Cryptic Diversity and Impacts of Domestication in the Black Soldier Fly ( Hermetia illucens ) Genome

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 major genetic clusters 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 sampled 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 hybridization 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.