References
Ahantarig, A., Trinachartvanit, W., Baimai, V., & Grubhoffer, L. (2013). Hard ticks and their bacterial endosymbionts (or would be pathogens). Folia Microbiologica, 58 (5), 419-428. doi: 10.1007/s12223-013-0222-1
Aksoy, S. (2000). Tsetse - A haven for microorganisms.Parasitology Today, 16 (3), 114-118. doi: 10.1016/S0169-4758(99)01606-3
Allen, J. M., Burleigh, J. G., Light, J. E., & Reed, D. L. (2016). Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice. PeerJ, 4, e2187. doi: 10.7717/peerj.2187
Amann, R., Krumholz, L., & Stahl, D. (1990). Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. Journal of Bacteriology, 172 (2), 762-770. doi: 10.1128/jb.172.2.762-770.1990
Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data.
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., … Meyer, F. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics, 9 (1), 75. doi: 10.1186/1471-2164-9-75
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., … Pyshkin, A. V. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19 (5), 455-477. doi: 10.1089/cmb.2012.0021
Baumann, P. (2005). Biology of bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annual Review of Microbiology, 59,155-189. doi: 10.1146/annurev.micro.59.030804.121041
Bennett, G. M., & Moran, N. A. (2013). Small, smaller, smallest: The origins and evolution of ancient dual symbioses in a phloem-feeding insect. Genome Biology and Evolution, 5 (9), 1675-1688. doi: 10.1093/gbe/evt118
Bennett, G. M., & Moran, N. A. (2015). Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole. Proceedings of the National Academy of Sciences of the United States of America, 112 (33), 10169-10176. doi: 10.1073/pnas.1421388112
Brewer, T. E., Albertsen, M., Edwards, A., Kirkegaard, R. H., Rocha, E. P., & Fierer, N. (2020). Unlinked rRNA genes are widespread among bacteria and archaea. The ISME Journal, 14 (2), 597-608. doi: 10.1038/s41396-019-0552-3
Boyd, B. M., Allen, J. M., Koga, R., Fukatsu, T., Sweet, A. D., Johnson, K. P., & Reed, D. L. (2016). Two bacterial genera, Sodalis andRickettsia , associated with the seal louseProechinophthirus fluctus (Phthiraptera: Anoplura). Applied and Environmental Microbiology, 82 (11), 3185-3197. doi: 10.1128/AEM.00282-16
Boyd, B. M., Allen, J. M., de Crécy-Lagard, V., & Reed, D. L. (2014). Genome sequence of Candidatus Riesia pediculischaeffi, endosymbiont of chimpanzee lice, and genomic comparison of recently acquired endosymbionts from human and chimpanzee lice. G3: Genes, Genomes, Genetics4 (11), 2189-2195. doi: 10.1534/g3.114.012567
Boyd, B. M., Allen, J. M., Nguyen, N. P., Vachaspati, P., Quicksall, Z. S., Warnow, T., … & Reed, D. L. (2017). Primates, lice and bacteria: speciation and genome evolution in the symbionts of hominid lice. Molecular Biology and Evolution34 (7), 1743-1757. doi: doi.org/10.1093/molbev/msx117
Carattoli, A., Zankari, E., García-Fernández, A., Larsen, M. V., Lund, O., Villa, L., … & Hasman, H. (2014). In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.Antimicrobial Agents and Chemotherapy, 58 (7), 3895-3903. doi: 10.1128/AAC.02412-14
Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution17 (4), 540-552. doi: 10.1093/oxfordjournals.molbev.a026334
Chen, X., Li, S., & Aksoy, S. (1999). Concordant evolution of a symbiont with its host insect species: molecular phylogeny of genusGlossina and its bacteriome-associated endosymbiont,Wigglesworthia glossinidiaJournal of Molecular Evolution48 (1), 49-58. doi: 10.1007/PL00006444
Clark, M. A., Moran, N. A., Baumann, P., & Wernegreen, J. J. (2000). Cospeciation between bacterial endosymbionts (Buchnera ) and a recent radiation of aphids (Uroleucon ) and pitfalls of testing for phylogenetic congruence. Evolution54 (2), 517-525. doi: 10.1111/j.0014-3820.2000.tb00054.x
Darling, A. E., Mau, B., & Perna, N. T. (2010). progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.PloS One, 5 (6), e11147. doi: 10.1371/journal.pone.0011147
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods9 (8), 772-772. doi: 10.1038/nmeth.2109
De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics34 (15), 2666-2669. doi: 10.1093/bioinformatics/bty149
Doudoumis, V., Blow, F., Saridaki, A., Augustinos, A., Dyer, N. A., Goodhead, I., … & Parker, A. G. (2017). Challenging theWigglesworthia , Sodalis , Wolbachia symbiosis dogma in tsetse flies: Spiroplasma is present in both laboratory and natural populations. Scientific Reports7 (1), 1-13. doi: 10.1038/s41598-017-04740-3
Douglas, A. E. (1989). Mycetocyte symbiosis in insects. Biological Reviews64 (4), 409-434. doi: 10.1111/j.1469-185X.1989.tb00682.x
Douglas, A. E. (2015). Multiorganismal insects: diversity and function of resident microorganisms. Annual Review of Entomology60 , 17-34. doi: 10.1146/annurev-ento-010814-020822
Edgar, R. C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods10 (10), 996. doi: 10.1038/nmeth.2604
Engel, P., & Moran, N. A. (2013). The gut microbiota of insects–diversity in structure and function. FEMS Microbiology Reviews37 (5), 699-735. doi: 10.1111/1574-6976.12025
Felsheim, R. F., Kurtti, T. J., & Munderloh, U. G. (2009). Genome sequence of the endosymbiont Rickettsia peacockii and comparison with virulent Rickettsia rickettsii : identification of virulence factors. PloS One4 (12), e8361. doi: 10.1371/journal.pone.0008361
Fukatsu, T., Hosokawa, T., Koga, R., Nikoh, N., Kato, T., Hayama, S. I., … & Tanaka, I. (2009). Intestinal endocellular symbiotic bacterium of the macaque louse Pedicinus obtusus : distinct endosymbiont origins in anthropoid primate lice and the old world monkey louse. Applied Environmental Microbiology75 (11), 3796-3799. doi: 10.1128/AEM.00226-09
Gauthier, J. P., Outreman, Y., Mieuzet, L., & Simon, J. C. (2015). Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA. PloS One10 (3), e0120664. doi: 10.1371/journal.pone.0120664
Gerhart, J. G., Moses, A. S., & Raghavan, R. (2016). AFrancisella -like endosymbiont in the Gulf Coast tick evolved from a mammalian pathogen. Scientific Reports6 , 33670. doi: 10.1038/srep33670
Guindon, S., & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology52 (5), 696-704. doi: 10.1080/10635150390235520
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology59 (3), 307-321. doi: 10.1093/sysbio/syq010
Guizzo, M. G., Parizi, L. F., Nunes, R. D., Schama, R., Albano, R. M., Tirloni, L., … & Gonzales, S. A. (2017). A Coxiella mutualist symbiont is essential to the development of Rhipicephalus microplusScientific Reports7 (1), 1-10. doi: 10.1038/s41598-017-17309-x
Hypša, V., & Křížek, J. (2007). Molecular evidence for polyphyletic origin of the primary symbionts of sucking lice (Phthiraptera, Anoplura). Microbial Ecology54 (2), 242-251. doi: 10.1007/s00248-006-9194-x
Jones, R. T., McCormick, K. F., & Martin, A. P. (2008). Bacterial communities of Bartonella -positive fleas: diversity and community assembly patterns. Applied and Environmental Microbiology74 (5), 1667-1670. doi: 10.1128/AEM.02090-07
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M. (2016). KEGG as a reference resource for gene and protein annotation. Nucleic Acids Research44 (D1), D457-D462. doi: 10.1093/nar/gkv1070
Katoh, K., Misawa, K., Kuma, K. I., & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research30 (14), 3059-3066. doi: 10.1093/nar/gkf436
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., … & Thierer, T. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics28 (12), 1647-1649. doi: 10.1093/bioinformatics/bts199
Kwong, W. K., & Moran, N. A. (2013). Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description ofSnodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicolagen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order ‘Enterobacteriales’ of the Gammaproteobacteria. International Journal of Systematic and Evolutionary Microbiology63 (6), 2008-2018. doi: 10.1099/ijs.0.044875-0
Lefort, V., Longueville, J. E., & Gascuel, O. (2017). SMS: smart model selection in PhyML. Molecular Biology and Evolution34 (9), 2422-2424. doi: 10.1093/molbev/msx149
Light, J. E., Smith, V. S., Allen, J. M., Durden, L. A., & Reed, D. L. (2010). Evolutionary history of mammalian sucking lice (Phthiraptera: Anoplura). BMC Evolutionary Biology10 (1), 292. doi: 10.1186/1471-2148-10-292
Manzano‐Marín, A., Szabó, G., Simon, J. C., Horn, M., & Latorre, A. (2017). Happens in the best of subfamilies: establishment and repeated replacements of co‐obligate secondary endosymbionts within Lachninae aphids. Environmental Microbiology19 (1), 393-408. doi: 10.1111/1462-2920.13633
Martinson, V. G., Moy, J., & Moran, N. A. (2012). Establishment of characteristic gut bacteria during development of the honeybee worker. Applied and Environmental Microbiology78 (8), 2830-2840. doi: 10.1128/AEM.07810-11
Martinů, J., Hypša, V., & Štefka, J. (2018). Host specificity driving genetic structure and diversity in ectoparasite populations: Coevolutionary patterns in Apodemus mice and their lice. Ecology and Evolution8 (20), 10008-10022. doi: 10.1002/ece3.4424
Meseguer, A. S., Manzano‐Marín, A., Coeur D’Acier, A., Clamens, A. L., Godefroid, M., & Jousselin, E. (2017). Buchnera has changed flatmate but the repeated replacement of co‐obligate symbionts is not associated with the ecological expansions of their aphid hosts. Molecular Ecology26 (8), 2363-2378. doi: 10.1111/mec.13910
Moran, N. A. (1996). Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proceedings of the National Academy of Sciences93 (7), 2873-2878. doi: 10.1073/pnas.93.7.2873
Moran, N. A., McCutcheon, J. P., & Nakabachi, A. (2008). Genomics and evolution of heritable bacterial symbionts. Annual Review of Genetics42 , 165-190. doi: 10.1146/annurev.genet.41.110306.130119
Munson, M. A., Baumann, L., & Baumann, P. (1993). Buchnera aphidicola (a prokaryotic endosymbiont of aphids) contains a putative 16S rRNA operon unlinked to the 23S rRNA-encoding gene: sequence determination, and promoter and terminator analysis. Gene137 (2), 171-178. doi: 10.1016/0378-1119(93)90003-L
Niebylski, M. L., Peacock, M. G., Fischer, E. R., Porcella, S. F., & Schwan, T. G. (1997). Characterization of an endosymbiont infecting wood ticks, Dermacentor andersoni , as a member of the genusFrancisellaApplied and Environmental Microbiology63 (10), 3933-3940. doi: 10.1128/AEM.63.10.3933-3940.1997
Noda, H., Munderloh, U. G., & Kurtti, T. J. (1997). Endosymbionts of ticks and their relationship to Wolbachia spp. and tick-borne pathogens of humans and animals. Applied and Environmental Microbiology63 (10), 3926-3932. doi: 10.1128/AEM.63.10.3926-3932.1997
Oteo, J. A., Portillo, A., Portero, F., Zavala-Castro, J., Venzal, J. M., & Labruna, M. B. (2014). ’Candidatus Rickettsia asemboensis’ and Wolbachia spp. in Ctenocephalides felis andPulex irritans fleas removed from dogs in Ecuador. Parasites & Vectors7 (1), 455. doi: 10.1186/s13071-014-0455-0
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology67 (5), 901-904. doi: 10.1093/sysbio/syy032
Říhová, J., Nováková, E., Husník, F., & Hypša, V. (2017).Legionella becoming a mutualist: Adaptive processes shaping the genome of symbiont in the louse Polyplax serrataGenome Biology and Evolution9 (11), 2946-2957. doi: 10.1093/gbe/evx217
Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., … & Huelsenbeck, J. P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology61 (3), 539-542. doi: 10.1093/sysbio/sys029
Sauer, C., Stackebrandt, E., Gadau, J., Hölldobler, B., & Gross, R. (2000). Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: proposal of the new taxon Candidatus Blochmannia gen. nov. International Journal of Systematic and Evolutionary Microbiology50 (5), 1877-1886. doi: 10.1099/00207713-50-5-1877
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., … & Tinevez, J. Y. (2012). Fiji: an open-source platform for biological-image analysis. Nature Methods9 (7), 676-682. doi: 10.1038/nmeth.2019
Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods9 (7), 671-675. doi: 10.1038/nmeth.2089
Yilmaz, L. S., Parnerkar, S., & Noguera, D. R. (2011). mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization. Applied and Environmental Microbiology77 (3), 1118-1122. doi: 10.1128/AEM.01733-10