食肉目哺乳动物（Carnivora）的分子进化研究
文献类型：学位论文
| 作者 | 于黎 |
| 学位类别 | 博士 |
| 答辩日期 | 2005-06 |
| 授予单位 | 中国科学院研究生院 |
| 授予地点 | 北京 |
| 导师 | 张亚平 |
| 关键词 | 肉目 犬型超科 熊科 猫科 系统发育分析 系统发育树 线粒体基因 核基因 哺乳动物 FGB基因第七内含子 |
| 其他题名 | Molecular evolution of the mammalian order Carnivora |
| 中文摘要 | 追溯生物界不同生物类型的起源及进化关系，即重建生物类群的系统发育树是进化生物学领域中一个十分重要的内容，并日益受到广泛的关注。美国和一些欧洲国家已率先启动了类似人类基因组计划的"生命之树，，计划（TreeofLife，TOL），将对生物学研究的发展产生深远影响。本研究瞄准了"生命之树"这一国际关注的焦点问题，选择具有重要进化理论意义和保护生物学价值的食肉目进行研究，除采用流行的多个线粒体基因外，还筛选多个有效的核基因标记，通过多基因序列数据的整合分析，构建可靠的食肉目分子系统树。此外，我们在食肉目部分物种的一个内含子区域发现了SINE家族的插入，考虑到这个内含子区域可能是SINE家族序列的一个插入热点，我们还增加了一些胎盘类哺乳动物目对这个内含子区域发生的多次SINE家族插入进行了详尽的进化研究。世界现生食肉目动物共计有11科280种，一般将它们归为两大超科，犬型超科（熊科，犬科，洗熊科，锄科，海狮科，海象科和海豹科）和猫型超科（灵猫科、猫科、鼠狗科和獴科）。犬型超科由于包含的物种种类繁多而且形态差异极"大，因此物种之间的系统发育关系方面争论颇多，难以解决。我们选用四个核基因序列片段和一个线粒体蛋白编码基因（共4417个碱基）对16个大型超科食肉目代表物种进行研究，探讨这一超科中科间的系统发育关系以及两个熊猫（大，小熊猫）的位置。结果表明不同基因在各分枝上表现出不同的解决能力，核基因和线粒体基因不含有冲突的，而是含有互补的系统发育信号，因而当把它们合并在一起进行系统发育分析时得到了一个大部分分枝都有很高支持程度的系统树拓扑结构。系统发育重建支持犬科是犬型超科中最早分歧的谱系，洗熊科和勃科的关系最近。小熊猫是洗熊科和触科的姐妹群，大熊猫是熊科中最早分歧的成员。鳍脚类（海狮科，海象科和海豹科）和熊科依次是由洗熊科，融科和小熊猫组成的进化枝最近的姐妹群。其中，鳍脚类和熊科的系统发育学位置在合并所有基因片段进行的ML和贝叶斯分析方法中都有较高的支持率和后验概率，但是在孵分析中的支持率却很低。因此，鳍脚类，熊科和由洗熊科，融科，小熊猫组成的进化枝三者之间的系统发育关系的解决将是以后食肉目犬型超科科水平系统发育学研究的趋势和重点。食肉目中不仅各科之间的进化关系扑朔迷离，科内的系统发育关系也很不清楚，尤其是熊科和猫科。因为这两个科都是在非常近期才发生物种分化的类群，代表了快速的进化辐射和间隔时间非常短的物种形成事件，因而重建科内各物种之间的系统发育关系对于系统学家来说是一项艰巨，极富挑战性的任务，也是造成熊科和猫科物种系统发育关系一直无法得到完全解决的重要原因。我们首次从两个核基因的角度，并与以前发表的五个线粒体基因数据进行单独和合并分析来探讨所有熊科物种（8个）的系统发育关系（约4kb）。结果不仅证实了目前普遍接受的观点，包括眼镜熊是除大熊猫以外最早分歧的熊科物种，以及棕熊和北极熊的姐妹群关系，而且进一步支持了亚洲黑熊和美洲黑熊之间的紧密关系，但是就在大多数以前的线粒体基因研究暗示懒熊极有可能是Ursus属中分歧最早的熊科物种时，我们的核基因分析提出新的假说，强烈支持懒熊和马来熊之间的姐妹群关系，使得懒熊和马来熊的系统发育位置又要成为将来熊科系统发育学研究中讨论的热点。另外，我们也探讨了核基因和线粒体基因表现出不一致系统发育信号的可能原因。猫科物种一般分成三大谱系：家猫谱系，豹谱系和虎猫谱系。其中由Panthera属和一些中等体型大小的猫类组成的豹谱系分化时间最近而且包含的物种最多，因此围绕它的系统发育学未解决的问题也最多。我们首次使用三个核基因对猫科中豹谱系部分物种系统发育关系进行探讨，同时还测定了两个完整线粒体编码基因，并结合以前发表的其它四个线粒体基因片段进行单独和结合分析，了解猫科豹谱系物种的进化历史。另外，我们还比较了这9个基因序列片段在进化特征和猫科系统发育关系应用价值方面的异同点。通过对14个猫科部分物种，主要为豹谱系物种的多个线粒体和核基因序列片段的综合分析，得到了一些非常有价值的重要结论，包括Panthera属的单源性以及Panthera属内部物种之间新的系统发育关系，云豹与Panthera属关系最近，美洲狮和猎豹是姐妹群，兔孙仍然属于家猫谱系等等。本研究中的核基因DNA在追溯如此近期才分化的猫科类群过程中积累的序列差异较少，因而贡献非常有限，它们可能会更适合用来解决食肉目中更高水平的物种之间系统发育关系。此外，当我们使用FGB基因第七内含子进行食肉目犬型超科各科和猫科部分物种的系统发育关系研究时，发现犬科代表物种和两个猫科物种中的不同位置上都发现了SINE片段的插入。我们又增加了除食肉目以外的部分哺乳动物目代表物种（共30个分类群）来进一步分析FGB基因第七内含子发生的多次SINEs家族插入事件。我们的结果表明：在所有哺乳动物内含子中的直源位置都发现了起源于tRNA的M琅元件，除了啮齿目。研究发现啮齿目小鼠中较高的序列变异速率以及大鼠中随着寄主DNA的大段丢失而发生了罕有的遗失是造成啮齿目中MIR缺失的原因。此外，在我们分析的12个哺乳动物目中，食肉目，偶蹄目和兔形目的FGB基因第七内含子不同位置还发现了至少五次谱系特异性SINE家族的独立插入事件。在食肉目中，三个独立的CANSINEs插入支持了这个SINE家族在食肉目所有类群中都有分布的假说（即"pan-camivores"假说）。研究中最重要的发现就是那些谱系特异的sINE家族有插入到己存在的MIRs内部或MIRs附近的强烈倾向，表明MIR很有可能是其它SINEs连续插入的"热点"区域，因而使这个内含子区域有如此多的逆转座子插入。我们认为SINEs要比以前所意识到的具有更大的插入"灵活性"和区域"特异性"。另外，本论文还重点介绍了现代系统发育学中常用的系统发育重建方法和策．略以及随着基因组时代的到来，"系统发育基因组学（P坤logenomics））'这门崭新的交叉学科在"重建生命之树"方面所具有的巨大优势和潜力。 |
| 英文摘要 | The study of evolutionary relationships among organisms is vital in evolutionary biology and receiving unprecedented attention in recent times. U.S.A and some European countries have initiated "The Tree of Life (TOL)" program which is going to have far-reaching impact on biological development. Aiming at this international focus, we attempt to conduct phylogenetic analyses of mammalian order Carnivora, an intriguing animal group with evolutionarily theoretic significance and conservation values. Besides popular mitochondrial (mt) genes, unlinked nuclear genes are also utilized as the source of characters in our study. The carnivore phylogeny was inferred from combined analyses of multiple mt and nuclear gene sequences. In addition, we unexpectedly observed SENEs insertion in an intronic region from some carnivoran species. Considering that this intronic region may be a hot spot for the insertions of SINEs, we also extended SINEs analyses of the same intron by including additional taxa from other placental orders of mammals beyond the Carnivora. Extant carnivores include 11 families and 280 species. In general, they are divided into two superfamilies: Caniformia (Ursidae, Canidae, Procyonidae, Mustelidae, Otariidae, Odobenidae and Phocidae) and Feliformia (Viverridae, Felidae, Hyaenidae and Herpestidae). The Caniformia is rather heterogeneous and morphologically diverse, and hence has had many controversial issues surrounding its phylogeny. We sequenced four nuclear and one protein-coding mt genes (4417bp in total) from 16 species within Caniformia to investigate interfamilial relationships and the placements of the two pandas. Phylogenetic results showed that nuclear and mt genes are phylogenetically complementary for the higher-level analyses, resulting in a well-supported tree topology for most branches when they were combined. The preferred hypothesis provides evidence in favor of the red panda as the closest taxon to the sister-grouping of Procyonidae and Mustelidae, followed by pinnipeds (i.e., Otariidae and Phocidae), Ursidae, and Canidae, the most basal lineage in the Caniformia. The giant panda was the earliest diverging member of Ursidae, Although the placements of pinnipeds and Ursidae were strongly supported in ML and Bayesian analyses of combined nuclear and mt genes, it was not in MP analysis. Therefore, the resolution of trichotomy among pinnipeds, Ursidae and the clade containing Procyonidae, Mustelidae and the red panda may be the emphases in future carnivore higher-level phylogeny. Not only interfamilial, but also intrafamilial relationships within Carnivora are subjects of debate, especially in case of Ursidae and Felidae. Because they represent typical examples of rapid evolutionary radiation and recent speciation events, so attempts to clarify relationships among the species within the two families have encountered challenge. We are among the first to employ two nuclear DNA data, together with previously published five mt data in both separate and combined analyses (about 4kb in total) to gain new insight into the phylogeny of Ursidae (8 bear species). Our study not only corroborated prior hypotheses, positioning the giant panda and spectacled bear most basaily and grouping the brown and polar bear together but also supported the close relatedness of Asiatic and American black bears. Notably, nuclear analyses suggested a novel sister-taxa association between sloth bear and sun bear with strong support, in contrast to those from the mt and combined analyses recognizing the sloth bear as the earliest diverging species among the ursine species. Thus, the precise positions of the sun and sloth bears in bear phylogeny still required confirmation by analyzing additional character information* In addition* we also discussed possible reasons for conflicting signals between nuclear and mt genes. The cat species of Felidae is generally assigned into the pantherine, domestic cat, and ocelot lineages. The pantherine lineage consists of five big cats of genus Panther a and a great many midsized cats species. As it is the most recently evolved and largest felid group in Felidae, the pantherine lineage has demonstrated greatest confusion in its phylogeny. We are the first to explore the potential of three nuclear genes in phylogenetic study of 14 cat species, mainly pantherine cats. Moreover, two complete protein-coding mt genes newly sequenced by us and four previously reported mtgenes were also added to our analyses. Evolutionary patterns of different genes and their values for resolution of low level feline questions were also discussed. Analyses of 9 genes from pantherine cats in a variety of combinations produced several valuable conclusions. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within the genus revealed a novel branching pattern. In addition, close association of the clouded leopard to Panthera, the phylogenetic redefinition of pallas cat within the domestic cat group, and the relatedness of puma and cheetah were all important finding in the resulting phytogenies. Our study demonstrate that nuclear DNA accumulated low sequence divergence in the event of tracking the evolutionary history for such a young lineage and consequently had limited phylogenetic contributions. They are expected to give better resolution at higher-level phylogeny of carnivores. An analysis of the nuclear p~fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of SINE insertion events. MIRs are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage -specific SINEs are also found to have independently inserted into this intron in Camivora, Artiodactyla and Lagomorpha. In Carnivora, the unique amplification pattern of CAN SINE provides important evidence for the "pan-carnivore" hypothesis. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs5 suggesting that the MIR element is a hot spot for successive insertions of other SINEs. Our study indicated that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. In the thesis, we also elaborately describe some tree reconstruction methods that were widely used in modem phylogenetics* and expatiate on enormous superiority and potential of a new synthesized discipline as a result of the genomic era coming, that is "Phylogenomics", to the reconstruction of "the Tree of Life". |
| 语种 | 中文 |
| 公开日期 | 2010-10-15 |
| 源URL | [http://159.226.149.42:8088/handle/152453/6181]  |
| 专题 | 昆明动物研究所_分子进化基因组学 |
| 推荐引用方式 GB/T 7714 | 于黎. 食肉目哺乳动物（Carnivora）的分子进化研究[D]. 北京. 中国科学院研究生院. 2005. |
入库方式： OAI收割
来源：昆明动物研究所
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