Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium

European Journal of Protistology

Volumn 40, Issue 1, 2004, Pages 21-48

  Cavalier Smith, Thomas ^a   Chao, Ema E Y ^a   Oates, Brian ^b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

'Mastigamoeba invertens'; 18S rRNA phylogeny; Amoebozoa; Discosea cl. nov.; Hyperamoeba; Phalansterium; Variosea cl. nov.

Indexed keywords

ACANTHAMOEBIDAE; AMOEBOZOA; CERCOZOA; DICTYOSTELIIDA; EUKARYOTA; FILAMOEBA; GEPHYRAMOEBA; HIMATISMENIDA; HYPERAMOEBA; LOBOSEA; MASTIGAMOEBA; MASTIGAMOEBA INVERTENS; MASTIGOPHORA (FLAGELLATES); MULTICILIA; MYCETOZOA; MYXOGASTRIA; PHALANSTERIUM; PHALANSTERIUM CONSOCIATUM; PHALANSTERIUM SOLITARIUM; PROTOSTELIDA; SARCODINA; SPONGOMONAS; THECAMOEBIDAE;

EID: 2942725903     PISSN: 09324739     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejop.2003.10.001     Document Type: Article

References (113)

1. Amaral Zettler L.A., Nerad T.A., O'Kelly C.J., Peglar M.T., Gillevet P.M., Silberman J.D., Sogin M.L. A molecular reassessment of the leptomyxid amoebae. Protist. 151:2000;275-282
2. Amaral Zettler L.A., Anderson O.R., Nerad T.A., Sogin M.L. The phylogenetic position of Comandonia operculata and its implications for the taxonomy of the genus Acanthamoeba. Billot-Bonef S., Cabanes P.A., Marciano-Cabral F., Pernin P., Pringuez E. IXth International Meeting on the Biology and Pathogenicity of Free-living Amoebae: proceedings. 2001;235-242 John Libbey Eurotext, Paris, France
3. Andersson J.O., Roger A.J. A cyanobacterial gene in nonphotosynthetic protists - an early chloroplast acquisition in eukaryotes? Curr. Biol. 12:2002;115-119
4. Baldauf S.L., Doolittle W.F. Origin and evolution of the slime molds (Mycetozoa). Proc. Natl Acad. Sci. USA. 94:1997;12007-12012
5. Baldauf S.L., Roger A.J., Wenk-Siefert I., Doolittle W.F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science. 290:2000;972-977
6. Bapteste E., Brinkmann H., Lee J.A., Moore D.V., Sensen C.W., Gordon P., Duruflé L., Gaasterland T., Lopez P., Müller M., Philippe H. The analysis of 100 genes supports the grouping of three highly divergent amoebae. Dictyostelium, Entamoeba, and Mastigamoeba Proc. Natl Acad. Sci. USA. 99:2002;1414-1419
7. 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. 18:2001;2306-2314
8. Brugerolle G. Organization of amitochondriate flagellates. Patterson D.J., Larsen J. The Biology of Free-Living Heterotrophic Flagellates. 1991;133-148 Clarendon Press, Oxford
9. Bütschli, O., 1885. Dr. H. G. Bronn's Klassen und Ordnungen des Thier-Reichs, Vol. 1, Abt. II Mastigophora. C. F. Winter, Heidelberg, p. 1016.
10. Cavalier-Smith T. The evolutionary origin and phylogeny of eukaryote flagella. Amos W.B., Duckett J.G. Prokaryotic and Eukaryotic Flagella. 35th Symposium of the Society of Experimental Biology. 1982;465-493 Cambridge University Press, Cambridge
11. Cavalier-Smith T. A 6-kingdom classification and a unified phylogeny. Schwemmler W., Schenk H.E.A. Endocytobiology II. 1983;l027-l034 de Gruyter, Berlin
12. Cavalier-Smith T. Endosymbiotic origin of the mitochondrial envelope. Schwemmler W., Schenk H.E.A. Endocytobiology II. 1983;265-279 de Gruyter, Berlin
13. Cavalier-Smith T. The simultaneous symbiotic origin of mitochondria, chloroplasts, and microbodies. Ann. N. Y. Acad. Sci. 503:1987;55-71
14. Cavalier-Smith T. The origin of eukaryotic and archaebacterial cells. Ann. N. Y. Acad. Sci. 503:1987;17-54
15. Cavalier-Smith T. Archamoebae. the ancestral eukaryotes? BioSystems. 25:1991;25-38
16. Cavalier-Smith T. Origin of the cytoskeleton. Hartman H., Matsuno K. The Origin and Evolution of the Cell. 1992;79-106 World Scientific Publishers, Singapore
17. Cavalier-Smith T. Kingdom Protozoa and its 18 phyla. Microbiol. Rev. 57:1993;953-994
18. Cavalier-Smith T. Percolozoa and the symbiotic origin of the metakaryote cell. Ishikawa H., Ishida M., Sato S. Endocytobiology. Vol. V:1993;399-406 University Press, Tübingen
19. Cavalier-Smith T. Zooflagellate phylogeny and classification. Tsitologiia. 37:1995;1010-1029
20. Cavalier-Smith T. Membrane heredity, symbiogenesis, and the multiple origins of algae. Arai R., Kato M., Doi Y. Biodiversity and Evolution. 1995;75-114 The National Science Museum Foundation, Tokyo
21. Cavalier-Smith, T., 1996/7. Amoeboflagellates and mitochondrial cristae in eukaryotic evolution: megasytematics of the new protozoan subkingdoms Eozoa and Neozoa. Arch. Protistenk. 147, 237-258.
22. Cavalier-Smith T. A revised six-kingdom system of life. Biol. Rev. Camb. Philos. Soc. 73:1998;203-266
23. Cavalier-Smith T. Neomonada and the origin of animals and fungi. Coombs G.H., Vickerman K., Sleigh M.A., Warren A. Evolutionary Relationships among Protozoa. 1998;375-407 Kluwer, London
24. Cavalier-Smith T. Flagellate megaevolution. the basis for eukaryote diversification Green J.R., Leadbeater B.S.C. The Flagellates. 2000;361-390 Taylor & Francis, London
25. Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 52:2002;297-354
26. Cavalier-Smith T. The excavate protozoan phyla Metamonada Grassé emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas). their evolutionary affinities and new higher taxa Int. J. Syst. Evol. Microbiol. 53:2003;1741-1758
27. Cavalier-Smith T. Protist phylogeny and the high-level classification of Protozoa. Eur. J. Protistol. 39:2003;338-348
28. Cavalier-Smith, T., Chao, E.E., 1996/7. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch. Protistenk. 147, 227-236.
29. Cavalier-Smith T., Chao E.E. Hyperamoeba rRNA phylogeny and the classification of the phylum Amoebozoa. J. Euk. Microbiol. 46:1999;5A
30. Cavalier-Smith T., Chao E.E. Phylogeny of Choanozoa, Apusozoa, and other Protozoa and early eukaryote megaevolution. J. Mol. Evol. 56:2003;540-563
31. Cavalier-Smith T., Chao E.E. Molecular phylogeny of centrohelid heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss. J. Mol. Evol. 56:2003;387-396
32. Cavalier-Smith T., Chao E.E. Phylogeny and classification of phylum Cercozoa (Protozoa). Protist. 154:2003;341-358
33. Cavalier-Smith T., Chao E.E., Allsopp M.T.E.P. The opalozoan Apusomonas is related to the common ancestor of animals, fungi, and choanoflagellates. Proc. R. Soc. London B. 261:1995;1-6
34. Chavez L.A., Balamuth W., Gong T. A light and electron microscopical study of a new, polymorphic free-living amoeba, Phreatamoeba balamuthi n. g., n. sp. J. Protozool. 33:1986;397-404
35. Cienkowski L. Über Palmellaceen und einige Flagellaten. Arch. Mikrosk. Anat. 7:1870;421-438
36. Corliss J.O. An interim utilitarian ("user friendly") hierarchical classification and characterisation of the protists. Acta. Protozool. 33:1994;1-51
37. Dacks J.B., Marinets A., Ford Doolittle W., Cavalier-Smith T., Logsdon J.M. Jr. Analyses of RNA polymerase II genes from free-living protists. phylogeny, long branch attraction, and the eukaryotic big bang Mol. Biol. Evol. 19:2002;830-840
38. Dawson S.C., Pace N.R. Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl Acad. Sci. USA. 99:2002;8324-8329
39. Drouin G., Moniz de Sa M., Zuker M. The Giardia lamblia actin gene and the phylogeny of eukaryotes. J. Mol. Evol. 41:1995;841-849
40. Edgcomb V.P., Simpson A.G., Zettler L.A., Nerad T.A., Patterson D.J., Holder M.E., Sogin M.L. Pelobionts are degenerate protists. insights from molecules and morphology Mol. Biol. Evol. 19:2002;978-982
41. Ekelund F. A study of the soil flagellate Phalansterium solitarium Sandon 1924 with preliminary data on its ultrastructure. Protistology. 2:2002;152-158
42. Furtago J.S., Olive L.S. Ultrastructural studies of protostelids. Cytobiologie. 2:1970;200-219
43. Goodkov A.V., Seravin L.N. New ideas on the nature of the giant amoeba Pelomyxa palustris; the position of this organism in the system of lower eukaryotes (Peloflagellata classis n.). Zool. Zh. 70:1991;5-16. (in Russian)
44. Grell K.G. Corallomyxa nipponica n. sp. and the phylogeny of plasmodial protists. Arch. Protistenk. 140:1991;303-320
45. Griffin J.L. Fine structure and taxonomic position of the giant amoeboid flagellate Pelomyxa palustris. J. Protozool. 35:1988;300-315
46. Gromov B.V. Algal parasites of Tsenkovsky's group of 'monad' genera, Aphelidium, Amoeboaphelidium and Pseudoaphelidium, as representatives of a new class. Zool. Zh. 79:2000;517-525. (in Russian)
47. Guhl B., Roos U.P. Microtubule centers and the interphase microtubule cytoskeleton in amoebae of the cellular slime molds (Mycetozoans) Acytostelium leptosomum and Protostelium mycophaga. Cell Motil. Cytoskeleton. 28:1994;45-58
48. Haeckel E. Generelle Morphologie der Organismen. 1866;Reimer, Berlin
49. Hibberd D.J. Ultrastructure of the colonial colourless flagellate Phalansterium digitatum Stein (Phalansteriida ord. nov.) and Spongomonas uvella Stein (Spongomonadida ord. nov.). Protistologica. 19:1983;523-535
50. Hinkle G., Sogin M.L. The evolution of the Vahlkampfiidae as deduced from 16S-like ribosomal RNA analysis. J. Eukaryot. Microbiol. 40:1993;599-603
51. Hinkle G., Leipe D.D., Nerad T.A., Sogin M.L. The unusually long small subunit ribosomal RNA of Phreatamoeba balamuthi. Nucleic Acids Res. 22:1994;465-469
52. Huelsenbeck J.P., Ronquist F. MRBAYES. Bayesian inference of phylogenetic trees Bioinformatics. 17:2001;754-755
53. Karpov S.A. Analysis of the orders Phalansteriida, Spongomonadida and Thaumatomonadida. Zool. Zhurn. 69:1990;5-12. (in Russian)
54. Karpov S.A. Cercomonads and their relationship to myxomycetes. Arch. Protistenkd. 158:1997;297-307
55. Karpov S.A. Protist Cell Structure. 2001;Tessa, St. Petersburg
56. Karpov S.A., Mylnikov A.P. Ultrastructure of the colourless flagellate Hyperamoeba flagellata. Eur. J. Protistol. 33:1997;349-355
57. Keeling P.J., Doolittle W.F. Alpha-tubulin from early diverging eukaryotic lineages and the evolution of the tubulin family. Mol. Biol. Evol. 13:1996;1297-1305
58. Kudryavtsev A.A. Description of Cochliopodium larifeli n. sp. (Lobosea, Himatismenida), an amoeba with peculiar scale structure, and notes on the diagnosis of the genus Cochliopodium (Hertwig and Lesser, 1874) Bark, 1974. Protistology. 1:1999;66-71
59. Kudryavtsev A.A. The first isolation of Cochliopodium gulosum Schaeffer, 1926 (Lobosea, Himatismenida) since its initial description. II. Electron microscopical study and redescription. Protistology. 1:2000;110-112
60. Lang B.F., O'Kelly C., Nerad T., Gray M.W., Burger G. The closest unicellular relatives of animals. Curr. Biol. 12:2002;1773-1778
61. Lee, J.J., Leedale, G., Bradbury, P., 2002 dated 2000. An Illustrated Guide to the Protozoa. Society of Protozoologists, Lawrence, KS.
62. Lemmermann E. Flagellatae 1. 1914;Gustav Fischer, Jena
63. Levine N.D., Corliss J.O., Cox F.E., Deroux G., Grain J., Honigberg B.M., Leedale G.F., Loeblich A.R. III, Lom J., Lynn D., Merinfeld E.G., Page F.C., Poljansky G., Sprague V., Vávra J., Wallace F.G. A newly revised classification of the Protozoa. J. Protozool. 27:1980;37-58
64. Lühe, 1913. as cited by J. O. Corliss (1984): The kingdom Protista and its 45 phyla. BioSystems 17, 87-126.
65. Margulis L. Five-kingdom classification and the origin and evolution of cells. Dobzhansky T., Hecht M.K., Steere W.C. Evolutionary Biology. Vol. 7:1974;45-78 Plenum Press, New York
66. Martin J.B., Laussmann T., Bakker-Grunwald T., Vogel G., Klein G. Neo-inositol polyphosphates in the amoeba Entamoeba histolytica. J. Biol. Chem. 275:2000;10134-10140
67. Meisterfeld, R., 2002 dated 2000. Order Arcellinida. In: Lee, J.J., Leedale, G., Bradbury, P. (Eds.), An Illustrated Guide to the Protozoa. Society of Protozoologists, Lawrence, KS, pp. 827-860.
68. Mikrjukov K.A., Mylnikov A.P. Protist Multicilia marina Cienk. Flagellate or a heliozoon? Doklady Acad. Nauk. 346:1996;136-139. (In Russian)
69. Mikrjukov K.A., Mylnikov A.P. The fine structure of a carnivorous multiflagellar protist, Multicilia marina Cienkowski, 1881 (Flagellata incertae sedis). Eur. J. Protistol. 34:1998;391-401
70. Milyutina I.A., Aleshin V.V., Mikrjukov K.A., Kedrova O.S., Petrov N.B. The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris. its rRNA predicted secondary structure and phylogenetic implication Gene. 272:2001;131-139
71. Minchin E.A. An Introduction to the Study of the Protozoa. 1922;Edward Arnold, London
72. Mitchison J.M. The Biology of the Cell Cycle. 1971;Cambridge University Press, Cambridge
73. Page F.C. An Illustrated Key to Freshwater and Soil Amoebae. 1976;Freshwater Biological Association, Ambleside
74. Page F.C. Marine Gymnamoebae. 1983;Institute of Terrestrial Ecology, Cambridge
75. Page F.C. A New Key to Freshwater and Soil Gymnamoebae with Instructions for Culture. 1988;Freshwater Biological Association, Ambleside, Cumbria
76. Page F.C., Blanton R.L. The Heterolobosea (Sarcodina: Rhizopoda), a new class uniting the Schizopyrenida and the Acrasidae (Acrasida). Protistologica. 21:1985;121-132
77. Patterson D.J. Protozoa. evolution and systematics Hausmann K., Hülsmann N. Progress in Protozoology: Proceedings of the IX International Congress in Protozoology. 1994;1-14 Gustav Fischer, Stuttgart
78. Patterson D.J. The diversity of eukaryotes. Am. Nat. 154:1999;S96-S124
79. Patterson D.J., Zölfell M. Heterotrophic flagellates of uncertain taxonomic position. Patterson D.J., Larsen J. The Biology of Free-living Heterotrophic Flagellates. 1991;427-476 Clarendon Press, Oxford
80. Peglar M.T., Amaral Zettler L.A., Anderson O.R., Nerad T., Gillevet P.M., Mullen T.E., Frasca S., Silberman J.D., O'Kelly C., Sogin M.L. Two small-subunit ribosomal RNA gene lineages within the subclass Gymnamoebia. J. Eukaryot. Microbiol. 50:2003;224-232
81. Philippe H. Opinion. long branch attraction and protist phylogeny Protist. 151:2000;307-316
82. Philippe H., Adoutte A. The molecular phylogeny of Eukaryota. solid facts and uncertainties Coombs G., Vickerman K., Sleigh M.A., Warren A. Evolutionary Relationships among Protozoa. 1998;25-56 Kluwer, London
83. Philippe H., Germot A. Phylogeny of eukaryotes based on ribosomal RNA. long-branch attraction and models of sequence evolution Mol. Biol. Evol. 17:2000;830-834
84. Philippe H., Germot A., Moreira D. The new phylogeny of eukaryotes. Curr. Opin. Genet. Dev. 10:2000;596-601
85. Posada D., Crandall K.A. MODELTEST. testing the model of DNA substitution Bioinformatics. 14:1998;817-818
86. Richards T.A., Hirt R.P., Williams B.A., Embley T.M. Horizontal gene transfer and the evolution of parasitic protozoa. Protist. 154:2003;17-32
87. Roger A.J., Smith M.W., Doolittle R.F., Doolittle W.F. Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3- phosphate dehydrogenase. J. Eukaryot. Microbiol. 43:1996;475-485
88. Rogerson, A., Patterson, D.J., 2002, dated 2000. The naked ramicristate amoebae (Gymnamoebae). In: Lee, J.J., Leedale, G.F., Bradbury, P. (Eds.), An Illustrated Guide to the Protozoa, Vol. II. Society of Protozoologists, Lawrence, KS, pp. 1023-1052.
89. Sandon H. Some protozoa from the soil and mosses of Spitzbergen. J. Linn. Soc. Zool. 35:1924;449-495
90. Sandon H. The Composition and Distribution of the Protozoan Fauna of the Soil. 1927;Oliver & Boyd, Edinburgh
91. Sawyer T.K., Griffin J. Acanthamoeba commandoni and A. astronyxis. taxonomic characteristics of mitotic nuclei, "centrosomes" and cysts J. Protozool. 18:1971;382-388
92. Schaudinn, F., 1899. Untersuchungen über den Generationswechsel von Trichosphaerium sieboldi. Abh. Königl. Preuss. Akad. Wiss., Berlin, Suppl. 1-93, 150-207.
93. Seravin L.N., Goodkov A.V. Golgi apparatus in the amoeba Pelomyxa palustris. Dokl. Akad. Nauk SSSR. 296:1987;249-250
94. Silberman J.D., Amaral-Zettler L.S., Nerad T.A., Caron D.A., Sogin M.L. The polyphyletic nature of amoebae. J. Eukaryot. Microbiol. 45:1998;A1
95. Silberman J.D., Simpson A.G., Kulda J., Cepicka I., Hampl V., Johnson P.J., Roger A.J. Retortamonad flagellates are closely related to diplomonads - implications for the history of mitochondrial function in eukaryote evolution. Mol. Biol. Evol. 19:2002;777-786
96. Simpson A.G.B., Bernard C., Fenchel T., Patterson D.J. The organization of Mastigamoeba schizophrenia n. sp. more evidence of ultrastructural idiosyncrasy and simplicity in pelobiont protists Eur. J. Protistol. 33:1997;87-98
97. Smirnov A.V., Goodkov A.V. An illustrated list of basic morphotypes of Gymnamoebia (Rhizopoda, Lobosea). Protistology. 1:1999;20-29
98. Sogin M.L. Early evolution and the origin of eukaryotes. Curr. Opin. Genet. Dev. 1:1991;457-463
99. Sogin M.L., Silberman J.D., Hinkle G., Morrison H.G. Problems with molecular diversity in the Eukarya. Roberts D.M., Sharp P., Alderson G., Collins M.A. Evolution of Microbial Life: Society for General Microbiology Symposium. 1996;167-184 Cambridge University Press, Cambridge
100. Spiegel F.W. Phylogenetic significance of the flagellar apparatus in protostelids (Eumycetozoa). BioSystems. 14:1981;491-499
101. Spiegel F.W. Phylum plasmodial slime moulds. class Protostelida Margulis L., Corliss J.O., Melkonian M., Chapman D.J. Handbook of Protoctista. 1990;484-497 Jones and Bartlett, Boston, MA
102. Spiegel F.W. A proposed phylogeny of the flagellate protostelids. BioSystems. 25:1991;113-120
103. Starmach K. Chrysophyceae und Haptophyceae. 1985;Gustav Fischer, Stuttgart
104. Stechmann A., Cavalier-Smith T. Rooting the eukaryote tree by using a derived gene fusion. Science. 297:2002;89-91
105. Stechmann A., Cavalier Smith T. The root of the eukaryote tree pinpointed. Curr. Biol. 13:2003;R665-R666
106. Stechmann A., Cavalier-Smith T. Phylogenetic analysis of eukaryotes using heat-shock protein Hsp90. J. Mol. Evol. 57:2003;408-419
107. Stiller J.W., Hall B.D. Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol. Biol. Evol. 16:1999;1270-1279
108. Swofford D.W. PAUP* 4.0b10. 1999;Sinauer, Sunderland, MS
109. Van de Peer Y., Baldauf S.L., Doolittle W.F., Meyer A. An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances. J. Mol. Evol. 51:2000;565-576
110. Walker G., Simpson A.G.B., Edgcomb V., Sogin M.L., Patterson D.J. Ultrastructural identities of Mastigamoeba punctachlora, Mastigamoeba simplex and Mastigella commutans and assessment of hypotheses of relatedness of the pelobionts (Protista). Eur. J. Protistol. 37:2001;25-49
111. Walker G., Silberman J.D., Karpov S.A., Preisfeld A., Foster P., Frolov A.O., Novozhilov Y., Sogin M.L. An ultrastructural and molecular study of Hyperamoeba dachnya, n. sp., and its relationship to the mycetozoan slime moulds. Eur. J. Protistol. 39:2003;319-336
112. Wright M., Moisand A., Mir L. Centriole maturation in the amoebae of Physarum polycephalum. Protoplasma. 105:1980;149-160
113. Zaman V., Zaki M., Howe J., Ng M., Leipe D.D., Sogin M.L., Silberman J.D. Hyperamoeba isolated from human feces. description and phylogenetic affinity Eur. J. Protistol. 35:1999;197-207