中国科学院昆明动物研究所机构知识库

物种如何形成及分化一直以来是进化生物学领域中十分重要的研究内容，并且日益受到广泛的关注。同时，了解物种的形成和分化机制也将为生物多样性的形成与保护提供帮助。分子遗传数据所含有的信息量要远大于表型数据，基因组测序技术的不断发展使得人们可以在较短的时间内获得海量的分子遗传数据，这使得进化生物学家们可以利用大量的DNA遗传变异信息来探讨影响物种种群内和物种之间遗传变异的各种因素。本文以两栖类中三个不同进化时间尺度的类群为研究对象，从种下和种上两个角度出发，分别利用基因组重测序和杂交富集的方法，探讨了不同进化时间尺度下两栖类的物种形成以及物种多样性形成问题。第一章，本文首先简要介绍了什么是物种，以及物种的形成机制和理论模型，接着介绍了如何从基因组的角度来解析物种的形成过程及其影响因素，最后介绍了种上的物种分化和多样性形成以及基因组技术在其中的应用。第二章，我们以青藏高原特有物种高山倭蛙为研究对象，利用基因组重测序的分析和方法，探讨了青藏高原复杂的地理环境、地质历史和生态环境对高山倭蛙的物种形成和群体分化的影响。我们的研究结果显示高山倭蛙东、西支系分别为两个不同的物种，东部内部支系的分化呈现与海拔相关的分化模式，选择和生态适应在高山倭蛙的种群分化和生殖隔离的形成中起主要推动作用。第三章，我们以两栖类物种多样性非常丰富（>1500种）且古老（~100Ma）的类群Natatanura为研究对象，通过探针杂交富集测序的方法，重建了该类群各主要支系的系统演化关系。基于此，我们重建并探讨了Natatanura的物种演化历史，发现冈瓦纳古陆的分离与后期重组对该类群的演化历史具有重要影响，该类群随印度板块的分离和漂移从冈瓦纳古陆扩散至劳亚大陆，其中印度板块在该类群的物种迁移扩散中扮演“脚踏石”的角色，从而拒绝从南极洲-澳大利亚-新几内亚扩散路径假说。后期由于大陆板块的重组又使得该类群能够多次独立返回至冈瓦纳大陆。第四章，建立在第三章中对Natatanura解决较好的骨干树基础上，我们挑选了其中的蛙科进行研究。该科是Natatanura类群中物种多样性非常丰富的一个科并且其系统发育关系在以往的研究中并没有得到很好解决。通过探针杂交富集测序的方法，我们不仅获得了目标核基因序列，同时也获得了线粒体基因组。线粒体突变速率过快（大约是目标核基因的15倍）以及蛙科早期物种的快速分化是导致线粒体基因组不能解决蛙科系统发育关系的主要原因。利用杂交富集的基因，我们重建了蛙科各主要支系的系统发育关系。基于此，我们对现有蛙科的分类进行重新评估并提出一些建议。此外，我们联合GenBank中目前已有蛙科物种的分子数据，重建了蛙科所有物种的演化历史，发现其演化历史与古气候温度的变化呈现正相关。 第五章，我们对本论文的工作进行了总结，并展望了未来的研究工作。

Processes that govern speciation and subsequently diversification is the central focus in evolutionary biology. The knowledge of these are keys to understanding the origin and patterns of diversification. Molecular genetic data, compared to phenotypic data, contain valuable information for testing hypotheses. The recent development in genome sequencing technology has enabled researchers to generate large amounts of sequence data. The availability of these data allowed evolutionary biologists to investigate the basis for intra- and inter-specific variations within and between populations. In this study, we employed population genome resequencing and anchored hybrid enrichment sequencing (AHE seq) approaches to examine the patterns of speciation and diversification in three groups of amphibians with different evolutionary time scales.In the first chapter, we introduced briefly the concept of species and the classical theoretical speciation models. Then, we unveiled patterns and processes of speciation from genomic perspective. Further, we introduced mechanisms of species differentiation and biodiversity formation, and the application of genomic approaches.In the second chapter, we used the Tibetan frog, Nanorana parkeri, endemic to Qinghai-Tibetan Plateau (QTP), as a model to investigate how the heterogeneous topography, complex paleoclimate history, and the inhospitable environmental conditions of QTP influenced population differentiation and speciation. Our results suggest that East and West lineages of the Tibetan frog are two distinctive species. Sub-lineages within East consisted of populations that differentiated to high (>3,700 m, E2 and E4) and low (<3,700 m, E1 and E3) elevations. Our study showed that natural selection seems a dominant factor that maintain and drive the continued population divergence and reproductive isolation in this species.In the third chapter, we used AHE seq approach to resolve the major lineage relationships within the Natatanuran frogs - a high species diversity (> 1500 extant species) and an ancient (~100 Ma) group of amphibians. We reconstructed and discussed the evolutionary history of Natatanura. Our result showed that the separation and subsequent tectonic reshuffle of the Gondwana Plate played a key role in the evolutionary history of this amphibian group. Analyses showed that Natatanuran frogs dispersed and radiated from Gondwana to Laurasia following the separation and drift of the Indian plate to Eurasian. During this process, the Indian plate acted as a “step-stone” in biotic exchanges between Laurasia and Gondwana. Our results reject the hypothesis of Antarctica-Australia-New Guinea dispersal route for this amphibian group. The later reorganization of the continental plate implies that Natatanuran frogs can dispersal back to Gondwana for several times.In the fourth chapter, based on the well resolved backbone relationship of Natatanura in Chapter three, we selected the Ranidae for further research. Ranidae is a species rich family in Natatanura with unresolved phylogenetic relationships. Using AHE seq approach, we obtained both target nuclear genes and mitochondrial genome. The rapid nucleotide substitution rate (~15 times faster than target nuclear genes) and the rapid diversification in the early stage seems likely factors that led to the failure of resolving the phylogenetic relationship of Ranidae using mitochondrial genome. Our target nuclear gene phylogeny resolved, for the first time, the phylogenetic relationships of Ranidae. Based on this, we presented the phylogenetic reconstruction of Ranidae and proposed several taxonomic change within this family. In addition, we combined all the molecular data in GenBank and reconstructed the evolutionary history of Ranidae species. Our study showed that the evolutionary history of Ranidae species strongly relates with the paleo-temperature changes.In chapter five, we summarized our work and offered recommendations for future researches.