Stork, N. E. How many species of insects and other terrestrial arthropods are there on Earth?. Annu. Rev. Entomol. 63, 31–45 (2018).
Stork, N. E., McBroom, J., Gely, C. & Hamilton, A. J. New approaches narrow global species estimates for beetles, insects, and terrestrial arthropods. Proc. Natl. Acad. Sci. U. S. A. 112, 7519–7523 (2015).
Lange, C. E. & Lord, J. C. Protistan entomopathogens. In Insect Pathology (eds. Vega, F. E. & Kaya, H. K.) 367–394 (Academic Press, 2012). https://doi.org/10.1016/B978-0-12-384984-7.00010-5.
Fabel, P., Radek, R. & Storch, V. A new spore-forming protist, Nephridiophaga blaberi sp. nov., in the Death’s head cockroach Blaberus craniifer. Eur. J. Protistol. 36, 387–395 (2000).
Ivanić, M. Die Entwicklungsgeschichte und die parasitäre Zerstörungsarbeit einer in den Zellen der Malpighischen Gefäße der Honigbiene (Apis mellifera) schmarotzenden Haplosporidie Nephridiophaga apis n. g. n. sp.. Cellule 45, 291–324 (1937).
Ormières, R. & Manier, J.-F. Observations sur Nephridiophaga forficulae (Léger, 1909). Ann. Parasitol. Hum. Comparée 48, 1–10 (1973).
Radek, R., Wellmanns, D. & Wolf, A. Two new species of Nephridiophaga (Zygomycota) in the Malpighian tubules of cockroaches. Parasitol. Res. 109, 473–482 (2011).
Radek, R. & Herth, W. Ultrastructural investigation of the spore-forming protist Nephridiophaga blattellae in the Malpighian tubules of the German cockroach Blattella germanica. Parasitol. Res. 85, 216–231 (1999).
Woolever, P. Life history and electron microscopy of a haplosporidian, Nephridiophaga blattellae (Crawley) n. comb, in the Malphigian tubules of the German Cockroach, Blattella germanica (L.). J. Protozool. 13, 622–642 (1966).
Radek, R., Klein, G. & Storch, V. The spore of the unicellular organism Nephridiophaga blattellae: ultrastructure and substances of the spore wall. Acta Protozool. 41, 169–181 (2002).
Purrini, K. & Weiser, J. Light and electron microscope studies on a protozoan, Oryctospora alata n. gen., n. sp. (Protista, Coelosporidiidae), parasitizing a natural population of the rhinoceros beetle, Oryctes monoceros Oliv. (Coleoptera, Scarabaeidae). Zool. Beitraege 332, 209–220 (1990).
Purrini, K. & Rohde, M. Light and electron microscope studies on two new protists, Coelosporidium schalleri n. sp. and Coelosporidium meloidorum n. sp. (Protista) infecting natural populations of the flea beetle, Podagrica fuscicornis, and flower beetle, Mylabris maculiventris. Zool. Anz. 220, 323–333 (1988).
Lange, C. E. Unclassified protists of arthropods: the ultrastructure of Nephridiophaga periplanetae (Lutz & Splendore, 1903) n. comb., and the affinities of the Nephridiophagidae to other protists. J. Eukaryot. Microbiol. 40, 689–700 (1993).
Perrin, W. S. Observations on the structure and life-history of Pleistophora periplanetæ, Lutz and Splendore. J. Cell Sci. 49, 615–633 (1906).
Sprague, V. Recent problems of taxonomy and morphology of Haplosporidia. J. Parasitol. 56, 327–328 (1970).
Wylezich, C., Radek, R. & Schlegel, M. Phylogenetische Analyse der 18S rRNA identifiziert den parasitischen Protisten Nephridiophaga blattellae (Nephridiophagidae) als Vertreter der Zygomycota (Fungi). Denisia 13, 435–442 (2004).
Radek, R. et al. Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota. MycoKeys 25, 31–50 (2017).
Evangelista, D. A. et al. An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea). Proc. R. Soc. B Biol. Sci. 286, 20182076 (2019).
Baumann, P., Moran, N. A. & Baumann, L. The evolution and genetics of aphid endosymbionts. Bioscience 47, 12–20 (1997).
Peek, A. S., Feldman, R. A., Lutz, R. A. & Vrijenhoek, R. C. Cospeciation of chemoautotrophic bacteria and deep sea clams. Proc. Natl. Acad. Sci. U. S. A. 95, 9962–9966 (1998).
Hosokawa, T., Kikuchi, Y., Nikoh, N., Shimada, M. & Fukatsu, T. Strict host-symbiont cospeciation and reductive genome evolution in insect gut bacteria. PLOS Biol. 4, e337 (2006).
Hughes, J., Kennedy, M., Johnson, K. P., Palma, R. L. & Page, R. D. M. Multiple cophylogenetic analyses reveal frequent cospeciation between pelecaniform birds and Pectinopygus lice. Syst. Biol. 56, 232–251 (2007).
Desai, M. S. et al. Strict cospeciation of devescovinid flagellates and Bacteroidales ectosymbionts in the gut of dry-wood termites (Kalotermitidae). Environ. Microbiol. 12, 2120–2132 (2010).
Wijayawardene, N. et al. Outline of fungi and fungus-like taxa. Mycosphere 11, 1060–1456 (2020).
Tedersoo, L., Anslan, S., Bahram, M., Kõljalg, U. & Abarenkov, K. Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach. Fungal Divers. 103, 273–293 (2020).
Crawley, H. Interrelationships of the Sporozoa. Am. Nat. 39, 607–624 (1905).
White, M. M. et al. Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia 98, 872–884 (2006).
Letcher, P. M., Powell, M. J., Churchill, P. F. & Chambers, J. G. Ultrastructural and molecular phylogenetic delineation of a new order, the Rhizophydiales (Chytridiomycota). Mycol. Res. 110, 898–915 (2006).
Van den Wyngaert, S., Rojas-Jimenez, K., Seto, K., Kagami, M. & Grossart, H.-P. Diversity and hidden host specificity of chytrids infecting colonial volvocacean algae. J. Eukaryot. Microbiol. 65, 870–881 (2018).
James, T. Y. et al. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98, 860–871 (2006).
Powell, M. J., Letcher, P. M., Chambers, J. G. & Roychoudhury, S. A new genus and family for the misclassified chytrid, Rhizophlyctis harderi. Mycologia 107, 419–431 (2015).
Letcher, P. M., Powell, M. J., Lopez, S., Lee, P. A. & McBride, R. C. A new isolate of Amoeboaphelidium protococcarum, and Amoeboaphelidium occidentale, a new species in phylum Aphelida (Opisthosporidia). Mycologia 107, 522–531 (2015).
Strassert, J. F. H. et al. Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. ISME J. 12, 304–308 (2018).
Jamy, M. et al. Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity. Mol. Ecol. Resour. 20, 429–443 (2020).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. Phylobayes mpi: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013).
Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).
Lloyd, D. & Harris, J. C. Giardia: highly evolved parasite or early branching eukaryote?. Trends Microbiol. 10, 122–127 (2002).
Burki, F. et al. Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in Rhizaria. Curr. Biol. 23, 1541–1547 (2013).
Abbott, C. L. Evolution: hidden at the end of a very long branch. Curr. Biol. 27, R271–R273 (2014).
Keeling, P. J. & Fast, N. M. Microsporidia: biology and evolution of highly reduced intracellular parasites. Annu. Rev. Microbiol. 56, 93–116 (2002).
Mozley-Standridge, S. E., Letcher, P. M., Longcore, J. E., Porter, D. & Simmons, D. R. Cladochytriales—a new order in Chytridiomycota. Mycol. Res. 113, 498–507 (2009).
Jerônimo, G. H., Jesus, A. L., Simmons, D. R., James, T. Y. & Pires-Zottarelli, C. L. A. Novel taxa in Cladochytriales (Chytridiomycota): Karlingiella (gen. nov.) and Nowakowskiella crenulata (sp. nov.). Mycologia 111, 506–516 (2019).
Gutiérrez, M. H., Jara, A. M. & Pantoja, S. Fungal parasites infect marine diatoms in the upwelling ecosystem of the Humboldt current system off central Chile. Environ. Microbiol. 18, 1646–1653 (2016).
Lepelletier, F. et al. Dinomyces arenysensis gen. et sp. nov. (Rhizophydiales, Dinomycetaceae fam. Nov.), a chytrid infecting marine dinoflagellates. Protist 165, 230–244 (2014).
Hassett, B. T. & Gradinger, R. Chytrids dominate arctic marine fungal communities. Environ. Microbiol. 18, 2001–2009 (2016).
Comeau, A. M., Vincent, W. F., Bernier, L. & Lovejoy, C. Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats. Sci. Rep. 6, 30120 (2016).
Lefèvre, E., Roussel, B., Amblard, C. & Sime-Ngando, T. The molecular diversity of freshwater picoeukaryotes reveals high occurrence of putative parasitoids in the plankton. PLoS ONE 3, e2324 (2008).
Fisher, M. C., Garner, T. W. J. & Walker, S. F. Global emergence of Batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host. Annu. Rev. Microbiol. 63, 291–310 (2009).
Powell, M. J. & Letcher, P. M. Chytridiomycota, Monoblepharidomycota, and Neocallimastigomycota. In Systematics and Evolution: The Mycota VII Part A (eds. McLaughlin, D. J. & Spatafora, J. W.) 141–175 (Springer, 2014). https://doi.org/10.1007/978-3-642-55318-9.
Cali, A., Becnel, J. J. & Takvorian, P. M. Microsporidia. In Handbook of the Protists: Second Edition (eds. Archibald, J. M. et al.) 1559–1618 (Springer, 2017). https://doi.org/10.1007/978-3-319-28149-0_27.
Powell, M. J. Chytridiomycota. In Handbook of the Protists: Second Edition (eds. Archibald, J. M. et al.) 1523–1558 (Springer, 2017). https://doi.org/10.1007/978-3-319-28149-0_18.
Schulte, R. D., Makus, C., Hasert, B., Michiels, N. K. & Schulenburg, H. Multiple reciprocal adaptations and rapid genetic change upon experimental coevolution of an animal host and its microbial parasite. Proc. Natl. Acad. Sci. U. S. A. 107, 7359–7364 (2010).
Ebert, D. Host-parasite coevolution: insights from the Daphnia-parasite model system. Curr. Opin. Microbiol. 11, 290–301 (2008).
Spurr, A. R. A low-viscosity epoxy resin embedding medium for electron microscopy. J. Ultrasructure Res. 26, 31–43 (1969).
Reynolds, E. S. The use of lead citrate at high pH as an electron-opaque stain in electron microscopy. J. Cell Biol. 17, 208–212 (1963).
Wurzbacher, C. et al. Introducing ribosomal tandem repeat barcoding for fungi. Mol. Ecol. Resour. 19, 118–127 (2019).
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
Roehr, J. T., Dieterich, C. & Reinert, K. Flexbar 3.0—SIMD and multicore parallelization. Bioinformatics 33, 2941–2942 (2017).
Nakamura, T., Yamada, K. D., Tomii, K. & Katoh, K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 34, 2490–2492 (2018).
Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71, 491–499 (1988).
Liu, H. & Beckenbach, A. T. Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects. Mol. Phylogenet. Evol. 1, 41–52 (1992).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
Shimodaira, H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51, 492–508 (2002).
Madeira, F. et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 47, W636–W641 (2019).
Le, V. S., Dang, C. C. & Le, Q. S. Improved mitochondrial amino acid substitution models for metazoan evolutionary studies. BMC Evol. Biol. 17, 136 (2017).
Source: Ecology - nature.com
