The genomics of thermal adaptation in a model pest insect

One sixth of the world's crop production is lost to pests and diseases each year. Rises in global temperatures are expected to cause dramatic shifts in the range and abundance of food pests, with potentially alarming consequences for global food supplies. To protect food security in the context of a changing climate therefore requires multidisciplinary research into how pest species adapt to their environments, drawing from the fields of molecular biology, genetics, ecology and evolutionary biology. Understanding how organisms adapt to high temperature is especially important, as temperature increases affect organisms in a wide range of ways, from their DNA to their complex social behaviours.

Combining the principles of Darwinian evolution with DNA sequencing is an excellent way of studying how pests adapt to temperature. Pest species usually have very short life-cycles, so can evolve rapidly in response to changing temperatures. Studying how pests evolve in response to temperature using DNA sequencing is a promising way forward because i) many of the characteristics and processes thought to be important for how pests adapt to temperature, such as body size, development and stress response, have a genetic basis; and ii) it will enable us to identify new genes, and new biological processes, involved in adapting to climate. At present, however, we know very little about what kinds of genes are involved in adapting to temperature, and less still about how rapidly these genes can evolve and allow pests to spread.

I will study how food pests adapt to temperature. My study organism will be the red flour beetle, a major pest of stored grain that causes enormous amounts of wheat, rice and corn to be discarded each year. It is also a "model species" for DNA research, with detailed genetic information available, and is easy to rear and study in the laboratory. I will study how red flour beetles evolve in response to extreme temperatures in real time, using replicated populations that have been maintained in the laboratory at high temperature for 60 generations. By sequencing the genomes of individual flour beetles adapted to living at extreme temperatures, I will identify the genes and biological processes that govern adaptation to temperature, and find out how these genes interact with one another. Additionally, because I have samples available from every generation since this experiment was set up, I will be able to look at how genes involved in adaptation to temperature evolve over time, and in doing so determine how rapidly these important genes can respond to changing temperature.

The proposed research will give us a better understanding of how DNA enables individuals and populations adapt to their environments. And, importantly, it will help us generate better predictions of where and when food pests are likely to spread as the global climate continues to change.

Understanding how pests adapt and respond to temperature at a genetic level is essential for maintaining food security in a changing climate. Changes in environmental temperature are expected to result in adaptive changes in genetically controlled traits, so determining the mechanistic basis of these changes will significantly improve models of when and where pest species are likely to spread. However, we still lack fundamental understanding of what types of genes and biological processes are involved in adapting to climate, how rapidly organisms are able to temperature from standing variation, and how genetic architecture influences adaptation to climate.

I will study the genomic basis of adaptation to temperature in the red flour beetle (Tribolium castaneum), a globally significant pest of stored products that is predicted to spread dramatically due to climate change. T. castaneum is also a model organism for genetic and developmental research, with a well annotated reference genome. I will use long-term, controlled selection lines that will have been maintained at high temperature for 60 generations. I will sequence individual genomes from these lines using a novel and cost-effective library preparation technique combined with low coverage sequencing. Using these data I will test how natural selection from extreme temperature shapes patterns of genomic variation in real time, and identify how linkage among genes, for example due to chromosomal inversions, influences genomic responses to extreme temperature. I will then use time-series analysis to map trajectories of genetic regions involved in adaptation to temperature, and determine how rapidly these key genetic regions evolve under natural selection. Finally, I will use experimentally manipulated gene flow to break up associations between genes under selection and linked neutral sites, which will enable me to identify the genes and biological processes involved in adaptation to temperature.

This proposal has potential for significant impact, both in terms of content and reach. First, because T. castaneum is an economically significant pest insect, research into the mechanistic basis of adaptation to temperature has potential benefits for industry in terms of pest management. Second, using a model insect to understand adaptation to temperature has important implications for how invasive species, as well as species of conservation concern, may respond to climate change. This proposal is therefore of relevance to conservation organisations and charities. Finally, this proposal is relevant to the general public, who are highly interested in both evolution and climate change, but are rarely exposed to how these two fields are inextricably linked.

I will register for schemes to interact with local schools, the public and policy makers (e.g. the Royal Society's pairing scheme). I will also organise a one-day symposium called "Controlling stored product pests: evidence-based approaches", with invited talks from pest-management companies, local authorities and academics. Finally, I will create a public performance, called 'Sex, Death and Global warming', which will take an informal approach to explaining the importance of evolution in the global warming debate, in an accessible way. I will present this talk at UEA, local venues, and national 'Skeptics in the Pub' meetings. I will accompany the talk with a series of non-academic articles on aspects of evolution and climate change, to be pitched to leading popular science publications. I have experience in communicating science to a wide range of non-academic audiences, both orally and in writing. This experience, combined with the excellent facilities for delivering impact at UEA, will ensure that the proposed activities reach their full potential.