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

Abstract

AbstractThe black soldier fly (Hermetia illucens) is the prime species in the developing global industry of insects as food and feed, but the genetic basis of its domestication has not been studied. 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 complex. Our study indicates that the most common populations used for commercial and academic applications are primarily derived from just one of these divergent lineages, originating from a wild North American progenitor. Despite insect farming practices only reaching mass production scale over the past two decades, we find that captive populations show strong genome-wide signatures of domestication. Selective sweeps are found in multiple independently domesticated populations but are not seen in wild populations and suggest five major domestication loci located on chromosomes two, four and five. These regions contain development, behaviour, reproduction, metabolism and immunity genes. Populations experiencing independent domestication events, in the early stages of domestication, also show evidence of convergent genome evolution with repeated signatures of domestication in these same regions. 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 reveals the genetic basis of ongoing domestication and provides a genomic platform for breeding and genetic surveillance in this novel agricultural species.