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题名	翼手目暗视觉适应性机制的研究和快速进化基因在黑腹果蝇发育中作用的整合分析
作者	刘鹤群
学位类别	博士
答辩日期	2015-07
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	适应性进化 翼手目 暗视觉 正选择 转录组测序 趋同/平行进化
其他题名	Studies on the Mechanism of Adaptation of Dim-light Vision among Chiroptera and Integrative Analysis of Rapid Evolution genes in the Development of Drosophila melanogaster
中文摘要	适应性进化是达尔文自然选择学说的核心，它主要是研究自然界的生物如何为了适应环境的变化而进化出一系列的结构和功能。分子生物学的诞生给适应性进化的研究带来了新的契机，使得人们能够从生物大分子的水平来揭示适应性进化的内在遗传机制。近年来，新一代测序技术的发展，大量基因组和转录组数据的涌现，使得从整个通路中多个分子、多个区域来揭示复杂性状的适应性进化遗传机制成为可能。另外，结合影像学、神经生物学等手段，可实现从结构、功能及分子机制等多方面系统地揭示适应性进化的机制。 翼手目（Chiroptera）俗称“蝙蝠”，是唯一能够飞行的哺乳动物，《物种起源》中就曾详细讨论蝙蝠是如何进化出飞行的能力，加之翼手目内存在在显著的感觉分化，使之成为适应性进化研究的绝佳素材。在本文研究篇的第一部分（第四章），我们首先着眼于翼手目内显著的感觉功能分化——暗视觉的分化，即：以旧大陆果蝠（Old-World fruit bats）为代表的大蝙蝠亚目，眼睛大，视觉发达；反之，小蝙蝠亚目，眼睛小，视觉退化，具有发达的回声定位能力；而同样隶属小蝙蝠亚目的墓蝠（Taphozous melanopogon），既具有发达的喉部回声定位能力，也使用视觉进行定位。为了更好地理解翼手目中这种暗视觉分化的机制，我们首先利用锰离子增强磁共振（MEMRI）成像技术扫描翼手目大脑结构，定位初级视觉皮层的位置，并发现视觉发达的大蝙蝠具有较大的上丘（参与视觉信息处理）（上下丘体积比约3:1），回声定位发达的小蝙蝠具有较大的下丘（参与听觉信息的处理）（上下丘体积比约为1:7），揭示了翼手目暗视觉分化的结构基础；接着我们利用闪光诱发电位技术，测得四种蝙蝠的视觉阈值，发现视觉能力的大小为：狐蝠科蝙蝠>墓蝠>中菊头蝠（小蝙蝠亚目，回声定位），进一步将视觉能力进行量化；最后利用转录组测序技术（RNA-seq），测得5种蝙蝠的视网膜转录组，检测了正选择、趋同/平行进化分析、表达上调等一系列适应性信号，并发现墓蝠眼部基因的转录组水平表达模式和狐蝠科更为相近。这项研究着眼于整个视觉通路，从结构、功能和分子机制等多角度系统得阐述了翼手目暗视觉分化的机制，为复杂性状的适应性进化研究提供了良好的范本。 嗜神经病毒是一类通过创口或者粘膜感染宿主外周神经系统，沿神经通路进入中枢神经系统，并特异性跨突触传播、感染的病毒统称，目前结合基因操纵手段改造后被广泛应用在神经环路的标记上。大脑是感觉信息加工处理的重要场所，磁共振成像的结果表明暗视觉能力不同的蝙蝠在大脑结构上存在差异，且已有研究报道，进化出飞行能力的蝙蝠内嗅皮层及背侧海马中与空间信息编码相关的Theta波段与大鼠是不同。由此，我们猜想感觉功能分化的翼手目内及翼手目和大鼠之间在大脑神经环路的连接上存在一定的差异。在研究篇的第二部分（第五章），我们尝试利用嗜神经病毒追踪系统，分别使用伪狂犬病毒（pseudorabies, PRV）和狂犬病毒（rabies, RV）改造后的单突触示踪系统标记视听觉神经环路和海马背侧神经环路。遗憾的是，这两种病毒系统在蝙蝠身上均不起作用，但这项研究为同类研究的开展提供了一定的参考作用。接着，我们测得视觉发达和回声定位发达的棕果蝠（Rousettus leschenaulti）和三叶蹄蝠（Aselliscus stoliczkanus）视听皮层及背腹侧海马等在内的不同脑区的转录组，通过基因共表达网络的构建，检测出和脑区相关的基因共表达模块（第六章）。 果蝇是人类研究的最为透彻的模式生物之一，被广泛应用在遗传、发育、生理和行为等方面的研究，是适应性进化研究极好的素材。前人对发育过程中引起表型差异的机制的研究表明调控序列的突变在表型进化中起着非常重要的作用。然而通过对基因组数据的分析，发现蛋白编码基因在进化中受到的正选择作用在表型进化中的作用被低估了。同样，新基因的作为进化革新的另一大重要原材料，在发育过程中引起了显著的表型变化。为此，我们使用目前已公布的黑腹果蝇59个不同发育时期及不同组织的转录组数据，通过基因共表达网络的分析，构建基因共表达模块，发现新基因（重复基因、孤儿基因和lncRNAs）和正选择基因富集的模块与某些表型特征形成的发育时期有显著的相关性（第七章）。 综上，本文利用闪光诱发电位、锰离子增强磁共振及转录组测序等多种方法，从结构、功能和分子机制等多个角度系统阐释翼手目内暗视觉适应性进化的机制（第四章）；为进一步揭示翼手目适应性进化的神经网络结构基础，利用嗜神经病毒示踪系统标记棕果蝠的神经环路，这一项研究为同类研究提供了一定的参考作用（第五章）；其后，我们利用转录组测序手段，测得视觉发达和回声定位发达的两种蝙蝠不同脑区的转录组，通过基因共表达网络的构建，检测出和脑区相关的基因共表达模块（第六章）；最后我们以模式动物果蝇为研究对象，利用其不同发育时期和不同组织的转录组数据，分析发现新基因和正选择基因在发育中起着重要作用（第七章）。
英文摘要	Adaptive evolution is the core of the Darwinian natural selection theory, which mainly aims at researching how the organisms evolve a series of structure and function to adapt the environment. The birth of molecular biology brings new chance to adaptive evolution for that we can explore the genetic basis of adaptive evolution from the biological macromolecule. With the advent of next generation of sequence, a lot of genome and transcriptome data are produced, that makes the research of genetic basis from multiple molecules and regions in the pathway possible. At the same time, we can explore the mechanism of adaptive evolution from the struture, function and molecule by combing the imageology and neurobiology. Bats (Chiroptera) are the only mammals that can fly, which were expounded in the orgin Orgin of speciesSpecies, and fantastic divergence of sensory is observed in bats, therefore, bats are excellent material for the research of adaptive evolution. In the first part of our research (Chapter 4), we forcused on the divergence of dim-light vision among bats. The Old-world fruit bats have developed vision, large eyes and don't use echolocation. While microbats have developed larynx echolocation and degraded eyes. Interestingly, the tomb bat(Taphozous melanopogon) belongs to microbat, can use larynx echolocation but perfer relying normal vison for navagation. In order to better understand the mechanism of the divergence of dim-ligth vision in bats, we used MEMRI (manganese-enhanced magnetic resonance imaging) to measure scan the brain anatomy of selected species of bats. As results, we described the location of primary visual cortex in bats. And we found that megabat has larger superior colliculus (SC, dealing with the visual stimulus,SC/IC approach to 3:1), while microbat has larger inferior colliculus (IC,dealing with auditory stimulus, SC/IC approach to 1:7) , that represents the difference of struture in the bats.Then, we measured the absolute visual threshold, (log cd/m2?s) of four species of bats by using the Flash-visual evoked potentials (f-VEP), and found that visual capacity of Pteropodidae was most robust, followed by Emballonuridae and then insectivorous bats. Finally, five transcriptomes from of five species of bats covering major groups of bats were sequenced. Positive selection, parallel/convergent evolution and up-expressed genes were detected, as well, similar patterns of gene expression were found in between Pteropodidae and Emballonuridae. Taken together, our study used a combination of imaging, electrophysiology, and RNA-seq methods to elaborate on the mechanism of visual divergence in bats and served as a model for adaptive evolution research. Neurotropic virus is a virus that is capable of infecting peripheral nervous system and spread from the neural pathway to the central pathway,nerve cells and are increasingly being exploited to trace the neurnal circuits. Brain participates in handling sensory information, and we have proved that difference of brain structure was existing in bats. Furthermore, theta rhythms f entorhinal cortex and hippocampus was different in between bats and rats, that implied that they might own varied mechanism of spatial information. Thus, we supposed that the neural circuit of different species of bats utilizing divergent strategies to navigation was different, as well, as the bats(fly) and rat varied (don't fly). In the second part of our study (Chapter 6), we injected pseudorabies(PRV) into the visual and auditory cortexes to trace the neural circuit of visual and auditory pathway of different species of bats. Then we utilized modificated rabies virus (RV) (monosynaptic tracing system) to trace the neural circuit of dorsal hippocampus. Unfortunately, these viruses didn’t work in bats. But, our this stduy served as a good reference for the similar research. In addition, we sequenced transcriptomes different brain sub-regions of Rousettus leschenaulti and Aselliscus stoliczkanus. We performed a weighted gene co-expression network analysisto detect modules highly corrected with sub-region of brain (Chapter 6). The Drosophila are one of model animals that were explored at most thoroughly, and are widely used in the study of genetics, development, physiology and behavior;are the good material for study of adaptive evolution. Predecessors proposed that the evolution of anatomy was influenced to a greater extent by changes in gene regulation than by changes in protein sequence.With the advent of large-scale genomic data, the role of positive selection in the evolution of protein coding sequences involved in phenotypic evolution is now known to have been underestimated. New genes also provide crucial material for evolutionary innovations. In this study (Chapter 7), we download transcriptomes data of 59 developmental stages and tissues, and carried out a weighted gene co-expression networks analysis, we found that new genes, including duplicated genes,orphan genes and lncRNAs, and positive genes played a role in development stages that might be responsible for specific phenotypic feature in Drosophila melanogaster. In summary, we first described the mechanism of divergence of dim-light vision among bats from the structure, function and molecule by using f-VEP, MEMRI and RNA-seq ( Chapter 4). Then, we used neurotropic virus to trace the neuronal circuits to better understand the neurtual circuits of differnet species of bats, and this study served as a reference of the similar research (Chapter). Transcriptomes of different brain sub-regions in of two species of bats were sequenced, and gene co-expression modules highly corrected with sub-regions were detected (Chapter 6).At last, after exploring the gene co-expression modules, we found that new genes and positive genes played a role in development stages that might be responsible for specific phenotypic feature in Drosophila melanogaster.
语种	中文
内容类型	学位论文
源URL	[http://159.226.149.26:8080/handle/152453/10138]
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	刘鹤群. 翼手目暗视觉适应性机制的研究和快速进化基因在黑腹果蝇发育中作用的整合分析[D]. 北京. 中国科学院研究生院. 2015.

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