The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species

Abstract Background The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA) and in order to gain insights into the phylogeography of the species. Results Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N = 1), Oriental (N = 4), and the Eastern Palearctic (N = 4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes. Conclusions Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species

Genetic diversity in a commercial black soldier fly, Hermetia illucens (Diptera: Stratiomydiae), population

Thesis (MSc)--Stellenbosch University, 2017.ENGLISH ABSTRACT: The applications of black soldier fly (BSF), Hermetia illucens, as a first-generation biotechnology address two global problems - the pressure on food security arising from unsustainable food production practices which exhausting fisheries resources by fishmeal production; and the vast accumulation of organic waste. Understanding the phenotypic and genetic changes experienced when establishing colonies of H. illucens is important for successfully establishing new colonies and managing already existing mass-rearing facilities. The aim of this study was to assess the changes in genetic diversity coupled with the phenotypic changes associated with colony establishment. Commercially-relevant phenotypic parameters were measured; including pupae weight, percentage eclosion, post-mating longevity, hatchability and egg clutch sizes over six successive generations (F0-F5). Hatchability, clutch size and pupae weight increased from F1 to F4, but a decline was apparent from F3 to F4. Post-mating longevity dramatically decreased from F1 (100%) to F4 (33%) and the F5 generation did not develop beyond the pre-pupae stage resulting in colony-collapse. The phenotypic changes can be explained by a combination of environmental, physiological and genetic effects. The positive trends observed during earlier generations (F0-F1) may reflect the population reacting to relaxed natural selection. While, at the end of the study period (F3-F5), natural selection in captivity resulted in a decrease in phenotypic variables. The colony collapse in the final generation, despite constant environmental conditions, possibly reflects the deleterious effects of random genetic drift and inbreeding depression. For the assessment of the genetic processes which may have resulted in the observed phenotypic changes, ten microsatellite markers were developed and characterised. Marker utility was tested on 37 wild individuals using three multiplex-PCR reactions. The number of alleles for each locus ranged from 4 to 21. Polymorphism information content ranged from 0.52 to 0.90, while observed and expected heterozygosity ranged from 0.30-0.65 and 0.55-0.91, respectively. Furthermore, the markers are useful in individual identification (PID = 1.2x10-11and PIDsib = 1.1x10-4) and parentage analysis (P1=1; P2 = 1). The markers proved useful in the assessment of genetic diversity and were used to understand the genetic mechanisms underlying phenotypic trends previously described. The assessment of genetic diversity revealed significant population differentiation as described by FST estimates across the experimental generations (P < 0.01), accompanied by a significant loss of genetic diversity. The final generation indicated a significantly higher number of private alleles and significantly lower observed heterozygosity in comparison to preceding generations (P < 0.05). Population bottlenecks and inbreeding were evident in the estimation of effective population size (Ne) and relatedness. Phenotypic parameters which significantly correlated (Pearson’s r) to changes in genetic diversity were pupation (%), clutch size, pupae weight and female post-mating longevity (P < 0.05). Results indicate the effects of inbreeding depression and genetic drift were amplified by a decrease in effective population size and increased relatedness amongst individuals. In summation, the assessment of changes in phenotypic measurements and genetic diversity during the establishment of an H. illucens colony, gave valuable insight into the genetic processes which occur during colony establishment; and are applicable to colony establishment and the management of already existing colonies.AFRIKAANSE OPSOMMING: Die toepassings van Hermetia illucens as 'n eerste-generasie biotegnologie is daarop gemik om twee probleme op te los; die druk op voedselsekerheid wat voortspruit uit onvolhoubare voedselproduksiepraktyke (bv. die uitputting van visseryhulpbronne om vismeel te produseer) en die opeenhoping van organiese afval. Dit is van waardevolle belang om die verandering van kommersiële-relevante fenotipes en mate van genetiese diversiteit tydens kolonie-stigting in H. illucens te verstaan en toe te pas wanneer nuwe kolonies gestig word of om reeds bestaande kolonies te bestuur. Die doel van hierdie studie was om die fenotipiese en genetiese veranderinge tydens kolonie-stigting te bestudeer. Kommersiële-relevante fenotipiese mates soos aanwysers van kolonie-fiksheid, -vrugbaarheid en -gesondheid was gemeet, insluitende papie-gewig, langslewendheid, uitbroeivermoë van eiers en eier-broeiselgroottes. Hierdie eienskappe was gemeet oor ses opeenvolgende geslagte (F0-F5). Uitbroeivermoë, eierbroeiselgroottes en papiegewig het toegeneem vanaf F1 tot F4, maar 'n afname word waargeneem vanaf F3 tot F4 vir al drie veranderlikes. Die langslewendheid van wyfies het ook dramaties afgeneem van F1 (100%) tot F4 (33%) en die F5 geslag het nie verder as die voor-papiese stadium ontwikkel nie, wat gelei het tot die ineenstorting van die kolonie. Die tendense in fenotipiese veranderinge kan verklaar word deur 'n kombinasie van omgewings-, fisiologiese- en genetiese effekte. Die positiewe tendense tydens vroeëre geslagte (F0-F1) kan toegeskryf word aan geleidelike aanpassing tot die kunsmatige omgewing. Daarteen, kan die afname in fenotipiese veranderlikes tydens die einde van die studietydperk (F3-F5) veroorsaak word deur die kolonie-onderhoudstrategie. Die ineenstorting van die kolonie in die sesde generasie, ten spyte van voortdurende konstante omgewingstoestande, verwys na die nadelige gevolge van genetiese drywing en gevolglike intelingsdepressie. Die volgende doelwit was om gereedskap te ontwikkelvir die ondersoek van genetiese verandering tydens massa-grootmaak. 'n Paneel van tien mikrosatelliet merkers was ontwikkel en gekarakteriseer. Die toepassing van mikrosatelliet genotipering was getoets in 37 wilde individue gdeur middel van drie multipleks-Polymerase Ketting Reaksie (PKR)-reaksies. Die aantal allele vir elke lokus het gewissel van 4 tot 21. Polimorfisme inligtinginhoud het gewissel van 0.52 tot 0.90, terwyl waargeneme en verwagte heterosigositeit gewissel het tussen 0.30-0.65 en 0.55-0.91, onderskeidelik. Die merkers was nuttig vir individuele identifikasie (PID = 1.2x10-11 en PIDsib = 1.1x10-4) asook ouerskap-analise (P1 = 1; P2 = 1). Die merkers wat hier aangebied word, sal nuttig wees vir verskeie toepassings, insluitend die beoordeling van genetiese diversiteit tydens die stigting van H. illucens kolonies. Die merkers was in die huidige studie gebruik om die geniese meganismes wat fenotipiese tendense dryf, te ondersoek. Betekenisvolle populasie-differensiasie soos beskryf deur FST skattings oor die eksperimentele geslagte (P < 0.01) was waargeneem, tesame met 'n beduidende verlies van alleliese rykheid en heterosigositeit. Die finale geslag het ook 'n aansienlike groter aantal private allele en laer heterosigositeit getoon, in vergelyking met vorige geslagte (P < 0.05). Die berekening van effektiewe populasiegrootte (Ne) en ondersoek na verwantskap dui op ʼn populasie bottelnek en inteling. Fenotipiese mates wat betekenisvolle korrelasier (Pearson se r) met veranderinge in genetiese diversiteit getoon het, was pupasie (%), eier-broeiselgrootte, papie-gewig en langslewendheid van wyfies na paring (P < 0.05). Die resultate dui aan dat die gevolge van intelingsdepressie en genetiese drywing versterk is deur 'n toenemende verwantskap tussen individue en klein effektiewe populasiegrootte. Ten slotte, die bevindinge van hierdie studie, sal nuttig wees in die toekomstige vestiging van H. illucens kolonies, asook vir die bestuur van reeds bestaande kolonies

Patterns of Genetic Diversity and Mating Systems in a Mass-Reared Black Soldier Fly Colony

The black soldier fly (BSF), Hermetia illucens, is a promising candidate for the emerging insect farming industry with favourable characteristics for both bioremediation and production of animal delivered nutritive and industrial compounds. The genetic management of commercial colonies will become increasingly important for the sustainability of the industry. However, r-selected life history traits of insects pose challenges to conventional animal husbandry and breeding approaches. In this study, the long-term genetic effects of mass-rearing were evaluated as well as mating systems in the species to establish factors that might influence genetic diversity, and by implication fitness and productivity in commercial colonies. Population genetic parameters, based on microsatellite markers, were estimated and compared amongst two temporal wild sampling populations and four generations (F28, F48, F52, and F62) of a mass-reared colony. Furthermore, genetic relationships amongst mate pairs were evaluated and parentage analysis was performed to determine the oc-currence of preferential mate choice and multiple paternity. The mass-reared colony showed a reduction in genetic diversity and evidence for inbreeding with significant successive generational genetic differentiation from the wild progenitor population. Population-level analysis also gave the first tentative evidence of positive assortative mating and genetic polyandry in BSF. The homoge-neity of the mass-reared colony seems to result from a dual action caused by small effective popu-lation size and increased homozygosity due to positive assortative mating. However, the high ge-netic diversity in the wild and a polyandrous mating system might suggest the possible restoration of diversity in mass-reared colonies through augmentation with the wild population