Cryptic diversity and signatures of domestication in the Black Soldier Fly (Hermetia illucens)

The Black Soldier Fly (Hermetia illucens) is the main species in the developing global industry of insects as food and feed, but little is known about its natural diversity or the genetic basis of its domestication. We obtained whole genome sequences for 54 individuals from both wild and captive populations. We identified two genetic lineages at least 3 million years divergent, revealing cryptic diversity within the species. Our study indicates that the most common populations used for commercial and academic applications are primarily derived from just one of these lineages, likely originating from a wild North American progenitor. We find that captive populations show strong reductions in genetic diversity, consistent with genome-wide effects of population bottlenecks and drift associated with rearing in captivity. Some limited evidence of gene flow between divergent lineages was observed, as well as evidence of hybridisation from domesticated populations into the wild. Our study suggests that natural genetic diversity could provide important variation for industrial purposes in this novel agricultural species. Author SummaryAnimals and plants have been domesticated by humans over thousands of years, shaping their genomes and yielding beneficial or improved traits for agriculture. Insect farming has recently reached industrial scales in order to recycle organic wastes into feed and food grade material. The Black Soldier Fly is the flagship insect species in this novel agriculture sector. However, the understanding of its evolutionary history and the genetic impact of intense farming has not been well studied to date. We examined whole genomes from populations sampled from across the worldwide distribution of Black Soldier Fly to investigate the impact of domestication and reveal the evolutionary history of the species. We found that farmed populations show distinct genomic regions showing reduced variation that could represent signatures of selection or demographic effects. We also identify two distinct lineages of Black Soldier Fly that have been diverging for millions of years, comparable to divergence between different species in other insect groups, yet show evidence of genetic exchange, indicating a lack of reproductive incompatibility in the populations tested. This work is the first to describe the genetic impact of domestication in the Black Soldier Fly and provide evolutionary insights using whole genomes. These results imply that considerable wild diversity could be harnessed for improving agricultural efficiency.