References

Adam, B. (1983). In search of the best strains of bees : Northern Bee Books.
Alburaki, M., Karim, S., Lamour, K., Adamczyk, J., & Stewart, S. D. (2019). RNA-seq reveals disruption of gene regulation when honey bees are caged and deprived of hive conditions. Journal of Experimental Biology, 222 (18), jeb207761.
Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome research, 19 (9), 1655-1664.
Ararso, Z., Ma, C., Qi, Y., Feng, M., Han, B., Hu, H., . . . Li, J. (2018). Proteome comparisons between hemolymph of two honeybee strains (Apis mellifera ligustica) reveal divergent molecular basis in driving hemolymph function and high royal jelly secretion. Journal of proteome research, 17 (1), 402-419.
Badaoui, B., Fougeroux, A., Petit, F., Anselmo, A., Gorni, C., Cucurachi, M., . . . Formato, G. (2017). RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae.PloS one, 12 (3), e0173438.
Bertolini, F., Cardoso, T. F., Marras, G., Nicolazzi, E. L., Rothschild, M. F., & Amills, M. (2018). Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats.Genetics Selection Evolution, 50 (1), 1-12.
Bieńkowska, M., Splitt, A., Węgrzynowicz, P., & Maciorowski, R. (2021). The Buzz Changes within Time: Native Apis mellifera mellifera Honeybee Subspecies Less and Less Popular among Polish Beekeepers Since 1980.Agriculture, 11 (7), 652.
Biscarini, F., Cozzi, P., Gaspa, G., & Marras, G. (2019). detectRUNS: an R package to detect runs of homozygosity and heterozygosity in diploid genomes.
Bouga, M., Alaux, C., Bienkowska, M., Büchler, R., Carreck, N. L., Cauia, E., . . . De la Rúa, P. (2011). A review of methods for discrimination of honey bee populations as applied to European beekeeping. Journal of Apicultural Research, 50 (1), 51-84.
Brascamp, E. W., & Bijma, P. (2014). Methods to estimate breeding values in honey bees. Genetics Selection Evolution, 46 (1), 1-15.
Browning, B. L., Zhou, Y., & Browning, S. R. (2018). A one-penny imputed genome from next-generation reference panels. The American Journal of Human Genetics, 103 (3), 338-348.
Büchler, R., Berg, S., & Le Conte, Y. (2010). Breeding for resistance to Varroa destructor in Europe. Apidologie, 41 (3), 393-408.
Burren, A., Neuditschko, M., Signer‐Hasler, H., Frischknecht, M., Reber, I., Menzi, F., . . . Flury, C. (2016). Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds. Animal genetics, 47 (6), 727-739.
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M., & Wilson, J. F. (2018). Runs of homozygosity: windows into population history and trait architecture. Nature Reviews Genetics, 19 (4), 220.
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4 (1), s13742-13015-10047-13748.
Chauzat, M.-P., Cauquil, L., Roy, L., Franco, S., Hendrikx, P., & Ribiere-Chabert, M. (2013). Demographics of the European apicultural industry. PloS one, 8 (11), e79018.
Cobey, S. W., Tarpy, D. R., & Woyke, J. (2013). Standard methods for instrumental insemination of Apis mellifera queens. Journal of Apicultural Research, 52 (4), 1-18.
Costa, C. P., Elias-Neto, M., Falcon, T., Dallacqua, R. P., Martins, J. R., & Bitondi, M. M. G. (2016). RNAi-mediated functional analysis of bursicon genes related to adult cuticle formation and tanning in the honeybee, Apis mellifera. PloS one, 11 (12), e0167421.
Cridland, J. M., Tsutsui, N. D., & Ramírez, S. R. (2017). The complex demographic history and evolutionary origin of the western honey bee, Apis mellifera. Genome biology and evolution, 9 (2), 457-472.
De la Rúa, P., Jaffé, R., Dall’Olio, R., Muñoz, I., & Serrano, J. (2009). Biodiversity, conservation and current threats to European honeybees. Apidologie, 40 (3), 263-284.
Dietemann, V., Pirk, C. W. W., & Crewe, R. (2009). Is there a need for conservation of honeybees in Africa? Apidologie, 40 (3), 285-295.
Ding, Z. Y., Wang, Y. H., Luo, Z. K., Lee, H. F., Hwang, J., Chien, C. T., & Huang, M. L. (2011). Glial cell adhesive molecule unzipped mediates axon guidance in Drosophila. Developmental Dynamics, 240 (1), 122-134.
Druml, T., Neuditschko, M., Grilz-Seger, G., Horna, M., Ricard, A., Mesarič, M., . . . Brem, G. (2018). Population networks associated with runs of homozygosity reveal new insights into the breeding history of the Haflinger horse. Journal of Heredity, 109 (4), 384-392.
Emerling, C. A., Huynh, H. T., Nguyen, M. A., Meredith, R. W., & Springer, M. S. (2015). Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution. Proceedings of the royal society B: biological sciences, 282 (1819), 20151817.
Estoup, A., Solignac, M., & Cornuet, J.-M. (1994). Precise assessment of the number of patrilines and of genetic relatedness in honeybee colonies. Proceedings of the Royal Society of London. Series B: Biological Sciences, 258 (1351), 1-7.
Even, N., Devaud, J.-M., & Barron, A. B. (2012). General stress responses in the honey bee. Insects, 3 (4), 1271-1298.
Geldmann, J., & González-Varo, J. P. (2018). Conserving honey bees does not help wildlife. Science, 359 (6374), 392-393.
Grilz-Seger, G., Druml, T., Neuditschko, M., Dobretsberger, M., Horna, M., & Brem, G. (2019). High-resolution population structure and runs of homozygosity reveal the genetic architecture of complex traits in the Lipizzan horse. BMC genomics, 20 (1), 174.
Grilz-Seger, G., Mesarič, M., Cotman, M., Neuditschko, M., Druml, T., & Brem, G. (2018). Runs of homozygosity and population history of three horse breeds with small population size. Journal of Equine Veterinary Science, 71 , 27-34.
Grilz-Seger, G., Neuditschko, M., Ricard, A., Velie, B., Lindgren, G., Mesarič, M., . . . Brem, G. (2019). Genome-wide homozygosity patterns and evidence for selection in a set of European and near eastern horse breeds. Genes, 10 (7), 491.
Guichard, M., Dainat, B., Eynard, S., Vignal, A., Servin, B., Consortium, B., & Neuditschko, M. (2021). Identification of quantitative trait loci associated with calmness and gentleness in honey bees using whole‐genome sequences. Animal genetics .
Guichard, M., Neuditschko, M., Fried, P., Soland, G., & Dainat, B. (2019). A future resistance breeding strategy against Varroa destructor in a small population of the dark honey bee. Journal of Apicultural Research, 58 (5), 814-823.
Guichard, M., Neuditschko, M., Soland, G., Fried, P., Grandjean, M., Gerster, S., . . . Brascamp, E. W. (2020). Estimates of genetic parameters for production, behaviour, and health traits in two Swiss honey bee populations. Apidologie .
Guo, Y., Fu, B., Qin, G., Song, H., Wu, W., Shao, Y., . . . Yu, L. (2019). Proteome analysis reveals a strong correlation between olfaction and pollen foraging preference in honeybees. International journal of biological macromolecules, 121 , 1264-1275.
Hao, Z., Lv, D., Ge, Y., Shi, J., Weijers, D., Yu, G., & Chen, J. (2020). RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Computer Science, 6 , e251.
Jones, J. C., Myerscough, M. R., Graham, S., & Oldroyd, B. P. (2004). Honey bee nest thermoregulation: diversity promotes stability.Science, 305 (5682), 402-404.
Kardos, M., Luikart, G., & Allendorf, F. W. (2015). Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees. Heredity, 115 (1), 63-72.
Klein, A.-M., Vaissiere, B. E., Cane, J. H., Steffan-Dewenter, I., Cunningham, S. A., Kremen, C., & Tscharntke, T. (2007). Importance of pollinators in changing landscapes for world crops. Proceedings of the royal society B: biological sciences, 274 (1608), 303-313.
Kofler, R., Pandey, R. V., & Schlötterer, C. (2011). PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics, 27 (24), 3435-3436.
Kryger, P. (1990). 4. Die Bedeutung der genotypischen Varianz für das hygienische Verhalten der Honigbiene. Apidologie, 21 (4), 332-333.
Kumar, S., Deng, C. H., Hunt, M., Kirk, C., Wiedow, C., Rowan, D., . . . Brewer, L. (2020). Homozygosity mapping reveals population history and trait architecture in self-incompatible pear (Pyrus spp.).Frontiers in Plant Science, 11 .
Li, H., Bob, H., Wysoker, A., Fennell, T., Ruan, J., Homer, N., . . . Durbin, R. (2009). The Sequence Alignment/Map (SAM) Format and.
Lichtenstein, L., Grübel, K., & Spaethe, J. (2018). Opsin expression patterns coincide with photoreceptor development during pupal development in the honey bee, Apis mellifera. BMC developmental biology, 18 (1), 1-11.
Lin, J., Yu, X.-Q., Wang, Q., Tao, X., Li, J., Zhang, S., . . . You, M. (2020). Immune responses to Bacillus thuringiensis in the midgut of the diamondback moth, Plutella xylostella. Developmental & Comparative Immunology, 107 , 103661.
Mastrangelo, S., Tolone, M., Sardina, M. T., Sottile, G., Sutera, A. M., Di Gerlando, R., & Portolano, B. (2017). Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep. Genetics Selection Evolution, 49 (1), 1-10.
Mattila, H. R., Rios, D., Walker-Sperling, V. E., Roeselers, G., & Newton, I. L. (2012). Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PloS one, 7 (3), e32962.
Mattila, H. R., & Seeley, T. D. (2014). Extreme polyandry improves a honey bee colony’s ability to track dynamic foraging opportunities via greater activity of inspecting bees. Apidologie, 45 (3), 347-363.
McDonnell, C. M., Alaux, C., Parrinello, H., Desvignes, J.-P., Crauser, D., Durbesson, E., . . . Le Conte, Y. (2013). Ecto-and endoparasite induce similar chemical and brain neurogenomic responses in the honey bee (Apis mellifera). BMC ecology, 13 (1), 25.
McQuillan, R., Leutenegger, A.-L., Abdel-Rahman, R., Franklin, C. S., Pericic, M., Barac-Lauc, L., . . . Tenesa, A. (2008). Runs of homozygosity in European populations. The American Journal of Human Genetics, 83 (3), 359-372.
Metzger, J., Karwath, M., Tonda, R., Beltran, S., Águeda, L., Gut, M., . . . Distl, O. (2015). Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses.BMC genomics, 16 (1), 764.
Momeni, J., Parejo, M., Nielsen, R. O., Langa, J., Montes, I., Papoutsis, L., . . . Charrière, J.-D. (2021). Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs. BMC genomics, 22 (1), 1-12.
Neuditschko, M., Khatkar, M. S., & Raadsma, H. W. (2012). NetView: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation. PloS one, 7 (10), e48375.
Neumann, P., Moritz, R. F., & van Praagh, J. (1999). Queen mating frequency in different types of honey bee mating apiaries. Journal of Apicultural Research, 38 (1-2), 11-18.
Nouvian, M., Mandal, S., Jamme, C., Claudianos, C., d’Ettorre, P., Reinhard, J., . . . Giurfa, M. (2018). Cooperative defence operates by social modulation of biogenic amine levels in the honey bee brain.Proceedings of the royal society B: biological sciences, 285 (1871), 20172653.
Oldroyd, B. P., Rinderer, T. E., Harbo, J. R., & Buco, S. M. (1992). Effects of intracolonial genetic diversity on honey bee (Hymenoptera: Apidae) colony performance. Annals of the Entomological Society of America, 85 (3), 335-343.
Parejo, M., Henriques, D., Pinto, M. A., Soland-Reckeweg, G., & Neuditschko, M. (2018). Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera.Journal of Apicultural Research, 57 (4), 504-506.
Parejo, M., Wragg, D., Gauthier, L., Vignal, A., Neumann, P., & Neuditschko, M. (2016). Using whole-genome sequence information to foster conservation efforts for the European Dark Honey Bee, Apis mellifera mellifera. Frontiers in Ecology and Evolution, 4 , 140.
Parejo, M., Wragg, D., Henriques, D., Charrière, J.-D., & Estonba, A. (2020). Digging into the genomic past of Swiss honey bees by whole-genome sequencing museum specimens. Genome biology and evolution, 12 (12), 2535-2551.
Parry, J. W., Carleton, K. L., Spady, T., Carboo, A., Hunt, D. M., & Bowmaker, J. K. (2005). Mix and match color vision: tuning spectral sensitivity by differential opsin gene expression in Lake Malawi cichlids. Current Biology, 15 (19), 1734-1739.
Pavan, S., Delvento, C., Mazzeo, R., Ricciardi, F., Losciale, P., Gaeta, L., . . . Ricciardi, L. (2021). Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight.Horticulture research, 8 (1), 1-12.
Purfield, D. C., Berry, D. P., McParland, S., & Bradley, D. G. (2012). Runs of homozygosity and population history in cattle. BMC genetics, 13 (1), 70.
Purfield, D. C., McParland, S., Wall, E., & Berry, D. P. (2017). The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PloS one, 12 (5), e0176780.
R Core Team. (2013). R: A language and environment for statistical computing (Version 3.6.1).
Rosenberg, N. A. (2004). DISTRUCT: a program for the graphical display of population structure. Molecular ecology notes, 4 (1), 137-138.
Rossi, M. L., Ghosh, A. K., & Bohr, V. A. (2010). Roles of Werner syndrome protein in protection of genome integrity. DNA repair, 9 (3), 331-344.
Rubinstein, M., Eshed, R., Rozen, A., Zviran, T., Kuhn, D. N., Irihimovitch, V., . . . Ophir, R. (2019). Genetic diversity of avocado (Persea americana Mill.) germplasm using pooled sequencing. BMC genomics, 20 (1), 1-10.
Ruttner, F. (1988). Biogeography and Taxonomy of Honeybees : Springer.
Ruttner, F. (1995). Von der ”dunklen” zur ”grauen” deutschen Landbiene.Imkerfreund, 95 (8), 16-18.
Ruttner, H. (1972). Technische Empfehlungen zur Methodik der Leistungsprüfung von Bienenvölkern. Paper presented at the Proceedings of Paarungskontrolle und Selektion bei der Honigbiene. Internationales Symposium. Lunz am See, Austria.
Seehuus, S.-C., Taylor, S., Petersen, K., & Aamodt, R. M. (2013). Somatic maintenance resources in the honeybee worker fat body are distributed to withstand the most life-threatening challenges at each life stage. PloS one, 8 (8), e69870.
Signer‐Hasler, H., Burren, A., Ammann, P., Drögemüller, C., & Flury, C. (2019). Runs of homozygosity and signatures of selection: A comparison among eight local Swiss sheep breeds. Animal genetics, 50 (5), 512-525.
Soares, M. P. M., Barchuk, A. R., Simões, A. C. Q., dos Santos Cristino, A., de Paula Freitas, F. C., Canhos, L. L., & Bitondi, M. M. G. (2013). Genes involved in thoracic exoskeleton formation during the pupal-to-adult molt in a social insect model, Apis mellifera. BMC genomics, 14 (1), 1-17.
Soland-Reckeweg, G., Heckel, G., Neumann, P., Fluri, P., & Excoffier, L. (2009). Gene flow in admixed populations and implications for the conservation of the Western honeybee, Apis mellifera. Journal of Insect Conservation, 13 (3), 317-328.
Steinig, E. J., Neuditschko, M., Khatkar, M. S., Raadsma, H. W., & Zenger, K. R. (2016). netview p: a network visualization tool to unravel complex population structure using genome‐wide SNP s. Molecular Ecology Resources, 16 (1), 216-227.
Tarpy, D., Nielsen, R., & Nielsen, D. (2004). A scientific note on the revised estimates of effective paternity frequency in Apis.Insectes Sociaux, 51 (2), 203-204.
Uzunov, A., Brascamp, E., & Büchler, R. (2017). The basic concept of honey bee breeding programs. Bee World, 94 (3), 84-87.
Valentine, M., Hogan, J., & Collier, S. (2014). The Drosophila Chmp1 protein determines wing cell fate through regulation of epidermal growth factor receptor signaling. Developmental Dynamics, 243 (8), 977-987.
Wallberg, A., Bunikis, I., Pettersson, O. V., Mosbech, M.-B., Childers, A. K., Evans, J. D., . . . Webster, M. T. (2019). A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds. BMC genomics, 20 (1), 275.
Watts, M. E., Williams, S. M., Nithianantharajah, J., & Claudianos, C. (2018). Hypoxia-induced MicroRNA-210 targets neurodegenerative pathways.Non-coding RNA, 4 (2), 10.
Wragg, D., Marti-Marimon, M., Basso, B., Bidanel, J.-P., Labarthe, E., Bouchez, O., . . . Vignal, A. (2016). Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly. Scientific reports, 6 (1), 1-13.
Yan, H., Jia, H., Gao, H., Guo, X., & Xu, B. (2013). Identification, genomic organization, and oxidative stress response of a sigma class glutathione S-transferase gene (AccGSTS1) in the honey bee, Apis cerana cerana. Cell Stress and Chaperones, 18 (4), 415-426.
Zhang, Q., Guldbrandtsen, B., Bosse, M., Lund, M. S., & Sahana, G. (2015). Runs of homozygosity and distribution of functional variants in the cattle genome. BMC genomics, 16 (1), 542.
Zou, Z., Lopez, D. L., Kanost, M. R., Evans, J. D., & Jiang, H. (2006). Comparative analysis of serine protease‐related genes in the honey bee genome: possible involvement in embryonic development and innate immunity. Insect molecular biology, 15 (5), 603-614.