Butler, J.M., 2014. Advanced topics in forensic DNA typing: interpretation. Academic Press, San Diego, CA.

Caballero, A., Bravo, I. and Wang, J., 2017. Inbreeding load and purging: implications for the short-term survival and the conservation management of small populations. Heredity 118: 177-185. https://doi.org/10.1038/hdy.2016.80

Cai, M., Li, L., Zhao, Z., Zhang, K., Li, F., Yu, C., Yuan, R., Zhou, B., Ren, Z., Yu, Z. and Zhang, J., 2022. Morphometric characteristic of black soldier fly (Hermetia illucens) Wuhan strain and its egg production improved by selectively inbreeding. Life 12. https://doi.org/10.3390/life12060873

Cai, Z., Hansen, L.S., Laursen, S.F., Nielsen, H.M., Bahrndorff, S., Tomberlin, J.K., Kristensen, T.N., Sørensen, J.G. and Sahana, G., 2024. Whole-genome sequencing of two captive black soldier fly populations: Implications for commercial production. Genomics: 110891.

Calfee, E., Agra, M.N., Palacio, M.A., Ramírez, S.R. and Coop, G., 2020. Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas. PLoS Genetics 16: e1009038.

Calus, M.P.L., Berry, D.P., Banos, G., Haas, Y.d. and Veerkamp, R.F., 2013. Genomic selection: the option for new robustness traits? Advances in Animal Biosciences 4: 618-625. https://doi.org/10.1017/S2040470013000186

Campbell, J.F., Athanassiou, C.G., Hagstrum, D.W. and Zhu, K.Y., 2022. *Tribolium castaneum*: A Model Insect for Fundamental and Applied Research. Annual Review of Entomology 67: 347-365. https://doi.org/10.1146/annurev-ento-080921-075157

Cantarel, B.L., Coutinho, P.M., Rancurel, C., Bernard, T., Lombard, V. and Henrissat, B., 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Research 37: D233-D238. https://doi.org/10.1093/nar/gkn663

Carter, M.J., Wilson, A.J., Moore, A.J. and Royle, N.J., 2019. The role of indirect genetic effects in the evolution of interacting reproductive behaviors in the burying beetle, *Nicrophorus vespilloides*. Ecology and Evolution 9: 998-1009. https://doi.org/10.1002/ece3.4731

Casillas, S. and Barbadilla, A., 2017. Molecular population genetics. Genetics 205: 1003-1035. https://doi.org/10.1534/genetics.116.196493

Castillo, D.M. and Barbash, D.A., 2017. Moving speciation genetics forward: modern techniques build on foundational studies in *Drosophila*. Genetics 207: 825-842. https://doi.org/10.1534/genetics.116.187120

Castillo-Juárez, H., Campos-Montes, G.R., Caballero-Zamora, A. and Montaldo, H.H., 2015. Genetic improvement of Pacific white shrimp [*Penaeus (Litopenaeus) vannamei*]: perspectives for genomic selection. Frontiers in Genetics 6: 93. https://doi.org/10.3389/fgene.2015.00093

Cavalli-Sforza, L.L. and Edwards, A.W., 1967. Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics 19: 233-257.

Chakravarthy, A.K., Jayasimha, G.T., Rachana, R.R. and Rohini, G., 2016. Insects as Human Food. In: Chakravarthy, A.K. and Sridhara, S. (eds.) Economic and ecological significance of arthropods in diversified ecosystems: sustaining regulatory mechanisms. Springer, Singapore, pp. 133-146. https://doi.org/10.1007/978-981-10-1524-3_7

Châline, N., Ratnieks, F.L., Raine, N.E., Badcock, N.S. and Burke, T., 2004. Non-lethal sampling of honey bee, Apis mellifera, DNA using wing tips. Apidologie 35: 311-318.

Chapuis, M.-P., Loiseau, A., Michalakis, Y., Lecoq, M., Franc, A. and Estoup, A., 2009. Outbreaks, gene flow and effective population size in the migratory locust, *Locusta migratoria*: a regional-scale comparative survey. Molecular Ecology 18: 792-800. https://doi.org/10.1111/j.1365-294X.2008.04072.x

Chapuis, M.-P., Pélissié, B., Piou, C., Chardonnet, F., Pagès, C., Foucart, A., Chapuis, E. and Jourdan-Pineau, H., 2021. Additive genetic variance for traits least related to fitness increases with environmental stress in the desert locust, *Schistocerca gregaria*. Ecology and Evolution 11: 13930-13947. https://doi.org/10.1002/ece3.8099

Chapuis, M.-P., Plantamp, C., Blondin, L., Pagès, C., Vassal, J.-M. and Lecoq, M., 2014. Demographic processes shaping genetic variation of the solitarious phase of the desert locust. Molecular Ecology 23: 1749-1763. https://doi.org/10.1111/mec.12687

Chapuis, M.P., Raynal, L., Plantamp, C., Meynard, C.N., Blondin, L., Marin, J.M. and Estoup, A., 2020. A young age of subspecific divergence in the desert locust inferred by ABC random forest. Molecular Ecology 29: 4542-4558.

Charlesworth, B. and Charlesworth, D., 1999. The genetic basis of inbreeding depression. Genetical Research 74: 329-340. https://doi.org/10.1017/S0016672399004152

Chen, B., Kou, Z., Jiang, Y., Luo, X., Li, P., Sun, K., Wang, W., Huang, Y. and Wang, Y., 2023. Intersex is required for female sexual development in *Hermetia illucens*. Insect Science 30: 901-911. https://doi.org/10.1111/1744-7917.13179

Cheng, J.Y., Stern, A.J., Racimo, F. and Nielsen, R., 2021. Detecting selection in multiple populations by modeling ancestral admixture components. Molecular Biology and Evolution 39: msab294. https://doi.org/10.1093/molbev/msab294

Choi, Y.J., Yi, J., Lee, C.-J., Kim, J.-W., Jeon, M.-J., Park, J.-S. and Cho, S.-J., 2022. Development of markers using microsatellite loci of two rove beetle species, *Paederus fuscipes* Curtis and *Aleochara (Aleochara) curtula* Goeze (Coleoptera: Staphylinidae), followed by analyses of genetic diversity and population structure. *Genes and Genomics* 44: 1471-1476.
Clarkson, C.S., Weetman, D., Essandoh, J., Yawson, A.E., Maslen, G., Manske, M., Field, S.G., Webster, M., Antão, T., MacInnis, B., Kwiatkowski, D. and Donnelly, M.J., 2014. Adaptive introgression between *Anopheles* sibling species eliminates a major genomic island but not reproductive isolation. Nature Communications 5: 4248. https://doi.org/10.1038/ncomms5248

Collard, B.C. and Mackill, D.J., 2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society London B: Biological Sciences 363: 557-572.

Colleau, J. and Moureaux, S., 2006. Gestion optimisée de la parenté et de la consanguïté dans les programmes de sélection des bovins laitiers. INRAE Productions Animales 19: 3-14.

Conner, J.K. and Hartl, D.L., 2004. A primer of ecological genetics, 425. Sinauer Associates, Sunderland, MA.

Costa, C., Lodesani, M. and BiBenefeld, K., 2012. Differences in colony phenotypes across different origins and locations: evidence for genotype by environment interactions in the Italian honeybee (*Apis mellifera ligustica*)? Apidologie 43: 634-642. https://doi.org/10.1007/s13592-012-0138-9

Costagli, S., Abenaim, L., Rosini, G., Conti, B. and Giovannoni, R., 2024. De Novo Genome Assembly at Chromosome-Scale of *Hermetia illucens* (Diptera: Stratiomyidae) via PacBio and Omni-C Proximity Ligation Technology. Insects 15: 133. https://doi.org/10.3390/insects15020133

Coudron, C.L., Adamaki-Sotiraki, C., Yakti, W., Pascual, J.J., Wicklicky, V., Sandrock, C., Van Peer, M., Athanassiou, C., Peguero, D., Rumbos, C.I., Naser El Deen, S., Veldkamp, T., Deruytter, D. and Cambra-López, M., 2025. Bugbook: Basic information and good practices on how to maintain stock populations for *Tenebrio molitor* and *Hermetia illucens* for research. Journal of Insects as Food and Feed. https://doi.org/10.1163/23524588-bja10240

Croze, M., Živković, D., Stephan, W. and Hutter, S., 2016. Balancing selection on immunity genes: review of the current literature and new analysis in *Drosophila melanogaster*. Zoology 119: 322-329. http://dx.doi.org/10.1016/j.zool.2016.03.004

Cruz-Tirado, J.P., Amigo, J.M. and Barbin, D.F., 2023. Determination of protein content in single black fly soldier (*Hermetia illucens* L.) larvae by near infrared hyperspectral imaging (NIR-HSI) and chemometrics. Food Control 143: 109266. https://doi.org/10.1016/j.foodcont.2022.109266

Csilléry, K., Blum, M.G., Gaggiotti, O.E. and François, O., 2010. Approximate Bayesian computation (ABC) in practice. Trends in Ecology and Evolution 25: 410-418.

de Carvalho, C.F., 2023. Epigenetic effects of climate change on insects. Current Opinion in Insect Science 57: 101029. https://doi.org/10.1016/j.cois.2023.101029

De Meeûs, T., McCoy, K.D., Prugnolle, F., Chevillon, C., Durand, P., Hurtrez-Bousses, S. and Renaud, F., 2007. Population genetics and molecular epidemiology or how to “débusquer la bête”. Infection, Genetics and Evolution 7: 308-332. https://doi.org/10.1016/j.meegid.2006.07.003

de Oliveira, D.S., Rosa, M.T., Vieira, C. and Loreto, E.L.S., 2021. Oxidative and radiation stress induces transposable element transcription in *Drosophila melanogaster*. Journal of Evolutionary Biology 34: 628-638. https://doi.org/10.1111/jeb.13762

De Wit, P., Pespeni, M.H., Ladner, J.T., Barshis, D.J., Seneca, F., Jaris, H., Therkildsen, N.O., Morikawa, M. and Palumbi, S.R., 2012. The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis. Molecular Ecology Resources 12: 1058-1067. https://doi.org/10.1111/1755-0998.12003

del Castillo, R.C., 2005. The quantitative genetic basis of female and male body size and their implications on the evolution of body size dimorphism in the house cricket *Acheta domesticus* (Gryllidae). Genetics and Molecular Biology 28: 843-848. https://doi.org/10.1590/S1415-47572005000500030

Deng, X., Liu, L., Deng, J. and Zha, X., 2023. Specific expression of antimicrobial peptides from the black soldier fly in the midgut of silkworms (*Bombyx mori*) regulates silkworm immunity. Insects 14: 443.

Deruytter, D., Coudron, C.L., Wicklicky, V., Naser El Deen, S., van Peer, M., Rumbos, C.I., Peguero, D., Adamaki-Sotiraki, C., Athanassiou, C.G., Veldkamp, T., Sandrock, C. and Yakti, W., 2025. BugBook: Considerations for designing and performing insect larvae production experiments. Journal of Insects as Food and Feed 11. https://doi.org/10.1163/23524588-bja10252

DiLeo, M.F., Nair, A., Kardos, M., Husby, A. and Saastamoinen, M., 2024. Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation. Proceedings of the National Academy of Sciences of the United States of America 121: e2309455121. https://doi.org/10.1073/pnas.2309455121

Diniz-Filho, J.A.F., Soares, T.N., Lima, J.S., Dobrovolski, R., Landeiro, V.L., de Campos Telles, M.P., Rangel, T.F. and Bini, L.M., 2013. Mantel test in population genetics. Genetics and Molecular Biology 36: 475-485.

Dong, Y., Xu, X., Qian, L., Kou, Z., Andongma, A.A., Zhou, L., Huang, Y. and Wang, Y., 2024. Genome-wide identification of yellow gene family in *Hermetia illucens* and functional analysis of yellow-y by CRISPR/Cas9. Insect Science 32: 115-126. https://doi.org/10.1111/1744-7917.13371

Donkpegan, A., Guigue, A., Boulanger, F., Brard-Fudulea, S., Haffray, P., Sourdioux, M. and Rouger, R., 2022. Development of genomic resources in black soldier fly (*Herme-
*tia illucens* L.) via throughput DNA pool sequencing. In: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP) Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. Wageningen Academic Publishers, Wageningen, pp. 2524-2527.

Dossey, A.T., Oppert, B., Chu, F.-C., Lorenzen, M.D., Scheffler, B., Simpson, S., Koren, S., Johnston, J.S., Kataoka, K. and Ide, K., 2023. Genome and genetic engineering of the house cricket (*Acheta domesticus*): a resource for sustainable agriculture. *Biomolecules* 13: 589.

Dowling, D.K. and Wolff, J.N., 2023. Evolutionary genetics of the mitochondrial genome: insights from *Drosophila*. *Genetics* 224. https://doi.org/10.1093/genetics/iyad036

Duffy, J.B., 2002. GAL4 system in *Drosophila*: A fly geneticist's swiss army knife. *Genesis* 34: 1-15. https://doi.org/10.1002/gene.10150

Dunkel, F.V. and Payne, C., 2016. Introduction to edible insects. In: Dossey, A.T., Morales-Ramos, J.A. and Rojas, M.G. (eds.) Insects as sustainable food ingredients. Academic Press, San Diego, CA, pp. 1-27. https://doi.org/10.1016/B978-0-12-802856-8.00001-6

Durand, E.Y., Patterson, N., Reich, D. and Slatkin, M., 2011. Testing for ancient admixture between closely related populations. *Molecular Biology and Evolution* 28: 2239-2252.

Edmands, S. and Timmerman, C.C., 2003. Modeling Factors Affecting the Severity of Outbreeding Depression. Conservation Biology 17: 883-892. https://doi.org/10.1046/j.1523-1739.2003.02026.x

Edwards, S.V., Robin, V., Ferrand, N. and Moritz, C., 2022. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. *Genome Biology and Evolution* 14: evab176.

Eleftheriou, E., Aury, J.-M., Vacherie, B., Istace, B., Belser, C., Noel, B., Moret, Y., Rigaud, T., Berro, F. and Gasparian, S., 2022a. Chromosome-scale assembly of the yellow meal-worm genome. *Open Research Europe* 1: 94.

Eleftheriou, E., Vacherie, B., Labadie, K., Athanassiou, C., Rigaud, T., Moret, Y., Lefebvre, T. and Madoui, M.-A., 2022b. *Tenebrio molitor* genomic structure among available populations. In: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP) Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. Wageningen Academic Publishers, Wageningen, pp. 2549-2551.

Ellen, E.D., Peeters, K., Verhoeven, M., Gols, R., Harvey, J.A., Wade, M.J., Dicke, M. and Bijma, P., 2016. Direct and indirect genetic effects in life-history traits of flour beetles (*Triolium castaneum*). *Evolution* 70: 207-217. https://doi.org/10.1111/evo.12835

English, G., Wanger, G. and Colombo, S.M., 2021. A review of advancements in black soldier fly (*Hermetia illucens*) production for dietary inclusion in salmonid feeds. *Journal of Agriculture and Food Research* 5: 100164. https://doi.org/10.1016/j.jafr.2021.100164

Eriksson, T. and Picard, C.J., 2021. Genetic and genomic selection in insects as food and feed. *Journal of Insects as Food and Feed* 7: 661-682. https://doi.org/10.3920/JIFF2020.0097

Evanno, G., Regnaut, S. and Goudet, J., 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. *Molecular Ecology* 14: 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x

Ewusie, E.A., Kwapong, P.K., Ofosu-Budu, G., Sandrock, C., Akumah, A., Nartey, E., Teye-Gaga, C., Agyarkwah, S.K. and Adamtey, N., 2018. Development of black soldier fly, *Hermetia illucens* (Diptera: Stratiomyidae) in selected organic market waste fractions in Accra, Ghana. *Asian Journal of Biotechnology and Bioresource Technology* 4: 1-16. https://doi.org/10.9734/AJB2T/2018/42371

Ewusie, E.A., Kwapong, P.K., Ofosu-Budu, G., Sandrock, C., Akumah, A.M., Nartey, E.K., Tetegaga, C. and Agyarkwah, S.K., 2019. The black soldier fly, *Hermetia illucens* (Diptera: Stratiomyidae): Trapping and culturing of wild colonies in Ghana. *Scientific African* 5: e00134. https://doi.org/10.1016/j.sciaf.2019.e00134

Excoffier, L. and Heckel, G., 2006. Computer programs for population genetics data analysis: a survival guide. *Nature Reviews Genetics* 7: 745-758. https://doi.org/10.1038/nrg1904

Excoffier, L. and Ray, N., 2008. Surfing during population expansions promotes genetic revolutions and structuration. *Trends in Ecology and Evolution* 23: 347-351.

Excoffier, L., Smouse, P.E. and Quattro, J.M., 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. *Genetics* 131: 479-491.

Extavour, C.G., Barry, S.K., Nakamura, T., Matsuoka, Y., Straub, C., Horch, H.W. and Extavour, C.G., 2019. Injecting *Grylulus bimaculatus* Eggs. *JoVE*: e59726. https://doi.org/10.3791/59726

Facchini, E., Shrestha, K., van den Boer, E., Junes, P., Sader, G., Peeters, K. and Schmitt, E., 2022. Long-Term Artificial Selection for Increased Larval Body Weight of *Hermetia illucens* in Industrial Settings. *Frontiers in genetics* 13: 865490. https://www.frontiersin.org/articles/10.3389/fgene.2022.865490/full

Faircloth, B.C., 2008. MSATCOMMANDER: Detection of microsatellite repeat arrays and automated, locus-specific primer design. *Molecular Ecology Resources* 8: 92-94.
Falconer, D.S., 1952. The Problem of Environment and Selection. The American Naturalist 86: 293-298. https://doi.org/10.1086/281736

Falconer, D.S. and MacKay, T.F.C., 1996. Introduction to Quantitative Genetics. Pearson Education, Harlow.

Falush, D., Stephens, M. and Pritchard, J.K., 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587. https://doi.org/10.1093/genetics/164.4.1567

Fernando, R. and Grossman, M., 1989. Marker assisted selection using best linear unbiased prediction. Genetics Selection Evolution 21: 467-477.

Fisher, R.A., 1958. Polymorphism and natural selection. Journal of Ecology 46: 289-293. https://doi.org/10.2307/2257396

Flasz, B., Ajay, A.K., Tarnawska, M., Babczyńska, A., Majchrzycki, Ł., Kędzierski, A., Napora-Rutkowski, Ł., Świerczek, E. and Augustyniak, M., 2023a. Multigenerational effects of graphene oxide nanoparticles on *Acheta domesticus* DNA stability. International Journal of Molecular Sciences 24: 12826. https://www.mdpi.com/1422-0067/24/16/12826

Flasz, B., Dziewięcka, M., Ajay, A.K., Tarnawska, M., Babczyńska, A., Kędzierski, A., Napora-Rutkowski, Ł., Ziętara, P., Świerczek, E. and Augustyniak, M., 2023b. Age- and lifespan-dependent differences in GO caused DNA damage in *Acheta domesticus*. International Journal of Molecular Sciences 24: 290. https://www.mdpi.com/1422-0067/24/1/290

Flatt, T., 2020. Life-history evolution and the genetics of fitness components in *Drosophila melanogaster*. Genetics 214: 3-48. https://doi.org/10.1534/genetics.119.300160

Fodor, I., Spoelstra, M., Calus, M.P.L. and Kamphuis, C., 2023. A systematic review of genotype-by-climate interaction studies in cattle, pigs, and chicken. Frontiers in Animal Science 4: 1324830. https://www.frontiersin.org/articles/10.3389/fanim.2023.1324830/full

Fong, J.J., Blom, M.P.K., Aowphol, A., McGuire, J.A., Sutcharit, C. and Soltis, P.S., 2023. Editorial: Recent advances in museomics: revolutionizing biodiversity research. Frontiers in Ecology and Evolution 11. https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2023.1188172

Fortes-Lima, C.A., Laurent, R., Thouzeau, V., Toupance, B. and Verdu, P., 2021. Complex genetic admixture histories reconstructed with Approximate Bayesian Computation. Molecular Ecology Resources 21: 1098-1117.

Fountain, T., Butlin, R.K., Reinhardt, K. and Otti, O., 2015. Outbreeding effects in an inbreeding insect, imex lectularius. Ecology and Evolution 5: 409-418. https://doi.org/10.1002/ece3.1373

Franco, A., Salvia, R., Scieuzo, C., Schmitt, E., Russo, A. and Falabella, P., 2022. Lipids from insects in cosmetics and for personal care products. Insects 13: 41.

François, O., Currat, M., Ray, N., Han, E., Excoffier, L. and Novembre, J., 2010. Principal component analysis under population genetic models of range expansion and admixture. Molecular Biology and Evolution 27: 1257-1268. https://doi.org/10.1093/molbev/msq010

François, O. and Jay, F., 2020. Factor analysis of ancient population genomic samples. Nature Communications 11: 4661. https://doi.org/10.1038/s41467-020-18335-6

Francuski, L. and Beukeboom, L.W., 2020. Insects in production – an introduction. Entomologia Experimentalis et Applicata 168: 422-431.

Frankham, R., 2005. Genetics and extinction. Biological Conservation 126: 131-140. https://doi.org/10.1016/j.biocon.2005.05.002

Frankham, R., Ballou, J.D. and Briscoe, D.A., 2004. A primer of conservation genetics. Cambridge University Press.

Frankham, R., Ballou, J.D., Eldridge, M.D.B., Lacy, R.C., Ralls, K., Dudash, M.R. and Fenster, C.B., 2011. Predicting the probability of outbreeding depression. Conservation Biology 25: 465-475. https://doi.org/10.1111/j.1523-1739.2011.01662.x

Franklin, I.R. and Frankham, R., 1998. How large must populations be to retain evolutionary potential? Animal Conservation 1: 69-70. https://doi.org/10.1111/j.1469-1795.1998.tb00228.x

Freeland, J.R., 2020. Molecular Ecology. Wiley, Chichester.

Freitas, M.V., Lemos, C.G., Ariede, R.B., Agudelo, J.F.G., Neto, R.R.O., Borges, C.H.S., Mastrochirico-Filho, V.A., Porto-Foresti, F., Iope, R.L., Batista, F.M., Brega, J.R.F. and Hashimoto, D.T., 2023. High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (*Piaractus mesopotamicus*). Aquaculture 562: 738847. https://doi.org/10.1016/j.aquaculture.2022.738847

Fu, C. and Yang, Y., 2023. iCAZyGFADB: an insect CAZyme and gene function annotation database. Database: baad086. https://doi.org/10.1093/database/baad086

Fu, G. and Yuna, Y., 2022. Phenotyping and phenomics in aquaculture breeding. Aquaculture and Fisheries 7: 140-146. https://doi.org/10.1016/j.aaf.2021.07.001

Fuentes-Pardo, A.P. and Ruzzante, D.E., 2017. Whole-genome sequencing approaches for conservation biology: advantages, limitations and practical recommendations. Molecular Ecology 26: 5369-5406. https://doi.org/10.1111/mec.14264

Gallagher, M.D. and Chen-Plotkin, A.S., 2018. The Post-GWAS era: from association to function. American Journal of Human Genetics 102: 717-730. https://doi.org/10.1016/j.ajhg.2018.04.002
Gamboa, M. and Watanabe, K., 2019. Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan. BMC Genomics 20: 84. https://doi.org/10.1186/s12864-019-5453-3

Gao, R., Li, C.-L., Tong, X.-L., Han, M.-J., Lu, K.-P., Liang, S.-B., Hu, H., Luan, Y., Zhang, B.-L. and Liu, Y.-Y., 2020. Identification, expression, and artificial selection of silkworm epigenetic modification enzymes. BMC Genomics 21: 1-11.

Gao, Z., Deng, W. and Zhu, F., 2019. Reference gene selection for quantitative gene expression analysis in black soldier fly (Hermetia illucens). PLoS ONE 14: e0221420.

Generalovic, T.N., McCarthy, S.A., Warren, I.A., Wood, J.M.D., Torrance, J., Sims, Y., Quail, M., Howe, K., Pipan, M., Durbin, R. and Jiggins, C.D., 2021. A high-quality, chromosome-level genome assembly of the black soldier fly (Hermetia illucens L.). G3 Genes|Genomes|Genetics 11: jkab085. https://doi.org/10.1093/g3journal/jkab085

Generalovic, T.N., Sandrock, C., Leonard, S., Schuldiner-Harpaz, T., Pipan, M., Welch, J.J. and Jiggins, C.D., 2025a. Variation in strain performance and estimates of heritability of body size indicate considerable potential for genetic improvement of the black soldier fly (Hermetia illucens). Entomologia Experimentalis et Applicata 173: 558-574. https://doi.org/10.1111/eea.13565

Generalovic, T.N., Sandrock, C., Roberts, B.J., Meier, J.I., Hauser, M., Warren, I.A., Pipan, M., Durbin, R. and Jiggins, C.D., 2023. Cryptic diversity and signatures of domestication in the Black Soldier Fly (Hermetia illucens). bioRxiv: 563413. https://www.biorxiv.org/content/early/2023/10/29/2023.10.21.563413

Generalovic, T.N., Zhou, W., Zhao, L.C., Leonard, S., Warren, I.A., Pipan, M. and Jiggins, C.D., 2025b. Repeatable phenotypic but not genetic response to selection on body size in the black soldier fly. bioRxiv: 640052. https://doi.org/10.1101/2025.02.25.640052

George, S., Gaddelapati, S.C. and Palli, S.R., 2019. Histone deacetylase 1 suppresses Krüppel homolog 1 gene expression and influences juvenile hormone action in Tribolium castaneum. Proceedings of the National Academy of Sciences of the United States of America 116: 17759-17764.

Giannetto, A., Oliva, S., Ceccon Lanes, C.F., de Araújo Pedron, F., Savastano, D., Baviera, C., Parrino, V., Lo Paro, G., Spanò, N.C., Cappello, T., Maisano, M., Mauceri, A. and Fasulo, S., 2020. Hermetia illucens (Diptera: Stratiomydae) larvae and prepupae: biomass production, fatty acid profile and expression of key genes involved in lipid metabolism. Journal of Biotechnology 307: 44-54. https://doi.org/10.1016/j.jbiotec.2019.10.015

Gianola, D. and Rosa, G.J.M., 2015. One hundred years of statistical developments in animal breeding. Annual Review

of Animal Biosciences 3: 19-56. https://doi.org/10.1146/annurev-animal-022114-110733

Gilbert, K.J., 2016. Identifying the number of population clusters with STRUCTURE: problems and solutions. Molecular Ecology Resources 16: 601-603. https://doi.org/10.1111/1755-0998.12521

Gilbert, K.J., Andrew, R.L., Bock, D.G., Franklin, M.T., Kane, N.C., Moore, J.S., Moyers, B.T., Renaut, S., Rennison, D.J. and Veen, T., 2012. Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the program STRUCTURE. Molecular Ecology 21: 4925-4930.

Glastad, K.M., Hunt, B.G. and Goodisman, M.A.D., 2019. Epigenetics in insects: genome regulation and the generation of phenotypic diversity. Annual Review of Entomology 64: 185-203. https://doi.org/10.1146/annurev-ento-011118-111914

Gligorescu, A., Chen, L., Jensen, K., Moghadam, N.N., Kristensen, T.N. and Sørensen, J.G., 2023. Rapid evolutionary adaptation to diet composition in the black soldier fly (Hermetia illucens). Insects 14: 821.

Gmel, A.I., Guichard, M., Dainat, B., Williams, G.R., Eynard, S., Vignal, A., Servin, B., Consortium, B. and Neuditschko, M., 2023. Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole-genome sequencing data. Ecology and Evolution 13: e9723.

Gold, M., Tomberlin, J.K., Diener, S., Zurbrugg, C. and Mathys, A., 2018. Decomposition of biowaste macronutrients, microbes, and chemicals in black soldier fly larval treatment: a review. Waste Management 82: 302-318. https://doi.org/10.1016/j.wasman.2018.10.022

Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W. and Fritz, M.H.-Y., 2010. A draft sequence of the Neandertal genome. Science 328: 710-722. https://doi.org/0.1126/science.1188021

Greenbaum, G., Templeton, A.R., Zarmi, Y. and Bar-David, S., 2014. Allelic richness following population founding events – a stochastic modeling framework incorporating gene flow and genetic drift. PLoS ONE 9: e115203.

Greenwood, M.P., Hull, K.L., Brink-Hull, M., Lloyd, M. and Rhode, C., 2021. Feed and host genetics drive microbiome diversity with resultant consequences for production traits in mass-reared black soldier fly (Hermetia illucens) larvae. Insects 12. https://doi.org/10.3390/insects12121082

Guichard, M., Dainat, B., Eynard, S., Vignal, A., Servin, B., Consortium, T.B. and Neuditschko, M., 2021. Identification of quantitative trait loci associated with calmness and gentleness in honey bees using whole-genome sequences. Animal Genetics 52: 472-481. https://doi.org/10.1111/age.13070

Guilliet, J., Baudouin, G., Pollet, N. and Filée, J., 2022. What complete mitochondrial genomes tell us about the evolu-
tionary history of the black soldier fly, *Hermetia illucens*. BMC Ecology and Evolution 22: 72. https://doi.org/10.1186/12862-022-02025-6

Gunther, D., Alford, R., Johnson, J., Neilsen, P., Zhang, L., Harrell, R. and Day, C., 2024. Transgenic black soldier flies for production of carotenoids. Insect Biochemistry and Molecular Biology 168: 104110. https://doi.org/10.1016/j.ibmb.2024.104110

Guo, B., Yin, J., Hao, W. and Jiao, M., 2019. Polyurethane foam induces epigenetic modification of mitochondrial DNA during different metamorphic stages of *Tenebrio molitor*. Ecotoxicology and Environmental Safety 183: 109461. https://doi.org/10.1016/j.ecoenv.2019.109461

Hagberg, L., Celemín, E., Irisarri, I., Hawlitschek, O., Bella, J.L., Mott, T. and Pereira, R.J., 2022. Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones. Molecular Ecology 31: 2384-2399. https://doi.org/10.1111/mec.16406

Hagler, J.R. and Jackson, C.G., 2001. Methods for marking insects: current techniques and future prospects. Annual Review of Entomology 46: 511-543. https://doi.org/10.1146/annurev.ento.46.1.511

Hamada, Y., Bando, T., Nakamura, T., Ishimaru, Y., Mito, T., Noji, S., Tomioka, K. and Ohuchi, H., 2015. Leg regeneration is epigenetically regulated by histone H3K27 methylation in the cricket *Gryllus bimaculatus*. Development 142: 2916-2927. https://doi.org/10.1242/dev.122598

Hansen, L.S., 2024. Selective breeding in insects for food and feed. Aarhus University, Aarhus.

Hansen, L.S., Bouwman, A.C., Sahana, G., Slagboom, M., Nielsen, H.M. and Ellen, E.D., 2025. Comparative evaluation of phenotypic, pedigree, and family-based selection in insect breeding using stochastic simulation. Animal 19: 101475. https://doi.org/10.1016/j.animal.2025.101475

Hansen, L.S., Laursen, S.F., Bahrndorff, S., Kargo, M., Sørensen, J.G., Sahana, G., Nielsen, H.M. and Kristensen, T.N., 2024a. Estimation of genetic parameters for the implementation of selective breeding in commercial insect production. Genetics Selection Evolution 56: 21. https://doi.org/10.1186/s12711-024-00894-7

Hansen, L.S., Laursen, S.F., Bahrndorff, S., Sørensen, J.G., Sahana, G., Kristensen, T.N. and Nielsen, H.M., 2024b. The unpaved road towards efficient selective breeding in insects for food and feed – a review. Entomologia Experimentalis et Applicata. https://doi.org/10.1111/eea.13526

Hartl, D.L., 2020. A primer of population genetics and genomics. Oxford University Press, Oxford.

Hawkins, G.A., 2017. Analysis of human genetic variations using DNA sequencing. In: Jalali, M., Saldanha, F.Y.L. and Jalali, M. (eds.) Basic Science Methods for Clinical

Researchers. Academic Press, Boston, MA, pp. 77-98. https://doi.org/10.1016/B978-0-12-803077-6.00005-9

Hayes, B.J., Daetwyler, H.D. and Goddard, M.E., 2016. Models for Genome × Environment interaction: examples in livestock. Crop Science 56: 2251-2259. https://doi.org/10.2135/cropsci2015.07.0451

Hayes, B.J., Lien, S., Nilsen, H., Olsen, H.G., Berg, P., Maceachern, S., Potter, S. and Meuwissen, T.H.E., 2008. The origin of selection signatures on bovine chromosome 6. Animal Genetics 39: 105-111. https://doi.org/10.1111/j.1365-2052.2007.01683.x

Hazarika, A.K. and Kalita, U., 2023. Human consumption of insects. Science 379: 140-141. https://doi.org/10.1126/science.abp8819

Hazkani-Covo, E., Zeller, R.M. and Martin, W., 2010. Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genetics 6: e1000834.

He, C., Holme, J. and Anthony, J., 2014. SNP genotyping: the KASP assay. Methods in Molecular Biology 1145: 75-86.

Hebert, P.D.N., Cywinska, A., Ball, S.L. and de Waard, J.R., 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B: Biological Sciences 270: 313-321. https://royalsocietypublishing.org/doi/abs/10.1098/rspb.2002.2218

Heckel, D.G., 2003. Genomics in pure and applied entomology. Annual Review of Entomology 48: 235-260. https://doi.org/10.1146/annurev.ento.48.091801.112624

Heckmann, L.-H., Sørensen, P.B., Krogh, P.H. and Sørensen, J.G., 2011. NORMA-Gene: a simple and robust method for qPCR normalization based on target gene data. BMC Bioinformatics 12: 250. https://doi.org/10.1186/1471-2105-12-250

Hedrick, P.W. and Garcia-Dorado, A., 2016. Understanding inbreeding depression, purging, and genetic rescue. Trends in Ecology and Evolution 31: 940-952. http://dx.doi.org/10.1016/j.tree.2016.09.005

Henderson, C.R., 1950. Estimation of genetic parameters. Annals of Mathematical Statistics 21: 309-310.

Hermisson, J. and Pennings, P.S., 2005. Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335-2352. https://doi.org/10.1534/genetics.104.036947

Heuel, M., Kreuzer, M., Gangnat, I., Frossard, E., Zurbrügg, C., Egger, J., Dortmans, B., Gold, M., Mathys, A., Jaster-Keller, J., Weigel, S., Sandrock, C. and Terranova, M., 2023. Low transfer of cadmium, lead and aflatoxin B1 to eggs and meat of laying hens receiving diets with black soldier fly larvae reared on contaminated substrates. Animal Feed Science and Technology 304: 115733. https://doi.org/10.1016/j.anifeedsci.2023.115733

Heuel, M., Kreuzer, M., Sandrock, C., Leiber, F., Mathys, A., Guggenbühl, B., Gangnat, I.D.M. and Terranova, M., 2022a.
Feeding value of black soldier fly larvae compared to soybean in methionine- and lysine-deficient laying hen diets. Journal of Insects as Food and Feed 8: 989-999. https://doi.org/10.3920/JIFF2021.0178

Heuel, M., Sandrock, C., Leiber, F., Mathys, A., Gold, M., Zurbrügg, C., Gangnat, I.D.M., Kreuzer, M. and Terranova, M., 2021. Black Soldier Fly larvae meal and fat can completely replace soybean cake and oil in diets for laying hens. *Poultry Science*: 101034. https://doi.org/10.1016/j.psj.2021.101034

Heuel, M., Sandrock, C., Leiber, F., Mathys, A., Gold, M., Zurbrügg, C., Gangnat, I.D.M., Kreuzer, M. and Terranova, M., 2022b. Black soldier fly larvae meal and fat as a replacement for soybeans in organic broilers diets: Effects on performance, body N retention, carcass, and meat quality. *British Poultry Science* 63: 650-661. https://doi.org/10.1080/00071668.2022.2053067

Hill, W.G. and Robertson, A., 1966. The effect of linkage on limits to artificial selection. *Genetics Research* 8: 269-294.

Hillary, V.E. and Ceasar, S.A., 2024. Using CRISPR-Cas9 to create knockout mutants in insects. *CABI Reviews* 19: 1. https://doi.org/10.1079/cabireviews.2024.0026

Hoffmann, L., Hull, K.L., Bierman, A., Badenhorst, R., Bester-van der Merwe, A.E. and Rhode, C., 2021. Patterns of genetic diversity and mating systems in a mass-reared black soldier fly colony. *Insects* 12. https://www.mdpi.com/2075-4450/12/6/480

Hohenlohe, P.A., Funk, W.C. and Rajora, O.P., 2021. Population genomics for wildlife conservation and management. *Molecular Ecology* 30: 62-82. https://doi.org/10.1111/mec.15720

Holliday, J., Hallerman, E. and Haak, D., 2019. Genotyping and sequencing technologies in population genetics and genomics. In: Rajora, O.P. (ed.) *Population genomics: Concepts, approaches and applications*. Springer, Cham, pp. 83-125.

Homchan, S., Kutanan, W. and Gupta, Y.M., 2024. A reproducible workflow for assembling the mitochondrial genome of *Acheta domesticus* (Orthoptera: Gryllidae). *Ecology and evolution* 14: e11696. https://doi.org/10.1002/ece3.11696

Houle, D., Govindaraju, D.R. and Omholt, S., 2010. Phenomics: the next challenge. *Nature Reviews Genetics* 11: 855-866. https://doi.org/10.1038/nrg2897

Hoy, M.A., 2019. Insect molecular genetics: an introduction to principles and applications. Elsevier, Amsterdam.

Hua, K., 2021. A meta-analysis of the effects of replacing fish meals with insect meals on growth performance of fish. *Aquaculture* 530: 735732. https://doi.org/10.1016/j.aquaculture.2020.735732

Huanca-Mamani, W., Rivera-Cabello, D. and Maita-Maita, J., 2015. A simple, fast, and inexpensive CTAB-PVP-Silica based method for genomic DNA isolation from single, small insect larvae and pupae. *Genetics and Molecular Research* 14: 8001-8007.

Hull, K.L., Greenwood, M.P., Lloyd, M., Bester-van der Merwe, A.E. and Rhode, C., 2023. Gene expression differentials driven by mass rearing and artificial selection in black soldier fly colonies. *Insect Molecular Biology* 32: 86-105. https://doi.org/10.1111/imb.12816

Hull, K.L., Greenwood, M.P., Lloyd, M., Brink-Hull, M., Bester-van der Merwe, A.E. and Rhode, C., 2024. Drivers of genomic diversity and phenotypic development in early phases of domestication in *Hermetia illucens*. *Insect Molecular Biology* 33: 756-776. https://doi.org/10.1111/imb.12940

Hwang, U.-W. and Kim, W., 1999. General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics. *Korean Journal of Parasitology* 37: 215-228. https://doi.org/10.3347/kjp.1999.37.4.215

Inoue, S., Watanabe, T., Hamaguchi, T., Ishimaru, Y., Miyawaki, K., Nikawa, T., Takahashi, A., Noji, S. and Mito, T., 2023. Combinatorial expression of ebony and tan generates body color variation from nymph through adult stages in the cricket, *Gryllus bimaculatus*. *PLoS ONE* 18: e0285934. https://doi.org/10.1371/journal.pone.0285934

Jensen, J.D., Kim, Y., DuMont, V.B., Aquadro, C.F. and Bustamante, C.D., 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. *Genetics* 170: 1401-1410.

Jensen, K., Kristensen, T., Heckmann, L.-H. and Sørensen, J., 2017. Breeding and maintaining high-quality insects. In: van Huis, A. and Tomberlin, J.K. (eds.) *Insects as food and feed: from production to consumtion*. Wageningen Academic Publishers, Wageningen, pp. 175-198.

Jensen, K., Thormose, S.F., Noer, N.K., Schou, T.M., Kargo, M., Gligorescu, A., Nørgaard, J.V., Hansen, L.S., Zaalberg, R.M., Nielsen, H.M. and Kristensen, T.N., 2025. Controlled and polygynous mating in the black soldier fly: advancing breeding programs utilizing quantitative genetic designs. *Journal of Insects as Food and Feed* 11: 1-11. https://doi.org/10.1163/23524588-bja10205

Ji, Y., Li, X., Ji, T., Tang, J., Qiu, L., Hu, J., Dong, J., Luo, S., Liu, S. and Frandsen, P.B., 2020. Gene reuse facilitates rapid radiation and independent adaptation to diverse habitats in the Asian honeybee. *Science Advances* 6: eabd3590.

Joosten, L., Lecocq, A., Jensen, A.B., Haenen, O., Schmitt, E. and Eilenberg, J., 2020. Review of insect pathogen risks for the black soldier fly (*Hermetia illucens*) and guidelines for reliable production. *Entomologia Experimentalis et Applicata* 168: 432-447.
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ron-
neberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A.,
Potapenko, A., Bridgland, A., Meyer, C., Kohl, S.A.A., Bal-
lard, A.J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain,
R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy,
E., Zielinski, M., Steinegger, M., Pacholska, M., Bergham-
mer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A.W.,
Kavukcuoglu, K., Kohli, P. and Hassabis, D., 2021. Highly
accurate protein structure prediction with AlphaFold.
Nature 596: 583-589. https://doi.org/10.1038/s41586-021-03819-2

Kadarmideen, H.N., 2014. Genomics to systems biology in ani-
mal and veterinary sciences: Progress, lessons and oppor-
tunities. Livestock Science 166: 232-248. https://doi.org/10.
1016/j.livsci.2014.04.028

Kamm, J., Terhorst, J., Durbin, R. and Song, Y.S., 2020. Effi-
ciently inferring the demographic history of many popu-
lations with allele count data. Journal of the American Sta-
tistical Association 115: 1472-1487. https://doi.org/10.1080
/01621459.2019.1635482

Kanaka, K., Sukhija, N., Goli, R.C., Singh, S., Ganguly, I.,
Dixit, S., Dash, A. and Malik, A.A., 2023. On the con-
cepts and measures of diversity in the genomics era. Cur-
rent Plant Biology 33: 100278. https://doi.org/10.1016/j.cpb
.2023.100278

Kapun, M., Mitchell, E.D., Kawecki, T.J., Schmidt, P. and Flatt, T., 2023. An Ancestral balanced inversion polymorphism confers global adaptation. Molecular Biology and Evolution 40: msad118. https://doi.org/10.1093/molbev/msad118

Kapun, M., Nunez, J.C., Bogaerts-Márquez, M., Murga-Moreno,
J., Paris, M., Outten, J., Coronado-Zamora, M., Tern, C.,
Rota-Stabelli, O. and Guerreiro, M.P.G., 2021. *Drosophila*
evolution over space and time (DEST): a new population
genomics resource. Molecular Biology and Evolution 38:
5782-5805. https://doi.org/10.1093/molbev/msab259

Kaur, S., Stinson, S.A. and di Cenzo, G.C., 2023. Whole genome assemblies of *Zophobas morio* and *Tenebrio molitor*. G3: Genes, Genomes, Genetics 13: jkad079.

Kawecki, T.J., Lenski, R.E., Ebert, D., Hollis, B., Olivieri, I. and Whitlock, M.C., 2012. Experimental evolution. Trends in Ecology and Evolution 27: 547-560. https://doi.org/10.1016/j.tree.2012.06.001

Kaya, C., Generalovic, T.N., Ståhls, G., Hauser, M., Samayoa,
A.C., Nunes-Silva, C.G., Roxburgh, H., Wohlfahrt, J., Ewusie,
E.A., Kenis, M., Hanboonsong, Y., Orozco, J., Carrejo, N.,
Nakamura, S., Gasco, L., Rojo, S., Tanga, C.M., Meier, R.,
Rhode, C., Picard, C.J., Jiggins, C.D., Leiber, F., Tomberlin,
J.K., Hasselmann, M., Blanckenhorn, W.U., Kapun, M. and
Sandrock, C., 2021. Global population genetic structure
and demographic trajectories of the black soldier fly, *Her-

metia illucens. BMC Biology 19: 94. https://doi.org/10.1186
/s12915-021-01029-w

Khamis, F.M., Ombura, F.L.O., Akutse, K.S., Subramanian, S.,
Mohamed, S.A., Fiaboe, K.K.M., Saijuntha, W., Van Loon,
J.J.A., Dicke, M., Dubois, T., Ekesi, S. and Tanga, C.M., 2020.
Insights in the global genetics and gut microbiome of
black soldier fly, *Hermetia illucens*: implications for ani-
mal feed safety control. Frontiers in Microbiology 11: 1538.
https://doi.org/10.3389/fmicb.2020.01538

Kidd, S., Sorrell, T. and Meyer, W., 2003. Isolation of two
molecular types of *Cryptococcus neoformans* var. *gattii*
from insect frass. Medical Mycology 41: 171-176.

Kikuchi, A., Nakazato, T., Ito, K., Nojima, Y., Yokoyama, T.,
Iwabuchi, K., Bono, H., Toyoda, A., Fujiyama, A., Sato, R.
and Tabunoki, H., 2017. Identification of functional enolase
genes of the silkworm *Bombyx mori* from public databases
with a combination of dry and wet bench processes. BMC
Genomics 18: 83. https://doi.org/10.1186/s12864-016-3455-y

Kimura, M., 1968. Evolutionary rate at the molecular level.
Nature 217: 624-626.

Klein, T.W., 1974. Heritability and genetic correlation: Sta-
tistical power, population comparisons, and sample size.
Behavior Genetics 4: 171-189. https://doi.org/10.1007
/BF01065758

Kortsmit, Y., Van der Bruggen, M., Wertheim, B., Dicke, M.,
Beukeboom, L. and Van Loon, J., 2023. Behaviour of two
fly species reared for livestock feed: optimising production
and insect welfare. Journal of Insects as Food and Feed 9:
149-169. https://doi.org/10.3920/JIFF2021.0214

Korunes, K.L. and Samuk, K., 2021. pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Molecular Ecology Resources 21: 1359-1368. https://doi.org/10.1111/1755-0998.13326

Kou, Z., Luo, X., Jiang, Y., Chen, B., Song, Y., Wang, Y., Xu, J., Tomberlin, J.K. and Huang, Y., 2023. Establishment of highly efficient transgenic system for black soldier fly (*Hermetia illucens*). Insect Science 30: 888-900. https://doi.org/10.1111/1744-7917.13147

Krafsur, E., Cummings, M., Endsley, M., Marquez, J. and Nason,
J., 2005. Geographic differentiation in the house fly esti-
mated by microsatellite and mitochondrial variation. Jour-
nal of Heredity 96: 502-512. https://doi.org/10.1093/jhered
/esi093

Kranzfelder, P., Ekrem, T. and Stur, E., 2016. Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae. Molecular Ecol-
ogy Resources 16: 353-363.

Kronenberger, J.A., Gerberich, J.C., Fitzpatrick, S.W., Broder,
E.D., Angeloni, L.M. and Funk, W.C., 2018. An experimen-
tal test of alternative population augmentation scenarios.
Conservation Biology 32: 838-848. https://doi.org/10.1111/cobi.13076

Kuehn, L.A., Lewis, R.M. and Notter, D.R., 2007. Managing the risk of comparing estimated breeding values across flocks or herds through connectedness: a review and application. *Genet. Sel. Evol.* 39: 225-247. https://doi.org/10.1051/gse:2007001

Kumar, H., Panigrahi, M., Chhotaray, S., Bhanuprakash, V., Shandilya, R., Sonwane, A. and Bhushan, B., 2018. Red flour beetle (*Tribolium castaneum*): from population genetics to functional genomics. *Vet World* 11: 1043-1046. https://doi.org/10.14202/vetworld.2018.1043-1046

Kurbalija, Z., Stamenkovic-Radak, M., Pertoldi, C. and Andjelkovic, M., 2010. Outbreeding causes developmental instability in *Drosophila subobscura*. *Evolutionary Ecology* 24: 839-864. https://doi.org/10.1007/s10682-009-9342-0

Lähteenmäki-Uutela, A., Marimuthu, S.B. and Meijer, N., 2021. Regulations on insects as food and feed: a global comparison. *Journal of Insects as Food and Feed* 7: 849-856.

Lander, E. and Kruglyak, L., 1995. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. *Nature Genetics* 11: 241-247. https://doi.org/10.1038/ng1195-241

Laudani, F., Campolo, O., Latella, I., Modafferi, A., Palmeri, V. and Giunti, G., 2024. Does *Hermetia illucens* recognize sibling mates to avoid inbreeding depression? *Entomologia Generalis*. http://dx.doi.org/10.1127/entomologia/2024/2746

Laursen, S.F., Hansen, L.S., Bahrndorff, S., Nielsen, H.M., Noer, N.K., Renault, D., Sahana, G., Sørensen, J.G. and Kristensen, T.N., 2021. Contrasting manual and automated assessment of thermal stress responses and larval body size in black soldier flies and houseflies. *Insects* 12. https://doi.org/10.3390/insects12050380

Laursen, S.F., Hansen, L.S., Bahrndorff, S., Nielsen, H.M., Sahana, G., Sørensen, J.G., Ørsted, M. and Kristensen, T.N., 2024. Genotype-by-environment interactions for mean performance and trait variation in house fly larvae reared on two diets. *Entomologia Experimentalis et Applicata*. https://doi.org/10.1111/eea.13530

Lavinia, P.D., Núñez Bustos, E.O., Kopuchian, C., Lijtmaer, D.A., García, N.C., Hebert, P.D.N. and Tubaro, P.L., 2017. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence. *PLoS ONE* 12: e0186845. https://doi.org/10.1371/journal.pone.0186845

Lawson, D.J., Van Dorp, L. and Falush, D., 2018. A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. *Nature Communications* 9: 3258.

Lecheta, M.C., Awde, D.N., O'Leary, T.S., Unfried, L.N., Jacobs, N.A., Whitlock, M.H., McCabe, E., Powers, B., Bora, K.,

Waters, J.S., Axen, H.J., Frietze, S., Lockwood, B.L., Teets, N.M. and Cahan, S.H., 2020. Integrating GWAS and Transcriptomics to Identify the Molecular Underpinnings of Thermal Stress Responses in *Drosophila melanogaster*. *Frontiers in Genetics* 11. https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00658

Lee, S.H., Goddard, M.E., Visscher, P.M. and van der Werf, J.H.J., 2010. Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits. *Genetics Selection Evolution* 42: 22. https://doi.org/10.1186/1297-9686-42-22

Legarra, A., Aguilar, I. and Misztal, I., 2009. A relationship matrix including full pedigree and genomic information. *Journal of Dairy Science* 92: 4656-4663. https://doi.org/10.3168/jds.2009-2061

Leite, N.A., Alves-Pereira, A., Corrêa, A.S., Zucchi, M.I. and Omoto, C., 2014. Demographics and Genetic Variability of the New World Bollworm (*Helicoverpa zea*) and the Old World Bollworm (*Helicoverpa armigera*) in Brazil. *PLoS ONE* 9: e113286. https://doi.org/10.1371/journal.pone.0113286

Lepais, O., Chancerel, E., Boury, C., Salin, F., Manicki, A., Taillebois, L., Dutech, C., Aissi, A., Bacles, C.F. and Daverat, F., 2020. Fast sequence-based microsatellite genotyping development workflow. *PeerJ* 8: e9085.

Leung, K., Beukeboom, L.W. and Zwaan, B.J., 2025. Inbreeding and outbreeding depression in wild and captive insect populations. *Annual Reviews Entomology* 70: 271-292. https://doi.org/10.1146/annurev-ento-022924-020221

Lewontin, R.C. and Krakauer, J., 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. *Genetics* 74: 175-195.

Li, J., Li, H., Jakobsson, M., Li, S., Sjödin, P. and Lascoux, M., 2012. Joint analysis of demography and selection in population genetics: where do we stand and where could we go? *Molecular Ecology* 21: 28-44.

Li, Y., 2021. Modern epigenetics methods in biological research. *Methods* 187: 104-113.

Liang, X., Duan, Q., Li, B., Wang, Y., Bu, Y., Zhang, Y., Kuang, Z., Mao, L., An, X. and Wang, H., 2024. Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep. *Proceedings of the National Academy of Sciences of the United States of America* 121: e2322291121.

Librado, P. and Orlando, L., 2022. Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics. *Bioinformatics* 38: 2070-2071. https://doi.org/10.1093/bioinformatics/btac046

Lillehammer, M., Bangera, R., Salazar, M., Vela, S., Erazo, E.C., Suarez, A., Cock, J., Rye, M. and Robinson, N.A., 2020. Genomic selection for white spot syndrome virus
resistance in whiteleg shrimp boosts survival under an
experimental challenge test. Scientific Reports 10: 20571.
https://doi.org/10.1038/s41598-020-77580-3

Lirakis, M. and Magalhães, S., 2019. Does experimental evolution produce better biological control agents? A critical review of the evidence. Entomologia Experimentalis et Applicata 167: 584-597. https://doi.org/10.1111/eea.12815

Liu, T., Li, Q., Kong, L. and Yu, H., 2017. Comparison of microsatellites and SNPs for pedigree analysis in the Pacific oyster *Crassostrea gigas*. Aquaculture International 25: 1507-1519.

Lo, I.H.Y. and Matthews, B.J., 2023. Design and validation of guide RNAs for CRISPR-Cas9 genome editing in mosquitoes. Cold Spring Harbor Protocols 9: pdb.top107688. https://doi.org/10.1101/pdb.top107688

Loewe, L. and Hill, W.G., 2010. The population genetics of mutations: good, bad and indifferent. Philosophical Transactions of the Royal Society B: Biological Sciences 365: 1153-1167. https://doi.org/10.1098/rstb.2009.0317

Lou, R.N., Jacobs, A., Wilder, A.P. and Therkildsen, N.O., 2021. A beginner's guide to low-coverage whole genome sequencing for population genomics. Molecular Ecology 30: 5966-5993.

Lourenço, F., Calado, R., Medina, I. and Ameixa, O.M., 2022. The potential impacts by the invasion of insects reared to feed livestock and pet animals in Europe and other regions: a critical review. Sustainability 14: 6361. https://doi.org/10.3390/su14106361

Lowe, W.H., Kovach, R.P. and Allendorf, F.W., 2017. Population genetics and demography unite ecology and evolution. Trends in Ecology and Evolution 32: 141-152. http://dx.doi.org/10.1016/j.tree.2016.12.002

Lu, C., Li, B., Zhao, A. and Xiang, Z., 2004. QTL mapping of economically important traits in Silkworm (Bombyx mori). Science in China Series C: Life Sciences 47: 477-484. https://doi.org/10.1007/BF03187107

Lu, L., Wan, Q., Xu, Y., Shen, H. and Yang, M., 2021. Proteomic study reveals major pathways regulating the development of black soldier fly. Journal of Proteome Research 20: 2216-2223. https://doi.org/10.1021/acs.jproteome.0c00736

Luikart, G., Ryman, N., Tallmon, D.A., Schwartz, M.K. and Allendorf, F.W., 2010. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics 11: 355-373.

Luo, Z., Yu, Y., Bao, Z., Xiang, J. and Li, F., 2022. Evaluation of genomic selection for high salinity tolerance traits in Pacific white shrimp *Litopenaeus vannamei*. Aquaculture 557: 738320. https://doi.org/10.1016/j.aquaculture.2022.738320

Ma, C., Huang, Z., Feng, X., Memon, F.U., Cui, Y., Duan, X., Zhu, J., Tettamanti, G., Hu, W. and Tian, L., 2024. Selective breed-

ing of cold-tolerant black soldier fly (*Hermetia illucens*)
larvae: Gut microbial shifts and transcriptional patterns.
Waste Management 177: 252-265. https://doi.org/10.1016/j
.wasman.2024.02.007

Ma, C., Yang, P., Jiang, F., Chapuis, M.P., Shali, Y., Sword, G.A. and Kang, L., 2012. Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust. Molecular Ecology 21: 4344-4358.

Ma, X., Christensen, O.F., Gao, H., Huang, R., Nielsen, B., Madsen, P., Jensen, J., Ostersen, T., Li, P., Shirali, M. and Su, G., 2021. Prediction of breeding values for group-recorded traits including genomic information and an individually recorded correlated trait. Heredity 126: 206-217. https://doi.org/10.1038/s41437-020-0339-3

Ma, X.Z., Cai, L.J., Wu, X.H., Zhao, S.Y., Li, C.B. and Deng, K.J., 2003. Overexpression of human genes in *Drosophila melanogaster* by using GAL4 UAS system. Acta Biochimica et Biophysica Sinica 35: 597-600.

Mackay, T.F.C., 2001. Quantitative trait loci in *Drosophila*. Nature Reviews Genetics 2: 11-20. https://doi.org/10.1038/35047544

Mackay, T.F.C., 2004. The genetic architecture of quantitative traits: lessons from *Drosophila*. Current Opinion in Genetics and Development 14: 253-257. https://doi.org/10.1016/j.gde.2004.04.003

Mackay, T.F.C., 2010. Mutations and quantitative genetic variation: lessons from *Drosophila*. Philosophical Transactions of the Royal Society B: Biological Sciences 365: 1229-1239. https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2009.0315

Mackay, T.F.C. and Huang, W., 2018. Charting the genotype-phenotype map: lessons from the *Drosophila melanogaster* Genetic Reference Panel. Wiley Interdisciplinary Review and Developmental Biology 7. https://doi.org/10.1002/wdev.289

MacLean, H.J., Hjort Hansen, J. and Sørensen, J.G., 2022. Validating the automation of different measures of high temperature tolerance of small terrestrial insects. Journal of Insect Physiology 137: 104362. https://doi.org/10.1016/j.jinsphys.2022.104362

Maji, S. and Garg, D., 2013. Progress in gene prediction: principles and challenges. Current Bioinformatics 8: 226-243. http://dx.doi.org/10.2174/1574893611308020011

Makkar, H.P.S., Tran, G., Henze, V. and Ankers, P., 2014. State-of-the-art on use of insects as animal feed. Animal Feed Science and Technology 197: 1-33. https://doi.org/10.1016/j.anifeedsci.2014.07.008

Malinsky, M., Svardal, H., Tyers, A.M., Miska, E.A., Genner, M.J., Turner, G.F. and Durbin, R., 2018. Whole-genome sequences of Malawi cichlids reveal multiple radiations
interconnected by gene flow. Nature Ecology and Evolution 2: 1940-1955.

Malmendal, A., Sørensen, J.G., Overgaard, J., Holmstrup, M., Nielsen, N.C. and Loeschcke, V., 2013. Metabolomic analysis of the selection response of *Drosophila melanogaster* to environmental stress: are there links to gene expression and phenotypic traits? Naturwissenschaften 100: 417-427.
https://doi.org/10.1007/s00114-013-1040-7

Marques de Castro, G., Hastenreiter, Z., Silva Monteiro, T.A., Martins da Silva, T.T. and Pereira Lobo, F., 2022. Cross-species prediction of essential genes in insects. Bioinformatics 38: 1504-1513. https://doi.org/10.1093/bioinformatics/btac009

Martin, S.H., Davey, J.W. and Jiggins, C.D., 2014. Evaluating the use of ABBA-BABA statistics to locate introgressed loci. Molecular Biology and Evolution 32: 244-257. https://doi.org/10.1093/molbev/msu269

Masel, J., 2011. Genetic drift. Current Biology 21: R837-R838.

Masuoka, Y., Cao, W., Jouraku, A., Sakai, H., Sezutsu, H. and Yokoi, K., 2022. Co-expression network and time-course expression analyses to identify silk protein regulatory factors in *Bombyx mori*. Insects 13: 131. https://doi.org/10.3390/insects13020131

Matsuoka, Y., Nakamura, T., Watanabe, T., Barnett, A.A., Tomonari, S., Ylla, G., Whittle, C.A., Noji, S., Mito, T. and Extavour, C.G., 2024. Establishment of CRISPR/Cas9-based knock-in in a hemimetabolous insect: targeted gene tagging in the cricket *Gryllus bimaculatus*. bioRxiv: 2021.2005.2010.441399. https://doi.org/10.1101/2021.05.10.441399

Mayo, O., 2008. A century of Hardy-Weinberg equilibrium. Twin Research on Human Genetics 11: 249-256. https://doi.org/10.1375/twin.11.3.249

Mei, Y., Jing, D., Tang, S., Chen, X., Chen, H., Duanmu, H., Cong, Y., Chen, M., Ye, X., Zhou, H., He, K. and Li, F., 2021. InsectBase 2.0: a comprehensive gene resource for insects. Nucleic Acids Research 50: D1040-D1045. https://doi.org/10.1093/nar/gkab1090

Meirmans, P.G., 2012. AMOVA-based clustering of population genetic data. Journal of Heredity 103: 744-750. https://doi.org/10.1093/jhered/ess047

Meirmans, P.G., 2015. Seven common mistakes in population genetics and how to avoid them. Molecular Ecology 24: 3223-3231. https://doi.org/10.1111/mec.13243

Meirmans, P.G. and Hedrick, P.W., 2011. Assessing population structure: FST and related measures. Molecular Ecology Resources 11: 5-18. https://doi.org/10.1111/j.1755-0998.2010.02927.x

Meuwissen, T.H., Hayes, B.J. and Goddard, M., 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.

Meuwissen, T.H.E., 1997. Maximizing the response of selection with a predefined rate of inbreeding. Journal of Animal Science 75: 934-940. https://doi.org/10.2527/1997.754934x

Meuwissen, T.H.E., Sonesson, A.K., Gebregiwergis, G. and Woolliams, J.A., 2020. Management of genetic diversity in the era of genomics. Frontiers in Genetics 11: 880. https://doi.org/10.3389/fgene.2020.00880

Meyermans, R., Broeckx, L., Mondelaers, J., Gorssen, W., Frooninckx, L., Janssens, S., Van Miert, S. and Buys, N., 2025. Exploring the potential of crossbreeding to enhance black soldier fly (*Hermetia illucens*) production. Journal of Insects as Food and Feed 11: 1-13. https://doi.org/10.1163/23524588-00001391

Miglior, F., Fleming, A., Malchiodi, F., Brito, L.F., Martin, P. and Baes, C.F., 2017. A 100-year review: identification and genetic selection of economically important traits in dairy cattle. Journal of Dairy Science 100: 10251-10271. https://doi.org/10.3168/jds.2017-12968

Mito, T. and Noji, S., 2008. The two-spotted cricket *Gryllus bimaculatus*: an emerging model for developmental and regeneration studies. Cold Spring Harbor Protocols: pdb.emol10. https://doi.org/10.1101/pdb.emol10

Moest, M., Van Belleghem, S.M., James, J.E., Salazar, C., Martin, S.H., Barker, S.L., Moreira, G.R.P., Mérot, C., Joron, M., Nadeau, N.J., Steiner, F.M. and Jiggins, C.D., 2020. Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation. PLoS Biology 18: e3000597. https://doi.org/10.1371/journal.pbio.3000597

Montejo-Kovacevich, G., Salazar, P.A., Smith, S.H., Gavilanes, K., Bacquet, C.N., Chan, Y.F., Jiggins, C.D., Meier, J.I. and Nadeau, N.J., 2021. Genomics of altitude-associated wing shape in two tropical butterflies. Molecular Ecology 30: 6387-6402. https://doi.org/10.1111/mec.16067

Montero-Mendieta, S., Tan, K., Christmas, M.J., Olsson, A., Vilà, C., Wallberg, A. and Webster, M.T., 2019. The genomic basis of adaptation to high-altitude habitats in the eastern honey bee (*Apis cerana*). Molecular Ecology 28: 746-760.

Montgomery, M.E., Woodworth, L.M., England, P.R., Briscoe, D.A. and Frankham, R., 2010. Widespread selective sweeps affecting microsatellites in *Drosophila* populations adapting to captivity: implications for captive breeding programs. Biological Conservation 143: 1842-1849.

Morales-Ramos, J.A., Kelstrup, H.C., Rojas, M.G. and Emery, V., 2019. Body Mass increase induced by eight years of artificial selection in the yellow mealworm (Coleoptera: Tenebrionidae) and life history trade-offs. Journal of Insect Science 19: 4. https://doi.org/10.1093/jisesa/iey110

Morales-Ramos, J.A., Rojas, M.G., Tweedy, D., Emery, V. and Kelstrup, H.C., 2022. Inheritance of two traits with high plasticity, developmental speed, and body size, in *Tenebrio*
*molitor* (Coleoptera: Tenebrionidae). Journal of Insect Science 22. https://doi.org/10.1093/jisesa/ieac075

Moretta, A., Salvia, R., Scieuzo, C., Di Somma, A., Vogel, H., Pucci, P., Sgambato, A., Wolff, M. and Falabella, P., 2020. A bioinformatic study of antimicrobial peptides identified in the black soldier fly (BSF) *Hermetia illucens* (Diptera: Stratiomyidae). Scientific Reports 10: 16875.

Morfin, N., Goodwin, P.H. and Guzman-Novoa, E., 2023. *Varroa destructor* and its impacts on honey bee biology. Frontiers in Bee Science 1. https://doi.org/10.3389/frbee.2023.1272937

Mossman, J.A., Biancani, L.M., Zhu, C.-T. and Rand, D.M., 2016. Mitonuclear epistasis for development time and its modification by diet in *Drosophila*. *Genetics* 203: 463-484.
https://doi.org/10.1534/genetics.116.187286

Mousseau, T.A. and Dingle, H., 1991. Maternal effects in insect life histories. Annual Review of Entomology 36: 511-534.
https://doi.org/10.1146/annurev.en.36.010191.002455

Mousseau, T.A. and Roff, D.A., 1987. Natural selection and the heritability of fitness components. Heredity 59: 181-197.
https://doi.org/10.1038/hdy.1987.113

Muchina, P., Kinyua, J., Khamis, F., Tanga, C.M., Gebreyesus, G., Cai, Z. and Sahana, G., 2025. The genomic landscape of *Hermetia illucens*: exploring the potential of the black soldier fly through molecular insights. Journal of Insects as Food and Feed 11: 1-26. https://doi.org/10.1163/23524588-bja10200

Mukherjee, K. and Vilcinskas, A., 2019. Chapter 14 - Transgenerational epigenetic inheritance in insects. In: Tollefsbol, T.O. (ed.) Translational Epigenetics, Transgenerational epigenetics. 2nd ed. Academic Press, San Diego, CA, pp. 315-329. https://doi.org/10.1016/B978-0-12-816363-4.00014-6

Mulder, H.A. and Bijma, P., 2005. Effects of genotype × environment interaction on genetic gain in breeding programs. Journal of Animal Science 83: 49-61. https://doi.org/10.2527/2005.83149x

Nakamura, Y., Tomonari, S., Kawamoto, K., Yamashita, T., Watanabe, T., Ishimaru, Y., Noji, S. and Mito, T., 2022. Evolutionarily conserved function of the even-skipped ortholog in insects revealed by gene knock-out analyses in *Gryllus bimaculatus*. Developmental Biology 485: 1-8. https://doi.org/10.1016/j.ydbio.2022.02.005

Nawoya, S., Geissmann, Q., Karstoft, H., Bjerge, K., Roseline, A., Katumba, A., Mwikirize, C. and Gebreyesus, G., 2025. Prediction of black soldier fly larval sex and morphological traits using computer vision and deep learning. Smart Agricultural Technology: 100953.

Nawoya, S., Ssemakula, F., Akol, R., Geissmann, Q., Karstoft, H., Bjerge, K., Mwikirize, C., Katumba, A. and Gebreyesus, G., 2024. Computer vision and deep learning in insects for

food and feed production: A review. Computers and Electronics in Agriculture 216: 108503.

Nguyen, T.N., Tran, T.B.N. and Tran, H.N., 2023. Genetic diversity of black soldier flies in Vietnam based on DNA COI sequence. Biodiversitas Journal of Biological Diversity 24: 6727-6732. https://doi.org/10.13057/biodiv/d241235

Nielsen, H.M., Amer, P.R. and Byrne, T.J., 2014. Approaches to formulating practical breeding objectives for animal production systems. Acta Agriculturae Scandinavica, Section A – Animal Science 64: 2-12. https://doi.org/10.1080/09064702.2013.827237

Nielsen, R., 2005. Molecular Signatures of Natural Selection. Annual Review of Genetics 39: 197-218. https://doi.org/10.1146/annurev.genet.39.073003.112420

Nielsen, R., Williamson, S., Kim, Y., Hubisz, M.J., Clark, A.G. and Bustamante, C., 2005. Genomic scans for selective sweeps using SNP data. Genome Research 15: 1566-1575.

Nielsen, S.V., Vaughn, A.H., Leppälä, K., Landis, M.J., Mailund, T. and Nielsen, R., 2023. Bayesian inference of admixture graphs on Native American and Arctic populations. PLoS Genetics 19: e1010410. https://doi.org/10.1371/journal.pgen.1010410

Nunez, J.C., Coronado-Zamora, M., Gautier, M., Kapun, M., Steindl, S., Ometto, L., Hoedjes, K.M., Beets, J., Wiberg, R.A.W., Mazzeo, G.R., Bass, D.J., Radionov, D., Kozeretska, I., Zinchenko, M., Protsenko, O., Serga, S., Amor-Jimenez, C., Casillas, S., Sanchez-Gracia, A., Patenkovic, A., Glaser-Schmitt, A., Barbadilla, A., Buendia-Ruiz, A.J., Bertelli, A.C., Kiss, B., Önder, B.S., Roldán Matrín, B., Wertheim, B., Deschamps, C., Arboleda-Bustos, C.E., Tinedo, C., Feller, C., Schlötterer, C., Lawler, C., Fricke, C., Vieira, C.P., Vieira, C., Obbard, D.J., Orengo, D., Vela, D., Amat, E., Loreto, E., Kerdaffrec, E., Durmaz Mitchell, E., Puerma, E., Staubach, F., Camus, F., Colinet, H., Hrcek, J., Sørensen, J.G., Abbott, J., Torro, J., Parsch, J., Vieira, J., Olmo, J.L., Khfif, K., Wojciechowski, K., Madi-Ravazzi, L., Kankare, M., Schou, M.F., Ladoukakis, M., Gomez-Julian, M.J., Espinosa-Jimenez, M.L., Garcia Guerreiro, M.P., Parakatselaki, M.-E., Savic Veselinovic, M., Tanaskovic, M., Stamenkovic-Radak, M., Paris, M., Pascual, M., Ritchie, M.G., Rera, M., Jelić, M., Hojat Ansari, M., Rakic, M., Merenciano, M., Hernandes, N., Gora, N., Rode, N., Rota-Stabelli, O., Sepulveda, P., Gibert, P., Carazo, P., Kohlmeier, P., Erickson, P.A., Vitalis, R., Torres, R., Guirao-Rico, S., Ramos-Onsins, S.E., Castillo, S., Paulo, T.F., Tyukmaeva, V., Alonso, Z., Alatortsev, V., Pasyukova, E., Mukha, D., Petrov, D., Schmidt, P., Flatt, T., Bergland, A.O. and Gonzalez, J., 2024. Footprints of worldwide adaptation in structured populations of *D. melanogaster* through the expanded DEST 2.0 genomic resource.
bioRxiv: 2024.2011.2010.622744. https://www.biorxiv.org/content/10.1101/2024.11.10.622744v1

Olson, K.M., Garrick, D.J. and Enns, R.M., 2006. Predicting breeding values and accuracies from group in comparison to individual observations. Journal of Animal Science 84: 88-92. https://doi.org/10.2527/2006.84188x

Omuse, E.R., Tonnang, H.E., Yusuf, A.A., Machekano, H., Egonyu, J.P., Kimathi, E., Mohamed, S.F., Kassie, M., Subramanian, S. and Onditi, J., 2024. The global atlas of edible insects: analysis of diversity and commonality contributing to food systems and sustainability. Scientific Reports 14: 5045. https://doi.org/10.1038/s41598-024-55603-7

Oonincx, D.G.A.B., Gold, M., Bosch, G., Guillaume, J.B., Rumbos, C.I., Naser El Deen, S., Sandrock, C., Bellezza Oddon, S., Athanassiou, C.G., Cambra-López, M., Pascual, J.J., Parodi, A.P., Spranghers, T. and Yakti, W., 2025. Bugbook: nutritional requirements for edible insect rearing. Journal of Insects as Food and Feed 11: 1-20. https://doi.org/10.1163/23524588-bja10226

Oppert, B., Dossey, A.T., Chu, F.-C., Šatović-Vukšić, E., Plohl, M., Smith, T.P.L., Koren, S., Olmstead, M.L., Leierer, D., Ragan, G. and Johnston, J.S., 2023. The genome of the yellow mealworm, *Tenebrio molitor*: it's bigger than you think. *Genes* 14: 2209. https://doi.org/10.3390/genes14122209

Ožana, S., Pyszko, P. and Dolný, A., 2020. Determination of suitable insect part for non-lethal DNA sampling: case study of DNA quality and regeneration capability of drag-onflies. Insect Conservation and Diversity 13: 319-327.

Palstra, F.P. and Ruzzante, D.E., 2008. Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence? Molecular Ecology 17: 3428-3447.

Pannell, J.R. and Charlesworth, B., 2000. Effects of metapopulation processes on measures of genetic diversity. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 355: 1851-1864.

Pastor, B., Martínez-Sánchez, A.S., Ståhls, G.A. and Rojo, S., 2014. Introducing improvements in the mass rearing of the housefly: biological, morphometric and genetic characterization of laboratory strains. Bull Entomol Res 104: 486-493. https://doi.org/10.1017/s000748531400025x

Paul, K., D'Ambrosio, J. and Phocas, F., 2022. Temporal and region-specific variations in genome-wide inbreeding effects on female size and reproduction traits of rainbow trout. Evolutionary Applications 15: 645-662. https://doi.org/10.1111/eva.13308

Pazmiño, M.F., Del Hierro, A.G. and Flores, F.J., 2023. Genetic diversity and organic waste degrading capacity of *Hermetia illucens* from the evergreen forest of the Equatorial Choco lowland. PeerJ 11: e14798. https://doi.org/10.7717/peerj.14798

Peer, K. and Taborsky, M., 2005. Outbreeding depression, but no inbreeding depression in haplodiploid ambrosia beetles with regular sibling mating. Evolution 59: 317-323. https://doi.org/10.1111/j.0014-3820.2005.tb00992.x

Peng, X., Liu, J., Li, B., Wang, S., Chen, B. and Zhang, D., 2023. An acyl carrier protein gene affects fatty acid synthesis and growth of *Hermetia illucens*. Insects 14: 300.

Peng, Y., Wang, K., Fu, W., Sheng, C. and Han, Z., 2018. Biochemical comparison of dsRNA degrading nucleases in four different insects. Frontiers in Physiology 9: 624.

Pentinsaari, M., Salmela, H., Mutanen, M. and Roslin, T., 2016. Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life. Scientific Reports 6: 35275. https://doi.org/10.1038/srep35275

Pérez-Enciso, M. and Steibel, J.P., 2021. Phenomes: the current frontier in animal breeding. Genetics Selection Evolution 53: 22. https://doi.org/10.1186/s12711-021-00618-1

Pérez-Pereira, N., Pouso, R., Rus, A., Vilas, A., López-Cortegano, E., García-Dorado, A., Quesada, H. and Caballero, A., 2021. Long-term exhaustion of the inbreeding load in *Drosophila melanogaster*. Heredity 127: 373-383. https://doi.org/10.1038/s41437-021-00464-3

Peripolli, E., Munari, D., Silva, M., Lima, A., Irgang, R. and Baldi, F., 2017. Runs of homozygosity: current knowledge and applications in livestock. Animal Genetics 48: 255-271.

Petronio Petronio, G., Pietrangelo, L., Cutuli, M.A., Magnifico, I., Venditti, N., Guarnieri, A., Abate, G.A., Yewhalaw, D., Davinelli, S. and Di Marco, R., 2022. Emerging Evidence on *Tenebrio molitor* Immunity: A focus on gene expression involved in microbial infection for host-pathogen interaction studies. Microorganisms 10: 1983.

Poveda, J., 2021. Insect frass in the development of sustainable agriculture. A review. Agronomy for Sustainable Development 41: 5. https://doi.org/10.1007/s13593-020-00656-x

Price, A.L., Zaitlen, N.A., Reich, D. and Patterson, N., 2010. New approaches to population stratification in genome-wide association studies. Nature Reviews Genetics 11: 459-463. https://doi.org/10.1038/nrg2813

Pritchard, J.K., Stephens, M. and Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959. https://doi.org/10.1093/genetics/155.2.945

Prokkola, J., Roff, D., Kärkkäinen, T., Krami, I. and Rantala, M.J., 2013. Genetic and phenotypic relationships between immune defense, melanism and life-history traits at different temperatures and sexes in *Tenebrio molitor*. Heredity 111: 89-96. https://doi.org/10.1038/hdy.2013.20

Pszczola, M., Strabel, T., Van Arendonk, J. and Calus, M., 2012. The impact of genotyping different groups of animals on accuracy when moving from traditional to genomic selection. Journal of Dairy Science 95: 5412-5421.
Pudlo, P., Marin, J.-M., Estoup, A., Cornuet, J.-M., Gautier, M. and Robert, C.P., 2016. Reliable ABC model choice via random forests. *Bioinformatics* 32: 859-866. https://doi.org/10.1093/bioinformatics/btv684

Purfield, D.C., Berry, D.P., McParland, S. and Bradley, D.G., 2012. Runs of homozygosity and population history in cattle. *BMC genetics* 13: 1-11.

Rabani, V., Cheatsazan, H. and Davani, S., 2019. Proteomics and lipidomics of black soldier fly (Diptera: Stratiomyi-dae) and blow fly (Diptera: Calliphoridae) larvae. *Journal of Insect Science* 19. https://doi.org/10.1093/jisesa/iez050

Reed, L.K., Williams, S., Springston, M., Brown, J., Freeman, K., DesRoches, C.E., Sokolowski, M.B. and Gibson, G., 2010. Genotype-by-diet interactions drive metabolic phenotype variation in *Drosophila melanogaster*. *Genetics* 185: 1009-1019. https://doi.org/10.1534/genetics.109.113571

Reed, R.D., Papa, R., Martin, A., Hines, H.M., Counterman, B.A., Pardo-Diaz, C., Jiggins, C.D., Chamberlain, N.L., Kro-nforst, M.R., Chen, R., Halder, G., Nijhout, H.F. and McMil-lan, W.O., 2011. optix drives the repeated convergent evolu-tion of butterfly wing pattern mimicry. *Science* 333: 1137-1141. https://doi.org/10.1126/science.1208227

Rehman, K.u., Hollah, C., Wiesotzki, K., Heinz, V., Aganovic, K., Rehman, R.u., Petrusan, J.-I., Zheng, L., Zhang, J., Sohail, S., Mansoor, M.K., Rumbos, C.I., Athanassiou, C. and Cai, M., 2023. Insect-derived chitin and chitosan: a still unex-ploited resource for the edible insect sector. *Sustainability* 15: 4864. https://doi.org/10.3390/su15064864

Reznick, D.N., 1991. Maternal effects in fish life histories. In: Dudley, E. (ed.) The unity of evolutionary biology. Dis-corides Press, Portland, OR, pp. 780-793.

Rhode, C., Badenhorst, R., Hull, K.L., Greenwood, M.P., Bester-van der Merwe, A.E., Andere, A.A., Picard, C.J. and Richards, C., 2020. Genetic and phenotypic consequences of early domestication in black soldier flies (*Hermetia illucens*). *Animal Genetics* 51: 752-762. https://doi.org/10.1111/age.12961

Rhode, C. and Greenwood, M.P., 2023. Antimicrobial pep-tide gene expression and the microbiome in Black Sol-dier Fly. *Insect Sci* 30: 1017-1021. https://doi.org/10.1111/1744-7917.13177

Rodríguez-Ramilo, S.T., Elsen, J.M. and Legarra, A., 2019. Inbreeding and effective population size in French dairy sheep: comparison between genomic and pedigree esti-mates. *Journal of Dairy Science* 102: 4227-4237. https://doi.org/10.3168/jds.2018-15405

Rousset, F., 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. *Genetics* 145: 1219-1228. https://doi.org/10.1093/genetics/145.4.1219

Rowe, G., Sweet, M. and Beebee, T.J.C., 2017. An introduction to molecular ecology. Oxford University Press, Oxford.

Ryder, J.J. and Siva-Jothy, M.T., 2001. Quantitative genetics of immune function and body size in the house cricket, *Acheta domesticus*. *Journal of Evolutionary Biology* 14: 646-653. https://doi.org/10.1046/j.1420-9101.2001.00302.x

Sae-Lim, P., Gjerde, B., Nielsen, H.M., Mulder, H. and Kause, A., 2016. A review of genotype-by-environment interaction and micro-environmental sensitivity in aquaculture species. *Reviews in Aquaculture* 8: 369-393. https://doi.org/10.1111/raq.12098

Sahana, G., Cai, Z., Sanchez, M.P., Bouwman, A.C. and Boi-chard, D., 2023. Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle. *Journal of Dairy Science* 106: 5218-5241. https://doi.org/10.3168/jds.2022-22694

San Jose, M., Doorenweerd, C. and Rubinoff, D., 2023. Genomics reveals widespread hybridization across insects with ramifications for species boundaries and invasive species. *Current Opinion in Insect Science* 58: 101052. https://doi.org/10.1016/j.cois.2023.101052

Sánchez-Guillén, R.A., Córdoba-Aguilar, A., Hansson, B., Ott, J. and Wellenreuther, M., 2016. Evolutionary consequences of climate-induced range shifts in insects. *Biological Reviews* 91: 1050-1064. https://doi.org/10.1111/brv.12204

Sandrock, C., Frauenfelder, N., Von Burg, S. and Vorburger, C., 2007. Microsatellite DNA markers for the aphid parasitoid *Lysiphlebus fabarum* and their applicability to related species. *Molecular Ecology Notes* 7: 1080-1083. https://doi.org/10.1111/j.1471-8286.2007.01783.x

Sandrock, C., Gouskov, A. and Vorburger, C., 2010. Ample genetic variation but no evidence for genotype specificity in an all-parthenogenetic host-parasitoid interaction. *Journal of Evolutionary Biology* 23: 578-585. https://doi.org/doi:10.1111/j.1420-9101.2009.01925.x

Sandrock, C., Leupi, S., Wohlfahrt, J., Kaya, C., Heuel, M., Ter-ranova, M., Blanckenhorn, W.U., Windisch, W., Kreuzer, M. and Leiber, F., 2022. Genotype-by-diet interactions for lar-val performance and body composition traits in the black soldier fly, *Hermetia illucens*. *Insects* 13. https://doi.org/10.3390/insects13050424

Sandrock, C., Razmjou, J. and Vorburger, C., 2011a. Climate effects on life cycle variation and population genetic archi-tecture of the black bean aphid, *Aphis fabae*. *Molecular Ecology* 20: 4165-4181. https://doi.org/10.1111/j.1365-294X.2011.05242.x

Sandrock, C., Schirrmeister, B.E. and Vorburger, C., 2011b. Evol-ution of reproductive mode variation and host associa-tions in a sexual-asexual complex of aphid parasitoids. *BMC evolutionary biology* 11: 348. https://doi.org/10.1186/1471-2148-11-348
Santos, M., Fowler, K. and Partridge, L., 1994. Gene-environment interaction for body size and larval density in *Drosophila melanogaster*: an investigation of effects on development time, thorax length and adult sex ratio. Heredity 72: 515-521. https://doi.org/10.1038/hdy.1994.69

Santostefano, F., Wilson, A.J., Niemelä, P.T. and Dingemanse, N.J., 2017. Indirect genetic effects: a key component of the genetic architecture of behaviour. Scientific Reports 7: 10235. https://doi.org/10.1038/s41598-017-08258-6

Saravanan, K., Panigrahi, M., Kumar, H., Bhushan, B., Dutt, T. and Mishra, B., 2020. Selection signatures in livestock genome: a review of concepts, approaches and applications. Livestock Science 241: 104257.

Schaeffer, L., 2006. Strategy for applying genome-wide selection in dairy cattle. Journal of Animal Breeding and Genetics 123: 218-223.

Schlötterer, C., Kofler, R., Versace, E., Tobler, R. and Franssen, S.U., 2015. Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity 114: 431-440. https://doi.org/10.1038/hdy.2014.86

Scieuzo, C., Franco, A., Salvia, R., Triunfo, M., Addeo, N.F., Vozzo, S., Piccolo, G., Bovera, F., Ritieni, A., Francia, A.D., Laginestra, A., Schmitt, E. and Falabella, P., 2023. Enhancement of fruit byproducts through bioconversion by *Hermetia illucens* (Diptera: Stratiomyidae). Insect Science 30: 991-1010. https://doi.org/10.1111/1744-7917.13155

Scieuzo, C., Nardiello, M., Farina, D., Scala, A., Cammack, J.A., Tomberlin, J.K., Vogel, H., Salvia, R., Persaud, K. and Falabella, P., 2021. *Hermetia illucens* (L.) (Diptera: Stratiomyidae) odorant binding proteins and their interactions with selected volatile organic compounds: An in silico approach. Insects 12: 814.

Scott, J.G., Warren, W.C., Beukeboom, L.W., Bopp, D., Clark, A.G., Giers, S.D., Hediger, M., Jones, A.K., Kasai, S., Leichter, C.A., Li, M., Meisel, R.P., Minx, P., Murphy, T.D., Nelson, D.R., Reid, W.R., Rinkevich, F.D., Robertson, H.M., Sackton, T.B., Sattelle, D.B., Thibaud-Nissen, F., Tomlinson, C., van de Zande, L., Walden, K.K.O., Wilson, R.K. and Liu, N., 2014. Genome of the house fly, *Musca domestica* L., a global vector of diseases with adaptations to a septic environment. Genome Biology 15: 466. https://doi.org/10.1186/s13059-014-0466-3

Sellem, E., Paul, K., Donkpegan, A., Li, Q., Masseron, A., Chauveau, A., Gagnepain-Germain, F. and Lefebvre, T., 2024. Multitrait genetic parameter estimates in a *Tenebrio molitor* reference population: high potential for breeding gains. Animal 18: 101197. https://doi.org/10.1016/j.animal.2024.101197

Sethuraman, A., Janzen, F.J., Weisrock, D.W. and Obrycki, J.J., 2020. Insights from population genomics to enhance and

sustain biological control of insect pests. Insects 11: 462. https://doi.org/10.3390/insects11080462

Shah, P.N., Niermans, K., Hoek-van den Hil, E.F., Dicke, M. and van Loon, J.J., 2024. Effects of aflatoxin B1 on metabolism-and immunity-related gene expression in *Hermetia illucens* L. (Diptera: Stratiomyidae). Pesticide Biochemistry and Physiology 202: 105944.

Shim, J.E., Lee, T. and Lee, I., 2017. From sequencing data to gene functions: co-functional network approaches. Animal Cells Systems (Seoul) 21: 77-83. https://doi.org/10.1080/19768354.2017.1284156

Shirai, Y., Piulachs, M.-D., Belles, X. and Daimon, T., 2022. DIPA-CRISPR is a simple and accessible method for insect gene editing. Cell Reports Methods 2: 100215. https://doi.org/10.1016/j.crmeth.2022.100215

Siddiqui, S.A., Süfer, Ö., Çalışkan Koç, G., Lutuf, H., Rahayu, T., Castro-Muñoz, R. and Fernando, I., 2024. Enhancing the bioconversion rate and end products of black soldier fly (BSF) treatment – a comprehensive review. Environment, Development and Sustainability 24: 9673-9741. https://doi.org/10.1007/s10668-023-04306-6

Signor, S.A., Abbasi, M., Marjoram, P. and Nuzhedin, S.V., 2017. Social effects for locomotion vary between environments in *Drosophila melanogaster* females. Evolution 71: 1765-1775. https://doi.org/10.1111/evo.13266

Silvaraju, S., Zhang, Q.-H., Kittelmann, S. and Puniamoorthy, N., 2024. Genetics, age, and diet influence gut bacterial communities and performance of black soldier fly larvae (*Hermetia illucens*). Animal Microbiome 6: 56. https://doi.org/10.1186/s42523-024-00340-5

Simões, P., Pascual, M., Coelho, M.M. and Matos, M., 2010. Divergent evolution of molecular markers during laboratory adaptation in *Drosophila subobscura*. Genetica 138: 999-1009. https://doi.org/10.1007/s10709-010-9486-4

Singh, T., Saratchandra, B. and Murthy, G.N., 2002. An analysis of heterosis in the silkworm, *Bombyx mori* (L.). International Journal of Industrial Entomology 5: 23-32.

Singh, V. and Verma, N.K., 2022. Gene expression data analysis using feature weighted robust fuzzy c-means clustering. IEEE Transactions in Nanobioscience 22: 99-105. https://doi.org/10.1109/tnb.2022.3157396

Slagboom, M., Nielsen, H.M., Kargo, M., Henryon, M. and Hansen, L.S., 2024. The effect of phenotyping, adult selection, and mating strategies on genetic gain and rate of inbreeding in black soldier fly breeding programs. Genetics Selection Evolution 56: 71. https://doi.org/10.1186/s42523-024-00340-5

Slavkin, H.C., 2014. From Phenotype to Genotype: Enter Genomics and Transformation of Primary Health Care around the World. J Dent Res 93: 3s-6s. https://doi.org/10.1177/0022034514533569
Smetana, S., Coudron, C., Deruytter, D., Francis, A., Pascual Juan, J., Klammsteiner, T., Lemke, N., Sandrock, C. and Zanoli, R., 2025. BugBook: Data analysis methods in studies of insects for food and feed. Journal of Insects as Food and Feed 11: 1-27. https://doi.org/10.1163/23524588-bja10209

Smetana, S., Spykman, R. and Heinz, V., 2021. Environmental aspects of insect mass production. Journal of Insects as Food and Feed 7: 553-571.

Smith, J.M. and Haigh, J., 1974. The hitch-hiking effect of a favourable gene. Genetics Research 23: 23-35. https://doi.org/10.1017/S0016672308009579

Song, J.-H., Chang, G.-D., Ji, S., Kim, S.-Y. and Kim, W., 2022. Selective breeding and characterization of a black meal-worm strain of *Tenebrio molitor* Linnaeus (Coleoptera: Tenebrionidae). Journal of Asia-Pacific Entomology 25: 101978. https://doi.org/10.1016/j.aspen.2022.101978

Sørensen, J.G., 2010. Application of heat shock protein expression for detecting natural adaptation and exposure to stress in natural populations. Current Zoology 56: 703-713. https://doi.org/10.1093/czoolo/56.6.703

Sørensen, J.G., Kristensen, T.N. and Loeschcke, V., 2003. The evolutionary and ecological role of heat shock proteins. Ecology Letters 6: 1025-1037. https://doi.org/10.1046/j.1461-0248.2003.00528.x

Srivastava, A.K., Williams, S.M. and Zhang, G., 2023. Heritability estimation approaches utilizing genome-wide data. Current Protocols 3: e734. https://doi.org/10.1002/cpzl.734

Stadtlander, T., Stamer, A., Buser, A., Wohlfahrt, J., Leiber, F. and Sandrock, C., 2017. *Hermetia illucens* meal as fish meal replacement for rainbow trout on farm. Journal of Insects as Food and Feed 3: 165-175. https://doi.org/10.3920/JIFF2016.0056

Stähls, G., Meier, R., Sandrock, C., Hauser, M., Šašić Zorić, L., Laiho, E., Aracil, A., Doderović, J., Badenhorst, R., Unadi-rekkul, P., Mohd Adom, N.A.B., Wein, L., Richards, C., Tomberlin, J.K., Rojo, S., Veselić, S. and Parviainen, T., 2020. The puzzling mitochondrial phylogeography of the black soldier fly (*Hermetia illucens*), the commercially most important insect protein species. BMC Evolutionary Biology 20: 60. https://doi.org/10.1186/s12862-020-01627-2

Storey, J.D. and Tibshirani, R., 2003. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America 100: 9440-9445. https://doi.org/10.1073/pnas.1530509100

Stork, N.E., 2018. How many species of insects and other terrestrial arthropods are there on Earth? Annual Review of Entomology 63: 31-45. https://doi.org/10.1146/annurev-ento-020117-043334

Suárez, D., Arribas, P., Jiménez-García, E. and Emerson, B.C., 2022. Dispersal ability and its consequences for popula-

tion genetic differentiation and diversification. Proceedings of the Royal Society London B: Biological Sciences 289: 20220489. https://doi.org/10.1098/rspb.2022.0489

Sui, Z., Wu, Q., Geng, J., Xiao, J. and Huang, D., 2024. CRISPR/Cas9-mediated efficient white genome editing in the black soldier fly *Hermetia illucens*. Molecular Genetics and Genomics 299: 5. https://doi.org/10.1007/s00438-023-02088-0

Sukmak, R., Suttinun, C., Kovitvadhi, U., Kovitvadhi, A. and Vongsangnak, W., 2024. Uncovering nutrients and energy related gene functions of black soldier fly *Hermetia illucens* strain KUP. Gene 896: 148045.

Sun, M., Oulabi, I. and Chen, L., 2015. CRISPR/Cas9 genome editing system in *Drosophila*. Advanced Techniques in Biology and Medicine S1: 003. https://doi.org/10.4172/2379-1764

Suravajhala, P., Kogelman, L.J. and Kadarmideen, H.N., 2016. Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare. Genetics Selection Evolution 48: 38. https://doi.org/10.1186/s12711-016-0217-x

Suzuki, Y., Niu, G., Hughes, G.L. and Rasgon, J.L., 2014. A viral over-expression system for the major malaria mosquito *Anopheles gambiae*. Scientific Reports 4: 5127. https://doi.org/10.1038/srep05127

Svedberg, J., Shchur, V., Reinman, S., Nielsen, R. and Corbett-Detig, R., 2021. Inferring adaptive introgression using hidden Markov models. Molecular Biology and Evolution 38: 2152-2165. https://doi.org/10.1093/molbev/msab014

Swindell, W.R. and Bouzat, J.L., 2006. Reduced inbreeding depression due to historical inbreeding in *Drosophila melanogaster*: evidence for purging. Journal of Evolutionary Biology 19: 1257-1264. https://doi.org/10.1111/j.1420-9101.2005.01074.x

Szmatoła, T., Gurgul, A., Ropka-Molik, K., Jasielczuk, I., Ząbek, T. and Bugno-Poniewierska, M., 2016. Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livestock Science 188: 72-80. https://doi.org/10.1016/j.livsci.2016.04.006

Szűcs, M., Melbourne, B.A., Tuff, T., Weiss-Lehman, C. and Hufbauer, R.A., 2017. Genetic and demographic founder effects have long-term fitness consequences for colonising populations. Ecology Letters 20: 436-444. https://doi.org/10.1111/ele.12743

Thalamuthu, A., Mukhopadhyay, I., Ray, A. and Weeks, D.E., 2005. A comparison between microsatellite and single-nucleotide polymorphism markers with respect to two measures of information content. BMC Genetics 6: S27. https://doi.org/10.1186/1471-2156-6-S1-S27

Thia, J.A., 2023. Guidelines for standardizing the application of discriminant analysis of principal components to
genotype data. Molecular Ecology Resources 23: 523-538.
https://doi.org/10.1111/1755-0998.13706

Tiffin, P. and Ross-Ibarra, J., 2014. Advances and limits of using population genetics to understand local adaptation. *Trends in Ecology and Evolution* 29: 673-680. http://dx.doi.org/10.1016/j.tree.2014.10.004

Toews, D.P.L. and Brelsford, A., 2012. The biogeography of mitochondrial and nuclear discordance in animals. *Molecular Ecology* 21: 3907-3930. https://doi.org/10.1111/j.1365-294X.2012.05664.x

Tomberlin, J.K., Klammsteiner, T., Lemke, N., Yadav, P. and Sandrock, C., 2025. BugBook: Black soldier fly as a model to assess behaviour of insects mass produced as food and feed. Journal of Insects as Food and Feed 11: 1-20.
https://doi.org/10.1163/23524588-bja10225

Tong, X., Han, M.-J., Lu, K., Tai, S., Liang, S., Liu, Y., Hu, H., Shen, J., Long, A., Zhan, C., Ding, X., Liu, S., Gao, Q., Zhang, B., Zhou, L., Tan, D., Yuan, Y., Guo, N., Li, Y.-H., Wu, Z., Liu, L., Li, C., Lu, Y., Gai, T., Zhang, Y., Yang, R., Qian, H., Liu, Y., Luo, J., Zheng, L., Lou, J., Peng, Y., Zuo, W., Song, J., He, S., Wu, S., Zou, Y., Zhou, L., Cheng, L., Tang, Y., Cheng, G., Yuan, L., He, W., Xu, J., Fu, T., Xiao, Y., Lei, T., Xu, A., Yin, Y., Wang, J., Monteiro, A., Westhof, E., Lu, C., Tian, Z., Wang, W., Xiang, Z. and Dai, F., 2022. High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation. Nature Communications 13: 5619. https://doi.org/10.1038/s41467-022-33366-x

Tran, L.N., Sun, C.K., Struck, T.J., Sajan, M. and Gutenkunst, R.N., 2024. Computationally efficient demographic history inference from allele frequencies with supervised machine learning. Molecular Biology and Evolution 41: msae077.

Triunfo, M., Tafi, E., Guarnieri, A., Scieuzo, C., Hahn, T., Zibek, S., Salvia, R. and Falabella, P., 2021. Insect chitin-based nanomaterials for innovative cosmetics and cosmeceuticals. Cosmetics 8: 40.

Turner, T.L., Stewart, A.D., Fields, A.T., Rice, W.R. and Tarone, A.M., 2011. Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in *Drosophila melanogaster*. PLoS Genetics 7: 1-10. https://doi.org/10.1371/journal.pgen.1001336

Urzúa-Traslaviña, C.G., Leeuwenburgh, V.C., Bhattacharya, A., Loipfinger, S., van Vugt, M.A.T.M., de Vries, E.G.E. and Fehrmann, R.S.N., 2021. Improving gene function predictions using independent transcriptional components. Nature Communications 12: 1464. https://doi.org/10.1038/s41467-021-21671-w

van Huis, A., 2013. Potential of insects as food and feed in assuring food security. *Annual Review of Entomology* 58: 563-583. https://doi.org/10.1146/annurev-ento-120811-153704

van Huis, A., 2020. Insects as food and feed, a new emerging agricultural sector: a review. Journal of Insects as Food and Feed 6: 27-44. https://doi.org/10.3920/JIFF2019.0017

van Huis, A. and Oonincx, D.G.A.B., 2017. The environmental sustainability of insects as food and feed. A review. *Agronomy for Sustainable Development* 37: 43. https://doi.org/10.1007/s13593-017-0452-8

van Huis, A., Rumbos, C.I., Oonincx, D.G., Rojo, S., Kovit-vadhi, A. and Gasco, L., 2025. From traditional to industrial use of insects as feed: a review. Journal of Insects as Food and Feed 11: 115-137. https://doi.org/10.1163/23524588-00001232

van Huis, A., Rumpold, B., Van der Fels-Klerx, H. and Tomberlin, J., 2021. Advancing edible insects as food and feed in a circular economy. Journal of Insects as Food and Feed 7: 935-948. https://doi.org/10.3920/JIFF2021.x005

van Huis, A. and Tomberlin, J.K., 2017. Insects as food and feed: from production to consumption. Wageningen Academic Publishers, Wageningen.

Vogel, H., Müller, A., Heckel, D.G., Gutzeit, H. and Vilcinskas, A., 2018. Nutritional immunology: Diversification and diet-dependent expression of antimicrobial peptides in the black soldier fly *Hermetia illucens*. *Developmental and Comparative Immunology* 78: 141-148. https://doi.org/10.1016/j.dci.2017.09.008

Vogel, M., Shah, P., Voulgari-Kokota, A., Maistrou, S., Aartsma, Y., Beukeboom, L., Salles, J.F., Van Loon, J., Dicke, M. and Wertheim, B., 2022. Health of the black soldier fly and house fly under mass-rearing conditions: innate immunity and the role of the microbiome. Journal of Insects as Food and Feed 8: 857-878.

Voight, B.F., Kudaravalli, S., Wen, X. and Pritchard, J.K., 2006. A map of recent positive selection in the human genome. PLoS Biology 4: e72.

Wackchaure, R., Ganguly, S. and Praveen, P.K., 2016. Genotype × Environment interaction in animal breeding: a review. In: Biodiversity conservation in changing climate. Lenin Media, Delhi, pp. 60-73.

Wallace, D.C. and Chalkia, D., 2013. Mitochondrial DNA Genetics and the Heteroplasmy Conundrum in Evolution and Disease. Cold Spring Harbor Perspectives in Biology 5. https://doi.org/10.1101/cshperspect.a021220

Wandeler, P., Hoeck, P.E. and Keller, L.F., 2007. Back to the future: museum specimens in population genetics. *Trends in Ecology and Evolution* 22: 634-642.

Wang, C., Zhao, T., Liu, X., Li, T., He, L., Wang, Q., Wang, L. and Zhou, L., 2024. CRISPR/Cas9-mediated mutagenesis of antennapedia in *Spodoptera frugiperda*. Insects 15: 16.

Wang, X., Fang, X., Yang, P., Jiang, X., Jiang, F., Zhao, D., Li, B., Cui, F., Wei, J. and Ma, C., 2014. The locust genome
provides insight into swarm formation and long-distance
flight. Nature Communications 5: 1-9.

Waples, R.S., 2024. Practical application of the linkage disequilibrium method for estimating contemporary effective population size: a review. Molecular Ecology Resources 24: e13879. https://doi.org/10.1111/1755-0998.13879

Waples, R.S. and Do, C., 2010. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications 3: 244-262. https://doi.org/10.1111/j.1752-4571.2009.00104.x

Waples, R.S. and Gaggiotti, O., 2006. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15: 1419-1439. https://doi.org/10.1111/j.1365-294X.2006.02890.x

Warr, E., Meredith, J.M., Nimmo, D.D., Basu, S., Hurd, H. and Eggleston, P., 2006. A tapeworm molecule manipulates vitellogenin expression in the beetle *Tenebrio molitor*. Insect Mol Biol 15: 497-505. https://doi.org/10.1111/j.1365-2583.2006.00663.x

Weber, J.L. and Wong, C., 1993. Mutation of human short tandem repeats. Human Molecular Genetics 2: 1123-1128. https://doi.org/10.1093/hmg/2.8.1123

Wice, E.W. and Saltz, J.B., 2023. Indirect genetic effects for social network structure in *Drosophila melanogaster*. Philosophical Transactions of the Royal Society B: Biological Sciences 378: 20220075. https://doi.org/10.1098/rstb.2022.0075

Williams, G., Foley, M.M. and Knight, K.L., 2023. Applied Biosystems' GlobalFiler™ PCR Amplification Kit. Methods in Molecular Biology 2685: 241-252. https://doi.org/10.1007/978-1-0716-3295-6_15

Wilson, I.D., Barker, G.L. and Edwards, K.J., 2003. Genotype to phenotype: a technological challenge. Annals of Applied Biology 142: 33-39. https://doi.org/10.1111/j.1744-7348.2003.tb00226.x

Wolc, A., Kranis, A., Arango, J., Settar, P., Fulton, J.E., O'Sullivan, N.P., Avendano, A., Watson, K.A., Hickey, J.M., de los Campos, G., Fernando, R.L., Garrick, D.J. and Dekkers, J.C.M., 2016. Implementation of genomic selection in the poultry industry. Animal Frontiers 6: 23-31. https://doi.org/10.2527/af.2016-0004

Woodward, J., 2014. Bi-allelic SNP genotyping using the TaqMan® assay. Crop Breeding: Methods and Protocols: 67-74.

Woodworth, L.M., Montgomery, M.E., Briscoe, D.A. and Frankham, R., 2002. Rapid genetic deterioration in captive populations: Causes and conservation implications. Conservation Genetics 3: 277-288. https://doi.org/10.1023/A:1019954801089

Woolliams, J., Gwaze, D., Meuwissen, T., Planchenault, D., Renard, J., Thibier, M. and Wagner, H., 1998. Secondary guidelines for the development of national farm animal genetic resources management plans – management of small populations at risk. FAO, Rome.

Wright, S., 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395-420.

Wu, C., Zhou, Y., Tian, T., Li, T.-J. and Chen, B., 2022. First report of complete mitochondrial genome in the subfamily Alleculinae and mitochondrial genome-based phylogenetics in Tenebrionidae (Coleoptera: Tenebrionoidea). Insect Science 29: 1226-1238. https://doi.org/10.1111/1744-7917.12983

Wu, H., Li, Z., Zhong, Z., Guo, Y., He, L., Xu, X., Mao, Y., Tang, D., Zhang, W., Jin, F. and Pang, R., 2024. Insect Cytochrome P450 Database: an integrated resource of genetic diversity, evolution and function. ESS Open Archive: 05145509. https://doi.org/10.22541/au.172115440.05145509/v1

Wynants, E., Frooninckx, X., Crauwels, S., Verreth, C., De Smet, J., Sandrock, C., Wohlfahrt, J., Van Schelt, J., Depraetere, S., Lievens, B., Van Miert, S., Claes, J. and Van Campenhout, L., 2019. Assessing the microbiota of black soldier fly larvae (*Hermetia illucens*) reared on organic waste streams on four different locations at laboratory and large scale. Microbial Ecology 77: 913-930. https://doi.org/10.1007/s00248-018-1286-x

Xia, J., Ge, C. and Yao, H., 2021. Antimicrobial peptides from black soldier fly (*Hermetia illucens*) as potential antimicrobial factors representing an alternative to antibiotics in livestock farming. Animals 11: 1937. https://doi.org/10.3390/ani11071937

Xia, S., 2020. Exploring the potential of genetic improvement of insects: A case study using the haplodiploid parasitoid wasp *Nasonia vitripennis*. Doctoral dissertation, Wageningen University and Research, Wageningen.

Xia, S., Kiss, G.B., Megens, H.-J., Groenen, M.A.M., Zwaan, B.J., Bijma, P. and Pannebakker, B.A., 2024. Genomic prediction in insects: a case study on wing morphology traits in the jewel wasp *Nasonia vitripennis*. bioRxiv: https://doi.org/10.1101/2024.10.09.617398

Xiang, H., Li, X., Dai, F., Xu, X., Tan, A., Chen, L., Zhang, G., Ding, Y., Li, Q. and Lian, J., 2013. Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication. BMC Genomics 14: 1-11.

Xu, Q., Wu, Z., Zeng, X. and An, X., 2020. Identification and expression profiling of chemosensory genes in *Hermetia illucens* via a transcriptomic analysis. Frontiers in Physiology 11: 720. https://doi.org/10.3389/fphys.2020.00720
Yadav, S., Daugherty, S., Shetty, A.C. and Eleftherianos, I., 2017. RNAseq analysis of the *Drosophila* response to the entomopathogenic nematode *Steinernema*. G3 Genes|Genomes|Genetics 7: 1955-1967. https://doi.org/10.1534/g3.117.041004

Yagound, B., Remnant, E.J., Buchmann, G. and Oldroyd, B.P., 2020. Intergenerational transfer of DNA methylation marks in the honey bee. Proceedings of the National Academy of Sciences of the United States of America 117: 32519-32527. https://doi.org/10.1073/pnas.2017094117

Yamaguchi, K., Kadota, M., Nishimura, O., Ohishi, Y., Naito, Y. and Kuraku, S., 2021. Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies. Molecular Ecology 30: 5923-5934.

Yang, J., Wang, D.-F., Huang, J.-H., Zhu, Q.-H., Luo, L.-Y., Lu, R., Xie, X.-L., Salehian-Dehkordi, H., Esmailizadeh, A. and Liu, G.E., 2024. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biology 25: 148.

Yokoi, K., Tsubota, T., Jouraku, A., Sezutsu, H. and Bono, H., 2021. Reference transcriptome data in silkworm *Bombyx mori*. Insects 12: 519. https://doi.org/10.3390/insects12060519

Yu, H., Spangler, M.L., Lewis, R.M. and Morota, G., 2017. Genomic relatedness strengthens genetic connectedness across management units. G3 Genes|Genomes|Genetics 7: 3543-3556. https://doi.org/10.1534/g3.117.300151

Yu, X., Yang, H., Liu, J., Qi, Y., Sun, L. and Tian, X., 2022. A strategy for a high enrichment of insect mitochondrial DNA for mitogenomic analysis. Gene 808: 145986. https://doi.org/10.1016/j.gene.2021.145986

Zaalberg, R.M., Nielsen, H.M., Noer, N.K., Schou, T.M., Jensen, K., Thormose, S., Kargo, M. and Slagboom, M., 2024. A bio-economic model for estimating economic values of important production traits in the black soldier fly (*Hermetia illucens*). Journal of Insects as Food and Feed 10: 1411-1421. https://doi.org/10.1163/23524588-00001126

Zhan, L., Paterson, I.G., Fraser, B.A., Watson, B., Bradbury, I.R., Nadukkalam Ravindran, P., Reznick, D., Beiko, R.G. and Bentzen, P., 2017. MEGASAT: automated inference of microsatellite genotypes from sequence data. Molecular Ecology Resources 17: 247-256. https://doi.org/10.1111/1755-0998.12561

Zhan, S., Fang, G., Cai, M., Kou, Z., Xu, J., Cao, Y., Bai, L., Zhang, Y., Jiang, Y., Luo, X., Xu, J., Xu, X., Zheng, L., Yu, Z., Yang, H., Zhang, Z., Wang, S., Tomberlin, J.K., Zhang, J. and Huang, Y., 2020. Genomic landscape and genetic manipulation of the black soldier fly *Hermetia illucens*, a natural waste recycler. Cell Research 30: 50-60. https://doi.org/10.1038/s41422-019-0252-6

Zhang, D.-X., Yan, L.-N., Ji, Y.-J., Hewitt, G.M. and Huang, Z.-S., 2009. Unexpected relationships of substructured populations in Chinese *Locusta migratoria*. BMC evolutionary biology 9: 1-12. https://doi.org/10.1186/1471-2148-9-144

Zhang, J., Shi, Z., Gao, Z., Wen, Y., Wang, W., Liu, W., Wang, X. and Zhu, F., 2021. Identification of three metallothioneins in the black soldier fly and their functions in Cd accumulation and detoxification. Environmental Pollution 286: 117146. https://doi.org/10.1016/j.envpol.2021.117146

Zhang, Q.-H., Silvaraju, S., Unadirekkul, P., Lim, N.W., Heng, C.W., Liu, M.H. and Puniamoorthy, N., 2024. Laboratory-adapted and wild-type black soldier flies express differential plasticity in bioconversion and nutrition when reared on urban food waste streams. Journal of the Science of Food and Agriculture 104: 1521-1530. https://doi.org/10.1002/jsfa.13039

Zhu, Z., Rehman, K.u., Yu, Y., Liu, X., Wang, H., Tomberlin, J.K., Sze, S.-H., Cai, M., Zhang, J., Yu, Z., Zheng, J. and Zheng, L., 2019. De novo transcriptome sequencing and analysis revealed the molecular basis of rapid fat accumulation by black soldier fly (*Hermetia illucens*, L.) for development of insectival biodiesel. Biotechnology for Biofuels 12: 194. https://doi.org/10.1186/s13068-019-1531-7

Zimmerman, S.J., Aldridge, C.L. and Oyler-McCance, S.J., 2020. An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern. BMC Genomics 21: 1-16.