Genomics of diversity and adaptation in great tits (Parus major)

这个进化遗传学项目将使用最先进的基因组学工具来研究生态模式生物大山雀（Parus major）的自然选择特征。这项研究将集中在一个汇编的数据集上，其中超过50万个单核苷酸多态性（SNP）标记已经在来自欧洲和亚洲20多个不同的大山雀种群的2000只鸟中进行了分类。博士项目有几个目标：首先，将描述大山雀种群的遗传结构，以深入了解当代种群的进化史。其次，将确定高分化的基因组区域，以推断局部适应是如何发生的。最后，将通过确定哪些表型性状受到基因组区域的影响，通过自然选择进行适应性进化，来研究局部适应的原因。该研究项目将最先进的基因组学技术与艰苦的野生鸟类生态研究相结合，以解决进化遗传学的基本问题-数量性状的遗传结构，面对选择时遗传变异的维持，以及局部适应的遗传基础。在许多方面，这个项目可以被认为是著名的人类单体基因组计划的生态等级物，其目的是产生一个大山雀单体基因组图，首先描述一种野生脊椎动物。这项生物信息学研究将利用生态学家、遗传学家和基因组生物学家的合作网络，研究整个物种分布的大山雀种群。主要负责人Jon Slate与Kai Zeng（谢菲尔德大学）、Ben Sheldon（牛津大学）、Marcel Visser（荷兰生态研究所）和Martien Groenen（瓦赫宁根大学）合作研究大山雀种群遗传学。研究小组定期交换资源、数据集和想法。此外，Kanchon Dasmahaptara在利用下一代基因组学数据集了解鳞翅目，特别是蝴蝶的基因流动、适应、物种形成和适应性渗透方面具有相当的专业知识。

This evolutionary genetics project will use state-of-the-art genomics tools to study signatures of natural selection in an ecological model organism, the great tit (Parus major). The study will focus on a complied dataset, where more than 500,000 single nucleotide polymorphism (SNP) markers have been typed in >2000 birds, from more than 20 different great tit populations across Europe and Asia. The PhD project has several objectives: First, the genetic structure of great tit populations will be described, to gain insight into the evolutionary history of contemporary populations. Second, genomic regions of high divergence will be identified, to infer how local adaptation has occurred. Finally, the causes of local adaptation will be investigated by identifying which phenotypic traits are affected by regions of the genome that have undergone adaptive evolution by natural selection. The research project combines state-of-the-art genomics technology with painstaking ecological studies of wild birds, to address fundamental topics in evolutionary genetics - the genetic architecture of quantitative traits, the maintenance of genetic variation in the face of selection, and the genetic basis to local adaptation. In many ways the project can be thought of as an ecological equivalent of the famous human HapMap genome projects, with the aim to produce a great tit HapMap, to first describe a wild vertebrate. This bioinformatics research will make use of a collaboration network of ecologists, geneticists and genome biologists studying great tit populations across the species entire distribution. The primary supervisor Jon Slate collaborates on great tit population genetics with Kai Zeng (Sheffield), Ben Sheldon (Oxford), Marcel Visser (Netherlands Institute of Ecology) and Martien Groenen (Wageningen University). The research groups regularly exchange resources, datasets and ideas. In addition, the co-supervisor, Kanchon Dasmahaptara has considerable expertise in using next-generation genomics datasets to understand gene flow, adaptation, speciation and adaptive introgression in lepidoptera, especially in Heliconius butterflies.