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东亚特有鲤科类群的DNA条形码研究及其系统发育分析
Alternative TitleDNA Barcoding and Molecular Phylogeny of the East Asian Endemic Cyprinids group
彭居俐
Subtype硕士
Thesis Advisor何舜平 ; 王丁
2007-06-19
Degree Grantor中国科学院水生生物研究所
Place of Conferral水生生物研究所
KeywordDna条形码 Co1基因 东亚特有鲤科鱼类 鲌亚科 鲌属
AbstractDNA条形码(DNA Barcoding)作为一种新兴的分类学技术引起了越来越多生物学家的关注。作为一种新的物种鉴定手段,DNA条形码由于其快速简便的操作过程能够广泛地进行科学应用,尤其是在保护生物学和生物多样性调查等领域。 DNA条形码技术是通过对一个标准目的基因的DNA序列进行分析从而对物种进行鉴定。用于DNA条形码研究的标准基因,一方面应该足够保守,能够利用通用引物进行大范围的扩增;另一方面应该有足够的变异来区分不同物种DNA序列从而进行鉴定。因此,在鉴定不同物种类群时需要选择有效的目的基因。近期备受研究者关注的DNA条形码基因为线粒体CO1基因序列。 东亚特有鲤科类群是鲤科鱼类在适应青藏高原隆起过程中形成的东亚季风性气候下而分化的一个类群。此类群经历了爆发式物种形成过程,因其特殊的物种分化模式,线粒体CO1基因能否在此类群中表现出足够的遗传差异,以及能否准确地对此类群物种进行鉴定有待进行研究探讨。本研究将验证线粒体CO1基因在东亚特有类群中进行DNA条形码研究的可行性,并且拟基于线粒体CO1基因序列探讨东亚特有鲤科鱼类的系统发育关系。 本论文的研究内容可大致分为2个部分: (1)分别以鲌属、鲌亚科和东亚特有鲤科类群为研究对象,检测线粒体CO1基因在这些类群中进行物种鉴定的可行性。可行性的分析主要从遗传距离差异和系统发育树结构两方面进行探讨。其中遗传距离分析均在MEGA3.0软件中进行,系统发育树的构建在PAUP和MrBayes软件中完成。对鲌属物种的DNA条形码研究而言,其种间遗传距离显著地大于种内遗传距离,并且同一物种的不同个体均形成高支持率的单系,说明在鲌属类群中线粒体CO1基因是一个有效的DNA条形码标准基因。鲌亚科类群的遗传距离结果显示物种的种间遗传距离大于种内遗传距离;得到的邻接树、最大简约树和贝叶斯树显示出同一物种的不同个体均 形成高支持率的单系。因此得出结论,线粒体CO1基因能够对鲌亚科物种进行有效的物种鉴定。对整个东亚特有鲤科鱼类平均种间遗传距离分析,发现其平均种间遗传距离显著大于鲌亚科平均种间遗传距离(鲌亚科平均种间遗传距离远大于平均种内遗传距离),据此推断线粒体CO1基因能在东亚特有类群中有效的进行物种鉴定。并且经论证DNA条形码在东亚特有鲤科鱼类中的有效性,为构建东亚特有鲤科鱼类的DNA条形码数据库奠定了基础。 (2)为探讨东亚特有鲤科类群的单系性以及其内部物种的系统发育关系,本研究将实验获得的线粒体CO1基因序列与GenBank中下载的序列相结合构建鲤科鱼类的系统发育树。系统发育树的拓扑结构显示鲤科鱼类分为三个类群,波鱼类群位于系统树的基部,鲃系与雅罗鱼系互为姊妹群。在雅罗鱼支系中,东亚特有鲤科鱼类的单系性得到重现,并且支持鲌类物种的单系性。但基于线粒体CO1基因序列的系统发育分析,东亚特有类群内部各分类单元的相互关系依然没有得到很好的解决,结果表明线粒体CO1基因无法提供足够的系统发育信息来解决东亚特有鲤科鱼类内部类群的系统发育关系。
Other AbstractDNA Barcoding is becoming more and more attractive to biologists as a new method to aid in species identification. As a new technology, DNA Barcoding is very simple and easy to operate. It has been widely used in scientific research, especially in the field of conservation biology and investigation of biodiversity. The core idea of DNA barcoding is based on the fact that species can be differentiated by short pieces of standard gene sequences. Generally, a genetic marker which could be used as a DNA Barcode should, on one hand, be conserved at some degree so that this genomic region could be amplified by universal primers for diverse taxa; on the other hand, be variable enough among taxa so that different species could be differentiated. It is very important to choose appropriate genetic markers for species identification. Recently the mitochondrial CO1 gene is already proving to be efficacious as a DNA barcode in a range of amimals. The East Asian Endemic Cyprinid group is a group of cyprinid fishes whose speciation may be linked to the evolution of East Asian monsoon which has been affected by uplift of the Qinghai-Tibetan plateau. Because of rapid evolutionary radiation of the East Asian endemic group, we wonder that the mitochondrial cytochrome oxidase subunit 1 (CO1) gene could be an efficient marker for DNA barcoding of this group. In this study, we wanted to discuss the consequences and potential of the CO1 gene as a marker for phylogenetic reconstruction and DNA barcoding of this endemic cyprinid group. The main work and conclusion of the present study were as the following: (1) In order to testify the validity of the mitochondrial CO1 gene for species identification, we performed our research at different levels, such as Genus Culter, Subfamily Cultrinae and the East Asian endemic Cyprinid group. The analyses were focused on genetic distance and the phylogentic relationship. Genetic distance was calculated in MEGA3.0 software, and phylogenetic trees were constructed with PAUP and MrBayes software. In Genus Culter, genetic distance within species is obviously lower than that between species. And in the phylogenetic trees, all individuals of each species formed a clade. Then the conculsion was that mitochondrial CO1 gene was a good marker in Culter DNA barcoding. The conclusion was the same when the research group turned to Subfamily Cultrinae. In Cultrinae, genetic distance between species was much higher than that within species, and all the topology of trees constructed with different methods displayed that all the individual of each species formed a clade. From the study of Cultrinae, we can draw a conclusion that the mitochondrial CO1 gene can effectively support the species identification. When we met the data of genetic variation of East Asian Cyprinid group, the mean sequence divergences between groups were higher than that between Cultrinae taxa,then we could conclude that CO1 gene was a valid marker for DNA barcoding of East Asian endemic Cyprinid taxa. For the validation of DNA barcoding in the endemic group being supported, it provided a strong platform to construct the Bank of DNA barcoding. (2) To assess support for the monophyly of East Asian endemic cyprinid taxa, we used the mitochondrial CO1 gene sequences for phylogenetic reconstruction of the family Cyprinidae. The phylogenetic analyses revealed three groups within Cyprinidae. The subfamily Danioninae was on the base, Barbine and Leuciscine formed sister group. Whitin Leuciscine, East Asian endemic Cyprinid taxa were recognized as a monophyly. Although the monophyly of Cultrins was strong supported, the relationships of each groups in East Asian endemic Cyprinid taxa were not well resolved. The result indicated that the mitochondrial CO1 gene sequence provided less phylogenetic information to resolve the relationship of this East Aisan cyprinid group.
Pages83
Language中文
Document Type学位论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/12190
Collection学位论文
Recommended Citation
GB/T 7714
彭居俐. 东亚特有鲤科类群的DNA条形码研究及其系统发育分析[D]. 水生生物研究所. 中国科学院水生生物研究所,2007.
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