were reconstructed with maximum parsimony, maximum likelihood and Bayesian methods. Under this phylogenetic framework, the divergence times of recovered clades were estimated using different methods under relaxed molecular clock. Our results were as follows. (1) The monophyly of Sinocyclocheilus was strongly supported and this genus could be subdivided into 6 major clades. (2) The polyphyly of cave species and the most basal position of S. jii were corroborated. (3) Relaxed molecular clock estimation suggested that Sinocyclocheilus originated in the late Miocene, about 11 million years ago (Mya), which is older than what have been assumed. (4) The origin and diversification of Sinocyclocheilus may be associated with the east Asian monsoons and fluctuations of pCO2. 2. The sequences of three opsin genes of 16 Sinocyclocheilus species and some other cyprinid fishes, including RH1, LWS-1 and SWS2, were obtained through cloning. A wide array of codon models implemented in PAML was used to infer the evolution of these opsin genes. The results were as follows. (1) No nonsense or frameshift mutations occurred in newly determined RH1 sequences. Sinocyclocheilus had a significantly higher ω than other cyprinid fishes compared, which might be the result of relaxation of purifying selection and could be ascribed to cave habit of the species of this genus. In contrast to previous hypotheses, both cave and surface/normal lineages exhibit a similar rate of molecular evolution. The RH1 of cave species may be still functional, although these species were highly adapted to cave environment. RH1 might have an unknown function in the absence of light, perhaps a role in circadian rhythms. (2) LWS-1 gene of Sinocyclocheilus possessed a vertebrate typical six exon/five intron structure. The splice junction signals (GT/AG) were conserved in all introns. There were many indels in introns of LWS-1, and there were nonsense mutation or frameshift deletion in coding regions of some sequences. Selective pressure analysis and site inspections suggested that LWS-1 gene of Sinocyclocheilus was affected by positive selection and divergent selection, and clade specific amino acids were found. The two duplicated LWS-1 may have different lmax. The pseudogenization of some sequences might be ascribed to genome duplication of Sinocyclocheilus, cave environment, or a mixture of the two. (3) SWS2 gene of Sinocyclocheilus possessed a five exon/four intron structure, which was identical to other vertebrate species. The splice junction signals (GT/AG) were conserved in all introns. There were many indels in these introns. But there were no nonsense mutation or frameshift deletion in the coding regions of newly determined SWS2 sequences. Selective pressure analysis showed that the evolution of SWS2 was dominated by negative selection. Both maximum likelihood analysis and site inspections implied that the function of the function of the two paralogs might not be diverged. So, the molecular evolution of opsin genes of Sinocyclocheilus is complicated and confusing.