Molecular Phylogeny of Cercomonadidae and Kinetid Patterns of Cercomonas and Eocercomonas gen. nov. (Cercomonadida, Cercozoa)

Protist

Volumn 157, Issue 2, 2006, Pages 125-158

  Karpov, Serguei A ^a   Bass, David ^b   Mylnikov, Alexander P ^c   Cavalier Smith, Thomas ^b  

^a HERZEN STATE PEDAGOGICAL UNIVERSITY OF RUSSIA   (Russian Federation)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c PAPANIN INSTITUTE FOR BIOLOGY OF INLAND WATERS   (Russian Federation)

Author keywords

18S rRNA phylogeny; centriolar transformation; Cercomonas; Eocercomonas; kinetid structure; Paracercomonas

Indexed keywords

BIKONTA; CERCOMONADIDA; CERCOMONADIDAE; CERCOMONAS; CERCOMONAS LONGICAUDA; CERCOZOA;

EID: 33646585781     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2006.01.001     Document Type: Article

References (71)

1. Al-Qassab S., Lee W.J., Murray S., Simpson A.G.B., and Patterson D.J. Flagellates from stromatolites and surrounding sediments in Shark Bay, Western Australia. Acta Protozool 41 (2002) 91-144
2. Arndt H., Dietrich D., Auer B., Cleven E.-J., Gräfenham T., Weitere M., and Mylnikov A.P. Functional Diversity in Aquatic Ecosystems. In: Leadbeater B.S., and Green J.C. (Eds). The Flagellates: Unity and Diversity (2000), Taylor & Francis, London 240-268
3. Archibald J.M., Longet D., Pawlowski J., and Keeling P.J. A novel polyubiquitin structure in Cercozoa and foraminifera: evidence for a new eukaryotic supergroup. Mol Biol Evol 20 (2003) 62-66
4. Bass D., and Cavalier-Smith T. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int J Syst Evol Microbiol 54 (2004) 2393-2404
5. Bass D., Moreira D., López-García P., Polet S., Chao E.E., von der Heyden S., Pawlowski J., and Cavalier-Smith T. Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist 156 (2005) 149-161
6. Cavalier-Smith T. Basal body and flagellar development during the vegetative cell cycle and the sexual cycle of Chlamydomonas reinhardii. J Cell Sci 16 (1974) 529-556
7. Cavalier-Smith T. A revised six-kingdom system of life. Biol Rev Cambridge Philos Soc 73 (1998) 203-266
8. Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 52 (2002) 297-354
9. 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
10. Cavalier-Smith T. Protist phylogeny and the high-level classification of Protozoa. Europ J Protistol 39 (2003) 338-348
11. Cavalier-Smith T., and Chao E.E. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch Protistenkd 147 (1996/7) 227-236
12. Cavalier-Smith T., and Chao E.E. Phylogeny and classification of phylum Cercozoa (Protozoa). Protist 154 (2003) 341-358
13. Cavalier-Smith T., and Chao E.E. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). J Mol Evol 62 (2006) 388-420
14. Cavalier-Smith T., Chao E.E., and Oates B. Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. Europ J Protistol 40 (2004) 21-48
15. Dujardin F. Histoire Naturelle des Zoophytes Infusoires (1841), Roret, Paris
16. Ekelund F., and Patterson D.J. Some heterotrophic flagellates from a cultivated soil in Australia. Arch Protistenkd 148 (1997) 461-478
17. Ekelund F., Daugbjerg N., and Fredslund L. Phylogeny of Heteromita, Cercomonas and Thaumatomonas based on SSU rDNA sequences, including the description of Neocercomonas jutlandica sp. nov., gen. nov. Europ J Protistol 40 (2004) 119-135
18. Finlay B.J. Global dispersal of free-living microbial eukaryote species. Science 296 (2002) 1061-1063
19. Finlay B.J., and Clarke K.J. Apparent global ubiquity of species in the protist genus Paraphysomonas. Protist 150 (1999) 419-430
20. Foissner W. Diversity and Ecology of Soil Flagellates. In: Patterson D.J., and Larsen J. (Eds). The Biology of Free-Living Heterotrophic Flagellates (1991), Clarendon Press, Oxford 93-112
21. Fromentel F.D.E. Études sur les Microzoaires ou Infusoires Proprement dit (1874), Masson, Paris
22. Hollande A. Etude Cytologique et Biologique de Quelques Flagellés Libres. Arch Zool exp générale 83 (1942) 1-268
23. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
24. Karpov S.A. Cercomonads and their relationship to myxomycetes. Arch Protistenkd 158 (1997) 297-307
25. Karpov S.A. Flagellate Phylogeny: an Ultrastructural Approach. In: Leadbeater B.S.C., and Green J.C. (Eds). The Flagellates: Unity, Diversity and Evolution (2000), Taylor & Francis, London 336-360
26. Karpov SA (ed) (2000b) Protista: Handbook on Zoology Pt 1. Nauka, St. Petersburg
27. Karpov S.A., and Fokin S.I. The structural diversity of flagellar transitional zone in heterotrophic flagellates and other protists. Tsitologia 37 (1995) 1038-1052
28. Karpov S.A., Ekelund F., and Moestrup Ø. Katabia gromovi nov. gen., nov. sp. - a new soil flagellate with affinities to Heteromita (Cercomonadida). Protistology 3 (2003) 30-41
29. Karpov S.A., Novozhilov Y.K., and Christiakova L.V. A comparative study of zoospore cytoskeleton in Symphytocarpus impexus, Arcyria cinerea and Lycogala epidendrum (Eumycetozoa). Protistology 3 (2003) 15-29
30. Keeling P.J. Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home?. Mol Biol Evol 18 (2001) 1551-1557
31. Kent W.S. A Manual of the Infusoria (1880-1882), Bogue, London
32. Klebs G. Flagellatenstudien. Zeit wiss Zool 55 (1892) 265-445
33. Krassilstschik I (1886) The materials to the natural history and taxonomy of flagellates. On Cercobodo laciniaegerens nov. gen. et nov. sp. Zapiski Novosibirskogoobschestva estestvoispytatelei. 2, 1, 211-245 (in Russian)
34. Lee W.J., and Patterson D.J. Heterotrophic flagellates (Protista) from marine sediments of Botany Bay, Australia. J Nat History 34 (2000) 483-562
35. Lemmermann E. Flagellatae 1 (1914), Gustav Fischer, Jena
36. Macdonald C.M., Darbyshire J.F., and Ogden C.G. The morphology of a common soil zooflagellate, Heteromita globosa Stein (Mastigophorea: Protozoa). Bull Br Mus Nat Hist (Zool) 31 (1977) 255-264 + 6 plates
37. Mignot J.-P., and Brugerolle G. Étude ultrastructurale de Cercomonas Dujardin (=Cercobodo Krassilstchick) protiste flagellé. Protistologica 11 (1975) 547-554
38. Moestrup Ø. The Flagellate Cytoskeleton: Introduction of a General Terminology for Microtubular Roots in Protists. In: Leadbeater B.S., and Green J.C. (Eds). The Flagellates: Unity, Diversity and Evolution (2000), Taylor & Francis, London 69-94
39. Mylnikov A.P. The biology and ultrastructure of amoeboid flagellates Cercomonadida ord. n. Zoologicheskii Zhurnal, Moscow 65 (1986) 683-692 (in Russian with English summary)
40. Mylnikov A.P. The peculiarities of ultrastructure Cercomonas varians. Tsitologiya 28 (1986) 414-417 (in Russian with English summary)
41. Mylnikov A.P. Ultrastructure of a colourless amoeboid flagellate, Cercomonas sp. Arch Protistenkd 131 (1986) 239-247
42. Mylnikov A.P. The ultrastructure of flagellate Cercomonas longicauda (Cercomonadida) Bot Zhurn 72 (1987) 750-753 (in Russian with English summary)
43. Mylnikov A.P. The cell structure of flagellate Cercomonas crassicauda. Biologia vnutrenih vod Inform bul 84 (1989) 22-26 (in Russian)
44. Mylnikov A.P. The rootlet flagellar system of cercomonads. Biologia vnutrenih vod Inform bul 84 (1989) 52-54 (in Russian)
45. Mylnikov A.P. The cell structure of flagellate Cercobodo cometa. Biologia vnutrenih vod Inform bul 86 (1990) 33-38 (in Russian)
46. Mylnikov A.P. The cell structure of the flagellate Cercomonas activus. Biologia vnutrenih vod Inform bul N 92 (1992) 14-19 (in Russian)
47. Mylnikov A.P. The structure of amoeboid flagellate Cercomonas sp. Biologia vnutrenih vod Inform bul N 94 (1992) 41-45 (in Russian)
48. Mylnikov A.P. Some taxonomic features of cercomonads. Biologia vnutrenih vod Inform bul 93 (1992) 35-39 (in Russian)
49. Mylnikov AP (1995). The Free-Living Heterotrophic Flagellates (Ultrastructure, Systematics and Biology). DSc Thesis. St. Petersburg: St. Petersburg State University (in Russian)
50. Mylnikov AP (2000). Class Cercomonadea Mylnikov, 1986 - Cercomonads. In Alimov AF, Stepanjantz SD, Karpov SA (eds) Protista, I: Handbook on Zoology. Nauka, St. Petersburg. pp. 411-417 (in Russian with English summary)
51. Mylnikov A.P. New amoeboid flagellates of the genus Cercomonas (Cercomonadida, Protozoa) from lakes of Spitzbergen island. Zoologicheski Zhurnal Moscow 81 (2002) 1187-1192 (in Russian with English summary)
52. Mylnikov A.P., Mylnikova Z.M., and Tsvetkov A.I. The fine structure of amoeboid flagellate Cercomonas plasmodialis Mylnikov. Biologia vnutrenih vod N 4 (2000) 29-35 (in Russian with English summary)
53. Mylnikov A.P., and Mylnikova Z.M. The main ultrastructure of amoeboid flagellate Cercomonas metabolicus Mylnikov, 1987. Biologiya Vnutrenih Vod N 2 (2001) 65-69 (in Russian with English summary)
54. Mylnikov A.P., and Karpov S.A. Review of the diversity and taxonomy of cercomonads. Protistology 3 (2004) 201-217
55. Nikolaev S.I., Berney C., Fahrni J.F., Bolivar I., Polet S., Mylnikov A.P., Aleshin V.V., Petrov N.B., and Pawlowski J. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci USA 101 (2004) 8066-8071
56. Polet S., Berney C., Fahrni J., and Pawlowski J. Small-subunit ribosomal RNA gene sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria. Protist 155 (2004) 53-63
57. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
58. Richards T.A., and Cavalier-Smith T. Myosin domain evolution and the primary divergence of eukaryotes. Nature 436 (2005) 1113-1118
59. Sandon H. The Composition and Distribution of the Protozoan Fauna of the Soil (1927), Oliver & Boyd, Edinburgh
60. Schuster F.L., and Pollack A. Ultrastructure of Cercomonas sp., a free-living amoeboid flagellate. Arch Protistenkd 120 (1978) 206-212
61. Simpson A.G.B., and Roger A.J. Excavata and the Origin of Amitochondriate Eukaryotes. In: Hirt R.P., and Horner D.S. (Eds). Organelles, Genomes, and Eukaryote Phylogeny, The Systematics Association Special Volume Series 68 (2004), CRC Press, Boca Raton, Florida 27-33
62. Skvortzov B.V. The flagellates of clear and polluted waters. New taxa of the genus Cercobodo Krassil: a colourless flagellate of Rhizomastigaceae, Pantostomatinae. Q J Taiwan Mus Taipei 30 (1977) 89-121
63. Stechmann A., and Cavalier-Smith T. Rooting the eukaryote tree by using a derived gene fusion. Science 297 (2002) 89-91
64. Stechmann A., and Cavalier Smith T. The root of the eukaryote tree pinpointed. Curr Biol 13 (2003) R665-R666
65. Stechmann A., and Cavalier-Smith T. Phylogenetic analysis of eukaryotes using heat-shock protein Hsp90. J Mol Evol 57 (2003) 408-419
66. Stein F.R. Der Organismus der Infusionsthiere, III: Der Organismus der Flagellaten I (1878), Engelmann, Leipzig
67. Swofford DW (1999) PAUP* 4.0b10. Sinauer, Sunderland, MS
68. Vickerman K., Appleton P.L., Clarke K.J., and Moreira D. Aurigamonas solis n. gen., n. sp., a soil-dwelling predator with unusual helioflagellate organisation and belonging to a novel clade within the Cercozoa. Protist 156 (2005) 335-354
69. von der Heyden S., and Cavalier-Smith T. Culturing and environmental DNA sequencing uncover hidden kinetoplastid biodiversity and a major marine clade within ancestrally freshwater Neobodo designis. Int J Syst Evol Microbiol 55 (2005) 2605-2621
70. Wuyts J., De Rijk P., Van de Peer Y., Pison G., Rousseeuw P., and De Wachter R. Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res 28 (2000) 4698-4708
71. Zhukov B.F. Atlas of Freshwater Heterotrophic Flagellates (1993), Russian Academy of Sciences, Institute of the Biology of Inland Waters, Rubinsk (in Russian)