Genetic differentiation in domesticated black soldier fly (Hermetia illucens) populations

The black soldier fly (BSF, Hermetia illucens) is widely used for waste bioconversion and sustainable protein production. However, domestication and prolonged captive rearing can rapidly alter genetic diversity and population structure. This study investigated how selective breeding, genetic drift, and relaxed selection have shaped genomic variation and effective population size in multiple BSF populations. Using genome-wide restriction site-associated DNA sequencing, we analysed population structure, heterozygosity, and selection signatures across 11 BSF populations, including 1 long-term domesticated line, 5 selectively bred lines (Line A to Line E), 3 wild-derived populations, and 2 commercial strains.

Despite shared origins, lines LA to LE diverged rapidly within 6 years. Principal component analysis and ADMIXTURE clustering (K = 11) revealed that LC to LE retained close genetic affinity, while LA and LB diverged markedly from each other and LC-LE. Demographic reconstructions using Stairway Plot showed that effective population sizes increased during the initial homogenized selective breeding phase (2018-2019) but declined after 2022, consistent with bottlenecks and relaxed selection. Wild-derived populations maintained higher heterozygosity and lower inbreeding coefficients than domesticated lines. Finally, genome-wide analyses identified 133 candidate genes under selection, including signatures of balancing selection and selective sweeps, reflecting divergent evolution under domestication.

These findings demonstrate that genetic differentiation occurs rapidly in BSF populations under domestication, driven by artificial selection, relaxation, genetic drift, and environmental adaptation. These results highlight the need for genetic monitoring in breeding programmes, including maintenance of large founder populations, periodic genetic assessment, and genetic rescue to preserve adaptive potential and reduce inbreeding risks.