| 其他摘要 | 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. |
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