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

Abstract

13 The black soldier fly (Hermetia illucens) is the prime species in the developing global 14 industry of insects as food and feed, but the genetic basis of its domestication has not been 15 studied. We obtained whole genome sequences for 54 individuals from both wild and captive 16 populations. We identified two genetic lineages at least 3 million years divergent, revealing 17 cryptic diversity within the species complex. Our study indicates that the most common 18 populations used for commercial and academic applications are primarily derived from just 19 one of these divergent lineages, originating from a wild North American progenitor. Despite 20 insect farming practices only reaching mass production scale over the past two decades, we 21 find that captive populations show strong genome-wide signatures of domestication. 22 Selective sweeps are found in multiple independently domesticated populations but are not 23 seen in wild populations and suggest five major domestication loci located on chromosomes 24 two, four and five. These regions contain development, behaviour, reproduction, metabolism 25 and immunity genes. Populations experiencing independent domestication events, in the 26 early stages of domestication, also show evidence of convergent genome evolution with 27 repeated signatures of domestication in these same regions. Some limited evidence of gene 28 flow between divergent lineages was observed, as well as evidence of hybridisation from 29 domesticated populations into the wild. Our study reveals the genetic basis of ongoing 30 domestication and provides a genomic platform for breeding and genetic surveillance in this 31 novel agricultural species. 32 Keywords: domestication, hybridisation, cryptic species, selective sweeps, introgression, 33 artificial selection. Institute of Organic Agriculture (FiBL), Frick, Switzerland; 3Georgina Mace Centre for the Living Planet, Faculty of Natural Sciences, Imperial College London, London, UK; 4Tree of Life Programme, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; 5California Department of Food and Agriculture, Plant Pest Diagnostics Branch, Sacramento, CA, USA; 6Better Origin, Entomics Biosystems Limited, Cambridge, UK; 7Department of Genetics, University of Cambridge, Cambridge, UK 1 bioRxiv preprint doi: https://doi.org/10.1101/2023.10.21.563413; this version posted October 29, 2023. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 34