References
R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. 2014. [http://www.R-project.org/].
Alberoni, D., F. Gaggìa, L. Baffoni, M. M. Modesto, B. Biavati, and D. Di Gioia. 2019. Bifidobacterium xylocopae sp. nov. and Bifidobacterium aemilianum sp. nov., from the carpenter bee (Xylocopa violacea) digestive tract. Systematic and Applied Microbiology42 :205-216.
Anderson, K. E., T. H. Sheehan, B. M. Mott, P. Maes, L. Snyder, M. R. Schwan, A. Walton, B. M. Jones, and V. Corby-Harris. 2013. Microbial ecology of the hive and pollination landscape: bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera). PLoS ONE 8 :e83125.
Barrows, E. M. 1980. Results of a survey of damage caused by the carpenter bee Xylocopa virginica (Hymenoptera: Anthophoridae). Proc. Entomol. Soc. Wash. 82 :44.
Bates, D., M. Maechler, and B. Bolker. 2011. lme4: Linear mixed-effects models using S4 classes.
Bezark, L. G. 2013. Field Guide to the Common Bees of California: Including Bees of the Western United States. The Pan-Pacific Entomologist 89 :266-266.
Billiet, A., I. Meeus, F. Van Nieuwerburgh, D. Deforce, F. Wäckers, and G. Smagghe. 2017. Colony contact contributes to the diversity of gut bacteria in bumblebees (Bombus terrestris). Insect science24 :270-277.
Bossert, S., E. A. Murray, E. A. B. Almeida, S. G. Brady, B. B. Blaimer, and B. N. Danforth. 2019. Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae. Molecular Phylogenetics and Evolution 130 :121-131.
Breed, M. D. 1976. The Evolution of Social Behavior in Primitively Social Bees: A Multivariate Analysis. Evolution 30 :234-240.
Bushnell, B. 2014. BBMap: a fast, accurate, splice-aware aligner. Lawrence Berkeley National Lab.(LBNL), Berkeley, CA (United States).
Callahan, B. J., J. Wong, C. Heiner, S. Oh, C. M. Theriot, A. S. Gulati, S. K. McGill, and M. K. Dougherty. 2019. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic acids research 47 :e103-e103.
Cohen, H., Q. S. McFrederick, and S. M. Philpott. 2020. Environment shapes the microbiome of the blue orchard bee, Osmia lignaria. Microbial Ecology 80 :897-907.
Daisley, B. A., and G. Reid. 2021. BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities. Msystems 6 :e00082-00021.
Engel, P., W. K. Kwong, Q. McFrederick, K. E. Anderson, S. M. Barribeau, J. A. Chandler, R. S. Cornman, J. Dainat, J. R. De Miranda, and V. Doublet. 2016. The bee microbiome: impact on bee health and model for evolution and ecology of host-microbe interactions. MBio 7 .
Ge, Y., Z. Jing, Q. Diao, J.-Z. He, and Y.-J. Liu. 2021. Host Species and Geography Differentiate Honeybee Gut Bacterial Communities by Changing the Relative Contribution of Community Assembly Processes. MBio12 :e00751-00721.
Gerling, D., P. D. Hurd Jr, and A. Hefetz. 1981. In-nest behavior of the carpenter bee, Xylocopa pubescens Spinola (Hymenoptera: Anthophoridae). Journal of the Kansas Entomological Society:209-218.
Gerling, D., H. Velthuis, and A. Hefetz. 1989. Bionomics of the large carpenter bees of the genus Xylocopa. Annual review of Entomology34 :163-190.
Giannini, T., S. Boff, G. Cordeiro, E. Cartolano, A. Veiga, V. Imperatriz-Fonseca, and A. Saraiva. 2015. Crop pollinators in Brazil: a review of reported interactions. Apidologie 46 :209-223.
Hammer, T. J., E. Le, A. N. Martin, and N. A. Moran. 2021. The gut microbiota of bumblebees. Insectes Sociaux 68 :287-301.
Kapheim, K. M., T.-Y. Chan, A. Smith, W. T. Wcislo, and P. Nonacs. 2016. Ontogeny of division of labor in a facultatively eusocial sweat bee Megalopta genalis. Insectes Sociaux 63 :185-191.
Kapheim, K. M., M. M. Johnson, and M. Jolley. 2021. Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees. Scientific reports 11 :2993.
Keasar, T. 2010. Large carpenter bees as agricultural pollinators. Psyche 2010 .
Killer, J., J. Kopečný, J. Mrázek, J. Havlík, I. Koppová, O. Benada, V. Rada, and O. Kofroňová. 2010. Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees. Syst Appl Microbiol 33 :359-366.
Koch, H., and P. Schmid-Hempel. 2011. Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proceedings of the National Academy of Sciences108 :19288-19292.
Kuznetsova, A., P. B. Brockhoff, and R. H. Christensen. 2017. lmerTest package: tests in linear mixed effects models. Journal of Statistical Software 82 :1-26.
Kwong, W. K., L. A. Medina, H. Koch, K.-W. Sing, E. J. Y. Soh, J. S. Ascher, R. Jaffé, and N. A. Moran. 2017. Dynamic microbiome evolution in social bees. Science Advances 3 :e1600513.
Kwong, W. K., M. I. Steele, and N. A. Moran. 2018. Genome Sequences of Apibacter spp., Gut Symbionts of Asian Honey Bees. Genome biology and evolution 10 :1174-1179.
Lane, D. J. 1991. 16S/23S rRNA sequencing. Pages 115-175 in E. Stackebrandt, and Goodfellow, M., editor. Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, NY.
Lee, F. J., D. B. Rusch, F. J. Stewart, H. R. Mattila, and I. L. Newton. 2015. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environmental microbiology 17 :796-815.
Liu, H., M. A. Hall, L. E. Brettell, M. Halcroft, J. Wang, S. Nacko, R. Spooner-Hart, J. M. Cook, M. Riegler, and B. Singh. 2021. Gut microbial diversity in stingless bees is linked to host wing size and is influenced by geography. bioRxiv:2021.2007.2004.451070.
Love, M., S. Anders, and W. Huber. 2013. Differential analysis of count data‚ the DESeq2 package.
Lucia, M., V. H. Gonzalez, and A. H. Abrahamovich. 2015. Systematics and biology of Xylocopa subgenus Schonnherria (Hymenoptera, Apidae) in Argentina. ZooKeys:129.
Lugli, G. A., C. Milani, F. Turroni, S. Duranti, L. Mancabelli, M. Mangifesta, C. Ferrario, M. Modesto, P. Mattarelli, K. Jiří, D. van Sinderen, and M. Ventura. 2017. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. BMC Genomics 18 :568.
Marshall, L. D., and J. Alcock. 1981. The evolution of the mating system of the carpenter bee Xylocopa varipuncta (Hymenoptera: Anthophoridae). Journal of Zoology 193 :315-324.
Martinson, V. G., B. N. Danforth, R. L. Minckley, O. Rueppell, S. Tingek, and N. A. Moran. 2011. A simple and distinctive microbiota associated with honey bees and bumble bees. Molecular Ecology20 :619-628.
McFall-Ngai, M., M. G. Hadfield, T. C. Bosch, H. V. Carey, T. Domazet-Lošo, A. E. Douglas, N. Dubilier, G. Eberl, T. Fukami, and S. F. Gilbert. 2013. Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences110 :3229-3236.
McFrederick, Q. S., and S. M. Rehan. 2019. Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes. Microbial Ecology77 :513-522.
McFrederick, Q. S., J. M. Thomas, J. L. Neff, H. Q. Vuong, K. A. Russell, A. R. Hale, and U. G. Mueller. 2017. Flowers and Wild Megachilid Bees Share Microbes. Microbial Ecology 73 :188-200.
McFrederick, Q. S., H. Q. Vuong, and J. A. Rothman. 2018. Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers. International Journal of Systematic and Evolutionary Microbiology 68 :1879-1884.
McFrederick, Q. S., W. T. Wcislo, M. C. Hout, and U. G. Mueller. 2014. Host species and developmental stage, but not host social structure, affects bacterial community structure in socially polymorphic bees. Fems Microbiology Ecology 88 :398-406.
McFrederick, Q. S., W. T. Wcislo, D. R. Taylor, H. D. Ishak, S. E. Dowd, and U. G. Mueller. 2012. Environment or kin: whence do bees obtain acidophilic bacteria? Molecular Ecology 21 :1754-1768.
McMurdie, P. J., and S. Holmes. 2013. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. Plos One 8 :e61217.
Michener, C. 1990. Castes in Xylocopine Bees. Pages 123-146 in E. W., editor. Social Insects: An Evolutionary Approach to Castes and Reproduction. Springer Verlag.
Moeller, A. H., S. Foerster, M. L. Wilson, A. E. Pusey, B. H. Hahn, and H. Ochman. 2016. Social behavior shapes the chimpanzee pan-microbiome. Science Advances 2 :e1500997.
Moran, N. A. 2015. Genomics of the honey bee microbiome. Current Opinion in Insect Science 10 :22-28.
Moran, N. A., H. Ochman, and T. J. Hammer. 2019. Evolutionary and ecological consequences of gut microbial communities. Annual Review of Ecology, Evolution, and Systematics 50 :451-475.
Näpflin, K., and P. Schmid-Hempel. 2016. Immune response and gut microbial community structure in bumblebees after microbiota transplants. Proceedings of the Royal Society B: Biological Sciences283 :20160312.
Oksanen, J., F. G. Blanchet, R. Kindt, P. Legendre, R. B. O’Hara, G. L. Simpson, P. Solymos, M. H. Stevens, and H. Wagner. 2012. vegan: Community Ecology Package.
Ostwald, M., R. A. Dahan, Z. Shaffer, and J. H. Fewell. 2021. Fluid nest membership drives variable relatedness in groups of a facultatively social bee. Frontiers in Ecology and Evolution:893.
Ostwald, M., B. Lyman, Z. Shaffer, and J. Fewell. 2020. Temporal and spatial dynamics of carpenter bee sociality revealed by CT imaging. Insectes Sociaux 67 :203-212.
Paliy, O., H. Kenche, F. Abernathy, and S. Michail. 2009. High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray. Applied and environmental microbiology75 :3572-3579.
Parmentier, A., I. Meeus, F. Van Nieuwerburgh, D. Deforce, P. Vandamme, and G. Smagghe. 2018. A different gut microbial community between larvae and adults of a wild bumblebee nest (Bombus pascuorum). Insect science25 :66-74.
Powell, J. E., V. G. Martinson, K. Urban-Mead, and N. A. Moran. 2014. Routes of acquisition of the gut microbiota of the honey bee Apis mellifera. Applied and Environmental Microbiology 80 :7378-7387.
Quail, M. A., M. Smith, P. Coupland, T. D. Otto, S. R. Harris, T. R. Connor, A. Bertoni, H. P. Swerdlow, and Y. Gu. 2012. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC genomics13 :1-13.
Quast, C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies, and F. O. Glöckner. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic acids research 41 :D590-D596.
Rothman, J. A., D. L. Cox-Foster, C. Andrikopoulos, and Q. S. McFrederick. 2020. Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees. Insects 11 :645.
Rubin, B. E., J. G. Sanders, J. Hampton‐Marcell, S. M. Owens, J. A. Gilbert, and C. S. Moreau. 2014. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure. MicrobiologyOpen3 :910-921.
Rubin, B. E. R., J. G. Sanders, K. M. Turner, N. E. Pierce, and S. D. Kocher. 2018. Social behaviour in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts. Royal Society open science5 :180369-180369.
Schliep, K. P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics 27 :592-593.
Subta, P., P. Yodsuwan, R. Yongsawas, A. In-on, N. Warrit, S. Panha, K. Khongphinitbunjong, P. Chantawannakul, K. Attasopa, and T. Disayathanoowat. 2020. Bacterial Communities in Three Parts of Intestinal Tracts of Carpenter Bees (Xylocopa tenuiscapa). Insects11 :497.
Tedersoo, L., M. Albertsen, S. Anslan, and B. Callahan. 2021. Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Applied and environmental microbiology87 :e00626-00621.
Tedersoo, L., A. Tooming‐Klunderud, and S. Anslan. 2018. PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. New Phytologist 217 :1370-1385.
Vásquez, A., and T. C. Olofsson. 2009. The lactic acid bacteria involved in the production of bee pollen and bee bread. Journal of apicultural research 48 :189-195.
Vickruck, J. L., and M. H. Richards. 2021. Competition drives group formation and reduces within nest relatedness in a facultatively social carpenter bee. Frontiers in Ecology and Evolution:840.
Voulgari-Kokota, A., Q. S. McFrederick, I. Steffan-Dewenter, and A. Keller. 2019. Drivers, diversity, and functions of the solitary-bee microbiota. Trends in microbiology 27 :1034-1044.
Wang, J., Q. Su, X. Zhang, C. Li, S. Luo, X. Zhou, and H. Zheng. 2020. Entomomonas moraniae gen. nov., sp. nov., a member of the family Pseudomonadaceae isolated from Asian honey bee gut, possesses a highly reduced genome. International Journal of Systematic and Evolutionary Microbiology 70 :165-171.
Wright, E. S. 2015. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC bioinformatics16 :1-14.
Yu, G., D. K. Smith, H. Zhu, Y. Guan, and T. T. Y. Lam. 2017. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 8 :28-36.
Zheng, J., S. Wittouck, E. Salvetti, C. M. Franz, H. Harris, P. Mattarelli, P. W. O’Toole, B. Pot, P. Vandamme, and J. Walter. 2020. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae.