Evolution under Domestication: Genetic differentiation in black soldier fly ( Hermetia illucens ) populations subjected to recent selective breeding

The black soldier fly (BSF; Hermetia illucens ) is widely utilized in commercial and research applications for waste bioconversion and sustainable protein production. However, prolonged captivity and artificial selection can shape genetic diversity, potentially influencing adaptability and long-term population stability. This study examined how recent selective breeding, genetic drift, and relaxed selection have influenced genetic differentiation in BSF populations over a short timeframe. Using mitochondrial cytochrome oxidase 1 ( CO1 ) and genome-wide RAD sequencing, population structure, heterozygosity, and selection signatures across eleven BSF populations, including selectively bred, wild-derived, and commercial strains were analysed. Results revealed that rapid genetic shifts have occurred within selectively bred populations (LA to LE) over ∼5 years, driven by artificial selection, subsequent relaxation, and environmental adaptation. The decline in effective population size (Ne) observed post-COVID-19 suggests recent bottlenecks, which may have further contributed to genetic drift and differentiation. While domesticated populations exhibited reduced genetic diversity and signs of inbreeding, wild-type population under short captivity retained higher heterozygosity. Genome-wide analyses further identified adaptive divergence among populations, with balancing selection and selective sweeps shaping genetic variation. Notably, despite shared ancestry, genetic differentiation persisted in selectively bred populations, reinforcing that selection and environmental pressures continue to influence their genomic landscape even after targeted selection was relaxed. These findings underscore the need to monitor genetic diversity in BSF breeding programs to maintain adaptability, enhance resilience, and mitigate risks from artificial selection and population collapse.