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题名	川金丝猴与滇金丝猴的群体遗传学研究
作者	潘登
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	川金丝猴（Rhinopithecusroxellana） 群体遗传学 保护遗传学 滇金丝猴（Rhinopithecusbieti） 溯祖理论 生物信息学 程序设计
其他题名	Population Genetics of the Sichuan and Yunnan Golden Monkeys
中文摘要	川金丝猴（RhinoPithecusroxellana）是我国著名的珍稀濒危保护动物，但是，现有的群体遗传学研究成果并不能满足科学合理的制定其遗传保护策略的要求。这主要是因为前人研究的遗传标记均是相对比较保守的功能基因，因此无法检测到足够的变异，进而也无法进行精细的分析。有鉴于此，我们选取了进化速率较快的线粒体控制区作为遗传标记，并对来自于三个主要栖息地的川金丝猴样本进行了群体遗传学研究。我们在线粒体控制区中观察到了大量的变异，这和前人的工作结果形成了强烈的反差。通过基于溯祖理论的最大似然法估算，我们得到现存川金丝猴群体的总的有效群体大小在700一2，300只以内，同时其最近共同祖先的年代在19，000-62，700年前左右。线粒体控制区的结果表明现存川金丝猴群体可能起源于眠山群体，我们称之为单起源假说，但是由于样本限制，多起源的可能性仍然存在。整个川金丝猴群体表现出显著的内部分化的信号，甚至氓山群体内部还存在一个序列分歧非常大的分枝，这可能是由其特殊的社群结构以及较弱的基因交流造成的，并且由于群体结构和分化信息的拮抗作用，我们并没有直接检测到瓶颈效应。通过和相关濒危与非濒危物种的比较，我们认为川金丝猴群体的遗传多样性水平并不低，提示其濒危的状态主要是由随机因素造成的而非遗传因素的结果。虽然我们在线粒体控制区中发现了大量的变异，但是前人在蛋白质电泳的研究中并未检出多态，同时，川金丝猴特殊的社群结构是否会影响其在核基因水平上的群体遗传结构也是十分有趣的问题，因此，为了从核基因组的角度进一步研究川金丝猴的遗传多样性，并实现对核基因和核外基因的比较，我们对样本的14个微卫星座位做了检测。我们发现这些微卫星座位均存在多态，所有地方群体的平均杂合度均大于0.5；地方群体间存在着显著的分化；地方群体间有效群体大小比率的估计值和群体大小比率的野外观测值非常接近。通过对比线粒体数据，我们认为川金丝猴的社群结构对其群体的遗传结构有着重要的影响，首先表现在核基因有更大的基因流水平，其次还表现在我们可以检测到眠山群体和秦岭群体在近期均经历了瓶颈效应，说明在核基因水平上群体结构信号的影响要弱于线粒体基因。但是，通过和其它物种比较，微卫星的数据却表明川金丝猴的遗传多样性水平并不高于其它的濒危动物，这和线粒体控制区的结果相反。这主要是当以微卫星为标记时，群体的历史动态对于当前群体的多态程度的影响力有限所致。微卫星的结果表明了保护川金丝猴群体的紧迫性。我们还通过细胞色素b基因证明了线粒体控制区中的巨大分歧不是由核假基因的造成的。巧合的是前人也在川金丝猴群体中对该基因进行过研究，但是结果却相反，即我们发现的变异水平远远高于他们的结果。为此，我们比较了两项工作的数据，我们推测在前人的工作中可能存在着潜在的测序错误。不过，如果没有出现污染的话，这两项工作的综合结果可以直接支持我们前面提到的单起源假说。此外，通过细胞色素b基因的分析，我们还估算出川金丝猴和滇金丝猴（R.bieti）的分歧时间大致在0.7-2.3百万年之间。镇金丝猴（R．biti）也是我国著名的濒危保护动物，它是川金丝猴的近缘种，其濒危等级甚至还要高于川金丝猴。迄今为止，关于滇金丝猴并基于DNA序列的的群体遗传学研究还没有见诸于报道。我们测定了来自于云南省维西县镇金丝猴群体样本的线粒体控制区全序列以及部分个体的细胞色素b全序列。在排除了核线粒体假基因存在的可能性之后，我们确认滇金丝猴维西群体内部也存在着两个序列分歧较大的分枝，但是，这可能是邻近群体迁移而来的产物。因此，如果考虑到群体结构和迁移的影响，我们认为维西群体的遗传多样性水平可能并不高。在以上的研究中，我们使用了大量的群体遗传学方法，但遗憾的是，目前还没有一套令人满意的侧重于群体遗传学分析的程序工具库。为了简化今后工作的复杂度和难度，我使用OCAAML语言编制了一套程序工具集（Pan'sToolKit，PTK）。OCAML是一门优秀的计算机语言，它既支持快速开发，又支持高速运行，是理想的算法实现语言。基于OCAML的PTK库集成了许多实用工具以及群体遗传学算法，尤其是溯祖理论的算法。PTK库不仅可以用于处理常规的实验数据，而且还可以用于辅助理论和算法的研究。
英文摘要	Sichuan Golden Monkey (Rhinopithecus roxellana) is one of the most famous endangered animals in China; however, our knowledge about its population genetic patterns could not meet the requirement of developing a sound genetic conservation plan, which is because the genetic markers used in previous studies are all conservative and thus result in the extreme poor polymorphisms. So, we analyzed a sample set with 35 samples from the three major habitats of R. roxellana using the mitochondrial control region (D-loop), a well-known fast evolving marker, to explore its population patterns. In contrast to previous studies, we found a lot of mutations. With the help of the maximum likelihood method based on the coalescent theory, we obtained that the effective population size for the whole population is within 700-2,300 and the time of the most recent common ancestor is about 19,000 - 62,700 years ago. Our results indicate that the extant populations may be originated from Minshan, or called the mono-origin hypothesis, however, due to the limited sample size; a multi-origin version is also tenable. The whole population is highly structured such that there is a very deep divergence within Minshan, which maybe result from the monkey's special social structures and the subsequent weak geneflows. Against by the signals of population structure, we could not detect the presence of bottlenecks directly from D-loop data. The comparisons with related species, both endangered and none-endangered, show that R. roxellantfs polymorphism level is not low, suggesting that its endangerment is impacted more by stochastic factors not genetic ones. Although a lot of variations were detected in D-loop, none was found in the study using protein electrophoresis on nuclear genes. It is interesting to know the influences of*, roxellamfs social structure on genetic patterns revealed by nuclear genes. Therefore, we scanned 14 microsatellite loci to further the evaluation of differences of impacts between mitochondria! and nuclear genes. Ail the microsatellite loci are polymorphic; all the average heterozygositis are above 0.5; significant population differentiations were detected among local populations; the estimated ratio of the effective population size among the three local populations is close to the corresponding census one. Compared with mitochondrial data, we conclude that the social structure is an important factor shaping the population genetic pattern of it roxellana, such that the geneflows reviewed by microsatellites are much stronger than those by D-loop and recent bottlenecks can be detected directly in both Minshan and Qinling local populations, which means the influences of population structure is less decisive than those in D-loop. Opposite with the case of D-loop, we found that the polymorphism level of the monkey revealed by microsatellite is no more that those of other endangered animals, which is mainly because that the influences of population history to polymorphism level is weak in microsatellites. The conclusions from microsatellites suggest the urgency of its conservation protection. While analyzing the D-loop data, we proved that the deep divergence is not raised by the presence of nuclear pseudo gene by constructing the gene tree of cytochrome b gene. Coincidently, cytochrome b gene was also studied in jR. roxellana previously; however, our results converse with those in previous work in that we found many variations while few were detected in the previous work. By comparing the data from both studies, we speculate that there maybe possible sequencing errors in the previous work. However, if no contaminations occurred, the combination of both works does give full support to the mono-origin hypothesis. As an additive result, the divergence time between Rsoxellana and RMeti was estimated in a range of 0.7-2.3 Myr. The study of Kroxellana provides a template for similar studies on related species such as the Yunnan Golden Monkey (RMeti), which is also a famous endangered primate in China and even more dangerous than Kroxellana. So far, studies on its population genetics based on DNA sequences are not available. We sequenced the whole mitochondria control region of the samples from Weixi, Yunan Province as well as the whole cytochrome b gene in some individuals. A deep divergence was observed within Weixi population and confirmed after obviating the possibility of being nuclear pseudo gene, which may be introduced from the neighboring local populations. So, if population structure and migration are to be considered, the true polymorphism level of Weixi population may be not as high as observed. In our studies, a lot of population genetic methods are used, however, until now, no satisfied programming library emphasizing on population genetics is publicly available. In order to simplify and help routine works, I made a toolkit library, named Pan's Tool Kit (PTK), mainly focused on population genetics using Objective Categorical Abstract Machine Language (OCAML). OCAML is an excellent programming language with both rapid development features and high runtime performance, which is an ideal language for implementing algorithms. Now, PTK has been incorporated with a lot of helpful utilities and population genetic algorithms, especially those in the area of coalescent theory. Although it is still under development, PTK is capable of solving problems in routine work and giving aid in theoretical study.
语种	中文
公开日期	2010-10-15
内容类型	学位论文
源URL	[http://159.226.149.42:8088/handle/152453/6172]
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	潘登. 川金丝猴与滇金丝猴的群体遗传学研究[D]. 北京. 中国科学院研究生院. 2005.

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