Adl, S. M. et al. Revisions to the classification, nomenclature, and diversity of eukaryotes. J. Eukaryot. Microbiol. 66, 4–119. https://doi.org/10.1111/jeu.12691 (2019).
Google Scholar
Smirnov, A. Amoebas, Lobose. In Encyclopedia of Microbiology (ed. Schaechter, M.) 191–212 (Elsevier, 2012).
Schaeffer, A. A. Taxonomy of the Amoebas: With Descriptions of Thirty-Nine New Marine and Freshwater Species (Carnegie Inst, 1926).
Page, F. C. The classification of “naked” amoebae (Phylum Rhizopoda). Arch. Protistenkd. 133, 199–217. https://doi.org/10.1016/S0003-9365(87)80053-2 (1987).
Google Scholar
Page, F. C. A New Key to Freshwater and Soil Gymnamoebae (Freshwater Biological Association, 1988).
Smirnov, A. V. & Goodkov, A. V. An illustrated list of basic morphotypes of Gymnamoebia (Rhizopoda, Lobosea). Protistology 1, 20–29 (1999).
Smirnov, A. V. & Brown, S. Guide to the methods of study and identification of soil gymnamoebae. Protistology 3, 148–190 (2004).
Bovee, E. C. & Jahn, T. L. Mechanisms of movement in taxonomy of Sarcodina. II. The organization of subclasses and orders in relationship to the classes Autotractea and Hydraulea. Am. Midland Nat. 73, 293–298. https://doi.org/10.2307/2423456 (1965).
Google Scholar
Bovee, E. C. & Jahn, T. L. Mechanisms of movement in taxonomy or sarcodina. III. Orders, suborders, families, and subfamilies in the superorder Lobida. Syst. Zool. 15, 229–240. https://doi.org/10.2307/sysbio/15.3.229 (1966).
Google Scholar
Bovee, E.C. & Sawyer, T.K. Marine Flora and Fauna of the Northeastern United States. Protozoa: Sarcodina: Amoebae. (NOAA Technical Report, 1979). https://doi.org/10.5962/bhl.title.63225.
Jahn, T. L. & Bovee, E. C. Mechanisms of movement in taxonomy of Sarcodina. I. As a basis for a new major dichotomy into two classes, Autotractea and Hydraulea. Am. Midl. Nat. 73, 30–40. https://doi.org/10.2307/2423319 (1965).
Google Scholar
Jahn, T. L., Bovee, E. C. & Griffith, D. L. Taxonomy and evolution of the Sarcodina: A reclassification. Taxon 23, 483–496. https://doi.org/10.2307/1218771 (1974).
Google Scholar
Cavalier-Smith, T., Chao, E.E.-Y. & Oates, B. Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. Eur. J. Protistol. 40, 21–48. https://doi.org/10.1016/j.ejop.2003.10.001 (2004).
Google Scholar
Smirnov, A. et al. Molecular phylogeny and classification of the lobose amoebae. Protist 156, 129–142. https://doi.org/10.1016/j.protis.2005.06.002 (2005).
Google Scholar
Amaral Zettler, L. A. et al. A molecular reassessment of the leptomyxid amoebae. Protist 151, 275–282. https://doi.org/10.1078/1434-4610-00025 (2000).
Google Scholar
Bolivar, I., Fahrni, J. F., Smirnov, A. & Pawlowski, J. SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): The origin of gymnamoebae revisited. Mol. Biol. Evol. 18, 2306–2314. https://doi.org/10.1093/oxfordjournals.molbev.a003777 (2001).
Google Scholar
Fahrni, J. F. et al. Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol. Biol. Evol. 20, 1881–1886. https://doi.org/10.1093/molbev/msg201 (2003).
Google Scholar
Cavalier-Smith, T. et al. Multigene phylogeny resolves deep branching of Amoebozoa. Mol. Phylogenet. Evol. 83, 293–304. https://doi.org/10.1016/j.ympev.2014.08.011 (2015).
Google Scholar
Cavalier-Smith, T., Chao, E. E. & Lewis, R. 187-gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution. Mol. Phylogenet. Evol. 99, 275–296. https://doi.org/10.1016/j.ympev.2016.03.023 (2016).
Google Scholar
Kang, S. et al. Between a pod and a hard test: The deep evolution of amoebae. Mol. Biol. Evol. 34, 2258–2270. https://doi.org/10.1093/molbev/msx162 (2017).
Google Scholar
Tekle, Y. I. & Wood, F. C. Longamoebia is not monophyletic: Phylogenomic and cytoskeleton analyses provide novel and well-resolved relationships of amoebozoan subclades. Mol. Phylogenet. Evol. 114, 249–260. https://doi.org/10.1016/j.ympev.2017.06.019 (2017).
Google Scholar
Tekle, Y. I., Wang, F., Wood, F. C., Anderson, O. R. & Smirnov, A. New insights on the evolutionary relationships between the major lineages of Amoebozoa. bioRxiv https://doi.org/10.1101/2022.02.28.482369 (2022).
Google Scholar
Van Wichelen, J. et al. A hotspot of amoebae diversity: 8 new naked amoebae associated with the planktonic bloom-forming cyanobacterium microcystis. Acta Protozool. 55, 61–87. https://doi.org/10.4467/16890027AP.16.007.4942 (2016).
Google Scholar
Janicki, C. Paramoebenstudien (P. pigmentifera Grassi und P. chaetognathi Grassi). Z. Wiss. Zool. 103, 449–518 (1912).
Volkova, E. & Kudryavtsev, A. A morphological and molecular reinvestigation of Janickina pigmentifera (Grassi, 1881) Chatton 1953—an amoebozoan parasite of arrow-worms (Chaetognatha). Int. J. Syst. Evol. Microbiol. 71, 005094. https://doi.org/10.1099/ijsem.0.005094 (2021).
Google Scholar
Page, F. C. Taxonomic criteria for limax amoebae, with descriptions of 3 new species of Hartmannella and 3 of Vahlkampfia. J. Protozool. 14, 499–521 (1967).
Google Scholar
Page, F. C. & Blanton, R. L. The Heterolobosea (Sarcodina: Rhizopoda), a new class uniting the Schizopyrenida and the Acrasidae (Acrasida). Protistologica 21, 121–132 (1985).
Laurin, V., Labbé, N., Parent, S., Juteau, P. & Villemur, R. Microeukaryote diversity in a marine methanol-fed fluidized denitrification system. Microb. Ecol. 56, 637–648. https://doi.org/10.1007/s00248-008-9383-x (2008).
Google Scholar
Page, F. C. A further study of taxonomic criteria for limax amoebae, with descriptions of new species and a key to genera. Arch. Protistenkd. 116, 149–184 (1974).
Page, F. C. Marine Gymnamoebae (Institute of Terrestrial Ecology, 1983).
Page, F. C. A light- and electron-microscopical comparison of limax and flabellate marine amoebae belonging to four genera. Protistologica 16, 57–78 (1980).
Kuiper, M. W. et al. Quantitative detection of the free-living amoeba Hartmannella vermiformis in surface water by using real-time PCR. Appl. Environ. Microbiol. 72, 5750–5756. https://doi.org/10.1128/AEM.00085-06 (2006).
Google Scholar
Smirnov, A., Chao, E., Nassonova, E. & Cavalier-Smith, T. A revised classification of naked lobose amoebae (Amoebozoa: Lobosa). Protist 162, 545–570. https://doi.org/10.1016/j.protis.2011.04.004 (2011).
Google Scholar
Page, F. C. & Blakey, S. M. Cell surface structure as a taxonomic character in the Thecamoebidae (Protozoa: Gymnamoebia). Zool. J. Linn. Soc. 66, 113–135. https://doi.org/10.1111/j.1096-3642.1979.tb01905.x (1979).
Google Scholar
Smirnov, A. V. & Goodkov, A. V. Paradermamoeba valamo gen. n., sp. n. (Gymnamoebia, Thecamoebidae)—a freshwater amoeba from bottom sediments. Zool. Zhurn. 72, 5–11 (1993) (In Russian with English summary).
Smirnov, A. & Goodkov, A. Ultrastructure and geographic distribution of the genus Paradermamoeba (Gymnamoebia, Thecamoebidae). Eur. J. Protistol. 40, 113–118. https://doi.org/10.1016/j.ejop.2003.12.001 (2004).
Google Scholar
Smirnov, A. V., Bedjagina, O. M. & Goodkov, A. V. Dermamoeba algensis n sp (Amoebozoa, Dermamoebidae)—an algivorous lobose amoeba with complex cell coat and unusual feeding mode. Eur. J. Protistol. 47, 67–78. https://doi.org/10.1016/j.ejop.2010.12.002 (2011).
Google Scholar
Bailey, G. B., Day, D. B. & McCoomer, N. E. Entamoeba motility: Dynamics of cytoplasmic streaming, locomotion and translocation of surface-bound particles, and organization of the actin cytoskeleton in Entamoeba invadens. J. Protozool. 39, 267–272. https://doi.org/10.1111/j.1550-7408.1992.tb01313.x (1992).
Google Scholar
Shiratori, T. & Ishida, K. I. Entamoeba marina n. sp.; a new species of Entamoeba isolated from tidal flat sediment of Iriomote Island, Okinawa, Japan. J. Eukaryot. Microbiol. 63, 280–286. https://doi.org/10.1111/jeu.12276 (2016).
Google Scholar
Lahr, D. J., Laughinghouse, H. D. IV., Oliverio, A. M., Gao, F. & Katz, L. A. How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth. BioEssays 36, 950–959. https://doi.org/10.1002/bies.201400056 (2014).
Google Scholar
Pomorski, P. et al. Actin dynamics in Amoeba proteus motility. Protoplasma 231, 31–41. https://doi.org/10.1007/s00709-007-0243-1 (2007).
Google Scholar
Rogerson, A., Anderson, O. R. & Vogel, C. Are planktonic naked amoebae predominately floc associated or free in the water column?. J. Plankton Res. 25, 1359–1365. https://doi.org/10.1093/plankt/fbg102 (2003).
Google Scholar
Kudryavtsev, A. Paravannella minima n. g. n. sp. (Discosea, Vannellidae) and distinction of the genera in the vannellid amoebae. Eur. J. Protistol. 50, 258–269. https://doi.org/10.1016/j.ejop.2013.12.004 (2014).
Google Scholar
Kudryavtsev, A., Völcker, E., Clauß, S. & Pawlowski, J. Ovalopodium rosalinum sp. nov., Planopodium haveli gen. nov, sp. nov., Planopodium desertum comb. nov. and new insights into phylogeny of the deeply branching members of the order Himatismenida (Amoebozoa). Int. J. Sys. Evol. Microbiol. 71, 004737. https://doi.org/10.1099/ijsem.0.004737 (2021).
Google Scholar
Blandenier, Q. et al. Mycamoeba gemmipara nov. gen., nov. sp., the first cultured member of the environmental Dermamoebidae clade LKM74 and its unusual life cycle. J. Eukaryot. Microbiol. 64, 257–265. https://doi.org/10.1111/jeu.12357 (2017).
Google Scholar
Kudryavtsev, A. & Volkova, E. Cunea russae n. sp. (Amoebozoa, Dactylopodida), another cryptic species of Cunea Kudryavtsev and Pawlowski, 2015, inhabits a continental brackish-water biotope. Eur. J. Protistol. 73, 125685. https://doi.org/10.1016/j.ejop.2020.125685 (2020).
Google Scholar
Schindelin, J. et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods 9, 676–682. https://doi.org/10.1038/nmeth.2019 (2012).
Google Scholar
Maniatis, T., Fritsch, E. F. & Sambrook, J. Molecular Cloning, A Laboratory Manual (Cold Spring Harbor Laboratory, 1982).
Kudryavtsev, A. & Pawlowski, J. Cunea n. g. (Amoebozoa, Dactylopodida) with two cryptic species isolated from different areas of the ocean. Eur. J. Protistol. 51, 197–209. https://doi.org/10.1016/j.ejop.2015.04.002 (2015).
Google Scholar
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. https://doi.org/10.1016/0378-1119(88)90066-2 (1988).
Google Scholar
Yoon, H. S. et al. Broadly sampled multigene trees of eukaryotes. BMC Evol. Biol. 8, 14. https://doi.org/10.1186/1471-2148-8-14 (2008).
Google Scholar
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2 (1990).
Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780. https://doi.org/10.1093/molbev/mst010 (2013).
Google Scholar
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973. https://doi.org/10.1093/bioinformatics/btp348 (2009).
Google Scholar
Gouy, M., Tannier, E., Comte, N. & Parsons, D. P. Seaview version 5: A multiplatform software for multiple sequence alignment, molecular phylogenetic analyses, and tree reconciliation. In Multiple Sequence Alignment. Methods in Molecular Biology (ed. Katoh, K.) 241–260 (Humana, 2021). https://doi.org/10.1007/978-1-0716-1036-7_15.
Google Scholar
Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313. https://doi.org/10.1093/bioinformatics/btu033 (2014).
Google Scholar
Ronquist, F. et al. MRBAYES 3.2: Efficient Bayesian phylogenetic inference and model selection across a large model space. Syst. Biol. 61, 539–542. https://doi.org/10.1093/sysbio/sys029 (2012).
Google Scholar
Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320. https://doi.org/10.1093/molbev/msn067 (2008).
Google Scholar
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