Population genomics and domestication of the Black Soldier Fly (Hermetia illucens L.)

Our global food chain is under considerable threat from a growing human population and climate change. Improving food security requires an increase in sustainable agricultural practices to alleviate this threat. Recent development of an insect livestock industry has promoted a circular approach to producing food and feed through the bioremediation of organic wastes. Central to this novel industry, the black soldier fly, *Hermetia illucens*, an insect with a polyphagous diet, global distribution, and large population sizes has seen rapid uptake in agricultural activity. Improved knowledge of the evolutionary history, genetic diversity and potential for genetic improvement of this species will be fundamental to the success of this important industry. I investigate the role of domestication and its impact on the genome of *H. illucens*. I developed a suite of high-quality genomic resources for this novel agricultural system and used this to investigate the genomic landscape of an inbred *H. illucens* population. I obtained whole-genome sequences for a total of 54 *H. illucens* and an outgroup taxon, *Ptecticus aurifer*. Phylogenetic patterns provide evidence for previously undescribed cryptic diversity within *H. illucens*. Genome-wide insights into wild and captive populations revealed genomic signatures of domestication in captive populations across the globe. In addition, I identified several genomic regions associated with domestication which appear to converge in populations experiencing parallel selective pressures across the globe. After documenting genetic diversity, I performed phenotypic characterisation for several domesticated strains. This work revealed both genotype- and family-environment interactions which suggested a genetic and heritable basis for the high phenotypic variation observed within the species. I next carried out experimental evolution for increased pupal size in a replicated design. I achieved considerable genetic gain for this phenotype and identified complex trait interactions including a trade-off between pupal size and development time. I also optimised genetic modification using CRISPR/Cas9 to generate a transgenic line of *yellow H. illucens* mutants. I used this loss-of-function line to explore the role of *yellow* in mating behaviour in this novel system. This work combines genetic, phenotypic, behavioural and experimental evolution studies to lay the foundation for the advancement of *Hermetia illucens* as a globally important agricultural system.

I acknowledge the funding I received for this industry CASE studentship (BB/M011194/1) project which was awarded by the Biotechnology and Biological Sciences Research Council (BBSRC).