Evolution and epigenetic regulation of host plant choice in a specialised herbivore, the global crop pest seed beetle Callosobruchus maculatus

草食性昆虫作为粮食作物的害虫，在调节植物群落中起着重要的作用，对农业生态系统有很大的影响。近年来，我们目睹了“超级害虫”的反复爆发，这是一种多面手食草动物，它们迅速占领了新的地区，并能够以新的植物类型为食。然而，昆虫改变寄主植物摄食策略（在专门性和通用性之间）的机制在很大程度上是未知的。因此，为了预测和控制新出现的害虫暴发，现在发现昆虫能够获得新宿主耐受性的机制是及时和关键的。这个博士项目将采用实验进化、建模和生理操作实验，采用跨学科的方法来理解饮食专业化和泛化进化的机制。实验将使用Callosobruchus maculatus模型系统进行，Callosobruchus maculatus是一种储存在豆科植物上的世界性害虫，在其系统地理记录中有很好的宿主转移记录，并且可以获得良好的基因组资源（Arnqvist等人未发表）。我们小组最近的工作表明，DNA甲基化是该物种宿主偏好的重要调节因子，但我们还不知道这在整个进化时间和适应新宿主的过程中是如何运作的。我们目前在实验室中维持着该物种的几个实验系，它们已经进化到表达不同程度的饮食普遍性。利用这些现有的谱系，学生将：1)通过实验施加新的环境，允许多面手和专门家系在多代的时间里殖民新的资源。我们将使用“进化和重排序”类实验协议来监测多个种群中几代人的等位基因频率，从而产生时间序列数据。Kosiol小组为实验进化研究的轨迹设计了高斯过程模型，学生将使用该模型来评估与这些进化转变相关的等位基因分化模式。2)利用现有的高甲基化或低甲基化DNA的药物，学生将研究DNA甲基化在适应新资源中的功能作用。然后，学生将确定DNA甲基化或缺乏甲基化如何影响引入新资源后对选择的等位基因反应的性质。3)学生将评估与寄主植物转移相关的DNMT1 （DNA甲基化酶1，负责将DNA甲基化标签转移到新合成的DNA链上的酶）基因表达的进化变化，首次量化进化过渡期间DNA甲基化活性的时间变化。学生也将有机会进行有针对性的测序，以评估候选位点启动子区域DNA甲基化模式的进化变化（例如，从上面的1和2）。本研究结果将为发现新的害虫防治机制，特别是防止害虫入侵新的作物品种提供潜在的数据支持。这项研究还将为进化过程提供新的、普遍的见解。学生将在实验进化、基因组技术（湿实验室和生物信息学）和统计建模方面获得宝贵的可转移技能。

Herbivorous insects play important roles in regulating plant communities, and have large effects on agro-ecosystems as pests on food crops. In recent years, we have witnessed repeated outbreaks of 'super-pests', generalist herbivores that have rapidly colonised new regions and are capable of feeding on novel plant types. However, the mechanisms by which insects switch their host plant feeding strategies (between specialism and generalism) are largely unknown. Thus it is now timely and critical to discover the mechanisms by which insects can gain tolerance of novel hosts, in order to predict and contain emerging pest outbreaks. This PhD project will employ experimental evolution, modelling, and physiological manipulative experiments, taking an interdisciplinary approach to understanding the mechanisms by which dietary specialisation and generalisation evolve.Experiments will be run using the model system Callosobruchus maculatus, a worldwide pest on stored legumes with well documented host shifts in its phylogeographic record, and for which good genomic resources are available (Arnqvist et al. unpublished). Recent work in our group suggests that DNA methylation is an important regulator of host preference in this species, but we do not yet know how this operates throughout evolutionary time and in the process of adaptation to novel hosts. We are currently maintaining several experimental lines of this species in the laboratory, which have been evolved to express various degrees of dietary generalism. Using these existing lines, the student will:1) Experimentally impose novel environments which allow generalist and specialist lineages of C. maculatus to colonise novel resources over multiple generations. We will use an 'evolve and resequence' class of experimental protocols to monitor allele frequencies over the generations in multiple populations resulting in time-series data. The Kosiol group has devised Gaussian process models for the trajectories of experimental evolution studies, which the student will use to evaluate patterns of allelic divergence associated with these evolutionary transitions. 2) Using well-established drugs that can hyper- or hypo-methylate DNA, the student will examine the functional role of DNA methylation on adaptation to novel resources. The student will then identify how DNA methylation, or lack of it, affects the nature of the allelic response to selection following introduction of novel resources.3) The student will assess evolved shifts in gene expression of DNMT1 (DNA methyltransferase 1, the enzyme responsible for transferring DNA methylation tags to newly-synthesised strands of DNA) associated with host plant shifts, quantifying for the first time temporal variation in DNA methylation activity during evolutionary transitions. The student will also have the opportunity to conduct targeted sequencing to assess evolutionary changes in the patterns of DNA methylation in promoter regions of candidate loci (e.g., from 1&2, above).Results of this study will provide data with the potential to support the discovery of new pest control mechanisms, especially to prevent pests from invading new crop varieties. This study will also provide new, general insight into the evolutionary process. The student will gain valuable and transferrable skills in experimental evolution, genomic techniques (wet lab and bioinformatics) and statistical modelling.