雉鸡的种群基因组学与适应性进化研究

Varied evolutionary forces, such as natural selection, neutral processes like genetic drift, as well as population demography can leave traces in the genome of an organism. To determine the relative importance of these forces on the non-model organisms at the molecular level is one of the challenges in current evolutionary biology. The Common Pheasant (Phasianus colchicus) is a widespread and abundant gamebird species in Eurasia. Different geographical populations diverged substantially in morphology, genetic and exhibit adaptation to contrasting climatic and conditions, e.g. lowland to plateau, northern temperate to tropic, monsoon to inland desert. Thus the common pheasant is an ideal species to investigate microevolution patterns and processes leading to intraspecific divergence and local adaptation. In the present project, we will use a novel Genotyping-by-Sequencing laboratory and analytical method, i.e. RAD-seq based on Next-Generation Sequencing technique to generate genome-wide single nucleotide polymorphisms for multiple representative geographical populations across China. Based on genomic sequence data, state-of-the-art bioinformatic and population genetic methods will be applied to investigate genomic patterns of population demography and local adaptation in unprecedented detail in the Common Pheasants. Moreover, we will identify candidate genes that might be associated with the morphological variations and climatic adaptation. Further some of selected candidate genes will be genotyped using Sanger sequencing for a larger data set covering in order to estimate their frequencies and geographic patterns. This work will contribute significantly to our understanding of the mechanisms of population divergence and the maintenance of genetic variability, and will therefore furnish novel insights into microevolution in non-model organisms. Findings of this project will provide genetic resources for common pheasants. Given the novel sequencing technology and comprehensive analytical framework applied herein, this project would also represent a repeatable research scheme that can be applied in population genomics studies in other wild species.

如何从基因组水平检测自然选择、中性过程和种群历史等力量对于生物微进化的影响是进化生物学所面临的挑战之一。广布于欧亚大陆的雉鸡（Phasianus colchicus）的不同地理种群具有明显的表型和遗传分化，形成对不同地理气候条件的适应，是研究物种分化和适应等微进化机制的理想物种。本项目拟采用基于高通量测序的简化基因组技术RAD-seq，结合生物信息学、种群遗传学方法对雉鸡的种群基因组学进行研究，系统性地探讨雉鸡分化过程中各种进化力量的模式与规律；特别是在基因组水平寻找与雉鸡表型变异及适应不同地理气候条件相关的候选基因，并在雉鸡世界分布区内的更大群体中验证这些基因的分布频率，旨在揭示广布生物遗传分化模式和适应机制。相关研究成果促进了对非模式生物微进化机制的深入理解，为建立与完善野生鸟类大规模种群基因组学和适应性进化研究提供可扩展性的解决方案，对保护和利用雉鸡种质资源具有重要价值。

广布于欧亚大陆的雉鸡(Phasianus colchicus)的不同地理种群形成明显的表型和遗传分化，具有对不同地理气候条件的适应，是研究物种分化和适应性进化等微进化机制的典型物种。本项目采用基于高通量测序的简化基因组技术RAD-seq技术开发了不同类型的分子标记，结合生物信息学、群体遗传学方法对雉鸡的群体结构、群体历史和适应性进化进行研究。本项目获得28个亚种共计1007号样本，是迄今为止最全、数量最多的雉鸡样品库。我们基于多基因系统地理学的分析发现，雉鸡分为八个系统进化支系，其中位于横断山脉的支系是雉鸡的祖先类群。推测雉鸡起源于中国西南部，从中、晚更新世开始向亚洲腹地和东亚地区扩散。青藏高原的隆起导致了亚洲内陆的干旱区及东亚南亚季风区的形成，山脉、沙漠的扩张促进中亚地区四个雉鸡支系的斑块化分布。在东亚地区，雉鸡呈东、西部分化以及岛屿促进了东部群体分化为三个支系。基于“隔离-迁移”模型估算支系之间的基因流，概括为邻域支系之间存在显著基因流和不同程度的基因渐渗，而异域支系之间存在较弱的基因流或者完全阻隔。除了东亚东部的群体明显扩张和塔里木盆地群体群体下降外，其他5个进化支的雉鸡的有效群体大小在历史上都比较稳定。同时，取得了一只雉鸡torquatus亚种的雄性个体进行全基因组从头测序，首次获得了一只高质量的雉鸡基因组（contig N50为178 Kb，scaffold N50为10.1 Mb），以此作为参考基因组，获得11个群体107只个体的简化基因组数据，进行群体遗传分析，证实了中国雉鸡群体内部的自西向东存在显著的遗传多样性分化，在亚洲季风性气候与大陆性气候分界线即中国中部地区存在着基因渐渗，并发现了与气候变化、羽色相关的候选基因。本研究提供了雉鸡的大量基因组资源和分子标记，初步揭示了气候变化如何影响雉鸡的起源、分化和适应性进化，对保护和利用雉鸡种质资源具有重要应用价值。