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

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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 unpublished).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.