Phylogenetic position of Multicilia marina and the evolution of Amoebozoa

International Journal of Systematic and Evolutionary Microbiology

Volumn 56, Issue 6, 2006, Pages 1449-1458

  Nikolaev, Sergey I ^a,b,d   Berney, Cédric ^b,e   Petrov, Nikolai B ^a   Mylnikov, Alexandre P ^c   Fahrni, José F ^b   Pawlowski, Jan ^b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b UNIVERSITY OF GENEVA   (Switzerland)

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

^d Centre Médical Universitaire   (Switzerland)

^e UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL SUBUNIT RIBOSOMAL RNA;

AMOEBA; ARCHAMOEBAE; ARTICLE; CELL CULTURE; CONOSEA; DNA EXTRACTION; FILAMOEBA NOLANDI; FLAGELLATE; GENE AMPLIFICATION; GEPHYRAMOEBA; MICROTUBULE; MOLECULAR CLONING; MOULD; MULTICILIA MARINA; MYCETOZOAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHALANSTERIUM SOLITARIUM; PHYLOGENY; PRIORITY JOURNAL; PROTOZOON; RNA SEQUENCE; SARCODINA; ULTRASTRUCTURE; UNINDEXED SEQUENCE;

AMOEBA; ANIMALS; CLONING, MOLECULAR; DINOFLAGELLIDA; DNA, PROTOZOAN; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, PROTOZOAN; RNA, RIBOSOMAL;

AMOEBOZOA; ARCHAMOEBAE; ARCHEZOA; CONOSA; FILAMOEBA NOLANDI; GEPHYRAMOEBA; LOBOSEA; MULTICILIA MARINA; MYCETOZOA; PHALANSTERIUM SOLITARIUM; PROTISTA;

EID: 33745307797     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.63763-0     Document Type: Article

References (47)

1. Amaral Zettler, L. A., Nerad, T. A., O'Kelly, C. J., Peglar, M. T., Gillevet, P. M., Silberman, J. D. & Sogin, M. L. (2000). A molecular reassessment of the leptomyxid amoebae. Protistologica 151, 275-282.
2. Amaral Zettler, L. A., Gómez, F., Zettler, E., Keenan, B. G., Amils, R. & Sogin, M. L. (2002). Microbiology: Eukaryotic diversity in Spain's River of Fire. Nature 417, 137.
3. Bapteste, E., Brinkmann, H., Lee, J. A. & 8 other authors (2002). The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A 99, 1414-1419.
4. Bolivar, I., Fahrni, J. F., Smirnov, A. & Pawlowski, J. (2001). SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of Gymnamoebae revisited. Mol Biol Evol 18, 2306-2314.
5. Bovee, E. C. (1965). An emendation of the amoeba genus Flabellula and a description of Vannella gen. nov. Trans Am Microsc Soc 84, 217-227.
6. Brugerolle, G. (1991). Flagellar and cytoskeletal systems in amitochondrial flagellates: Archamoeba, Metamonada, and Parabasalia. Protoplasma 164, 70-90.
7. Brugerolle, G. & Müller, M. (2000). Amitochondriate flagellates. In The Flagellates: Unity, Diversity and Evolution, pp. 166-189. Edited by J. R. Green & B. S. C. Leadbeater. London: Taylor & Francis.
8. Brugerolle, G. & Patterson, D. J. (2000). Order Pelobiontida Page, 1976. In An Illustrated Guide to the Protozoa, 2nd edn, pp. 1097-1103. Edited by J. J. Lee, G. F. Leedale & P. Bradbury. Lawrence, KS: Society of Protozoologists.
9. Brugerolle, G., Bricheux, G., Philippe, H. & Coffea, G. (2002). Collodictyon triciliatum and Diphylleia rotans (= Aulacomonas submarina) form a new family of flagellates (Collodictyonidae) with tubular mitochondrial cristae that is phylogenetically distant from other flagellate groups. Protist 153, 59-70.
10. Cavalier-Smith, T. (1998). A revised six-kingdom system of life. Biol Rev Camb Philos Soc 73, 203-266.
11. Cavalier-Smith, T. (2000). Flagellate megaevolution: the basis for eukaryote diversification. In The Flagellates: Unity, Diversity and Evolution, pp. 361-390. Edited by J. R. Green & B. S. C. Leadbeater. London: Taylor & Francis.
12. Cavalier-Smith, T. (2002). The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 52, 297-354.
13. Cavalier-Smith, T. (2003). Protist phylogeny and the high-level classification of Protozoa. Eur J Protistol 39, 338-348.
14. Cavalier-Smith, T. (2004). Only six kingdoms of life. Proc R Soc Lond B Biol Sci 271, 1251-1262.
15. Cavalier-Smith, T. & Chao, E. E.-Y. (2003). Molecular phylogeny of centrohelid Heliozoa, a novel lineage of bikont Eukaryotes that arose by ciliary loss. J Mol Evol 56, 387-396.
16. Cavalier-Smith, T., Chao, E. E.-Y. & Oates, B. (2004). Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. Eur J Protistol 40, 21-48.
17. Cienkowski, L. (1881). An account on the White Sea excursion in 1880. Proc St-Petersb Imp Soc Nat 12, 130-171 (in Russian).
18. De Rijk, P. & De Wachter, R. (1997). Rna Viz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res 25, 4679-4684.
19. Edgcomb, V. P., Simpson, A. G. B., Amaral Zettler, L., Nerad, T. A., Patterson, D. J., Holder, M. E. & Sogin, M. L. (2002). Pelobionts are degenerate protists: insights from molecules and morphology. Mol Biol Evol 19, 978-982.
20. Ekelund, F. (2002). A study of the soil flagellate Phalansterium solitarium Sandon 1924 with preliminary data on its ultrastructure. Protistology 2, 152-158.
21. Fahrni, J. F., Bolivar, I., Berney, C., Nassonova, E., Smirnov, A. & Pawlowski, J. (2003). Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol Biol Evol 20, 1881-1886.
22. Fiore-Donno, A.-M., Berney, C., Pawlowski, J. & Baldauf, S. L. (2005). Higher-order phylogeny of plasmodial slime molds (Myxogastria) based on elongation factor 1-α and small subunit rRNA gene sequences. J Eukaryot Microbiol 52, 201-210.
23. Goodkov, A. V. & Seravin, L. N. (1991). 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, 5-16 (in Russian).
24. Griffin, J. L. (1988). Fine structure and taxonomic position of the giant amoeboid flagellate Pelomyxa palustris. J Protozool 35, 300-315.
25. Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696-704.
26. Hinkle, G., Leipe, D. D., Nerad, T. A. & Sogin, M. L. (1994). The unusually long small subunit ribosomal RNA of Phreatamoeba balamuthi. Nucleic Acids Res 22, 465-469.
27. Huelsenbeck, J. P. & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
28. Kudo, R. (1954). Protistology, pp. 333-338. Springfield, IL: Charles C. Thomas.
29. Lanave, C., Preparata, G., Saccone, C. & Serio, G. (1984). A new method for calculating evolutionary substitution rates. J Mol Evol 20, 86-93.
30. Larsen, N., Olsen, G. J., Maidak, B. L., McCaughey, M. J., Overbeek, R., Macke, T. J., Marsh, T. L. & Woese, C. R. (1993). The ribosomal database project. Nucleic Acids Res 21, 3021-3023.
31. Mikrjukov, K. A. & Mylnikov, A. P. (1996). Protist Multicilia marina Cienk. Flagellate or a Heliozoon? Dokl Acad Nauk 346, 136-139 (in Russian).
32. Mikrjukov, K. A. & Mylnikov, A. P. (1998). The fine structure of a carnivorous multiflagellar protist, Multicilia marina Cienkowski 1881 (Flagellata Incertae sedis). Eur J Protistol 34, 391-401.
33. Milyutina, I. A., Aleshin, V. V., Mikrjukov, K. A., Kedrova, O. S. & Petrov, N. B. (2001). The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication. Gene 272, 131-139.
34. Nikolaev, S. I., Berney, C., Fahrni, J. F., Bolivar, I., Polet, S., Mylnikov, A. P., Aleshin, V. V., Petrov, N. B. & Pawlowski, J. (2004). The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci U S A 101, 8066-8071.
35. Nikolaev, S. I., Mitchell, E. A. D., Petrov, N. B., Berney, C., Fahrni, J. & Pawlowski, J. (2005). The testate lobose amoebae (order Arcellinida Kent, 1880) finally find their home within Amoebozoa. Protist 156, 191-202.
36. Patterson, D. J., Vørs, N., Simpson, A. G. B. & O'Kelly, C. (2000). Residual free-living and predatory heterotrophic flagellates. In An Illustrated Guide to the Protozoa, 2nd edn, pp. 1302-1328. Edited by J. J. Lee, G. F. Leedale & P. Bradbury. Lawrence, KS: Society of Protozoologists.
37. Peglar, M. T., Amaral Zettler, L. A., Anderson, O. R. & 7 other authors (2003). Two new small-subunit ribosomal RNA gene lineages within the subclass gymnamoebia. J Eukaryot Microbiol 50, 224-232.
38. Richards, T. A. & Cavalier-Smith, T. (2005). Myosin domain evolution and the primary divergence of eukaryotes. Nature 436, 1113-1118.
39. Rodriguez, F., Oliver, J. F., Martin, A. & Medina, J. R. (1990). The general stochastic model of nucleotide substitution. J Theor Biol 142, 485-501.
40. Simpson, A. G. B., Bernard, C., Fenchel, T. & Patterson, D. J. (1997). The organization of Mastigamoeba schizophrenia n. sp.: more evidence of ultrastructural idiosyncrasy and simplicity in pelobiont protists. Eur J Protistol 33, 87-98.
41. Smirnov, A., Nassonova, E., Berney, C., Fahrni, J., Bolivar, I. & Pawlowski, J. (2005). Molecular phylogeny and classification of the lobose amoebae. Protist 156, 129-142.
42. Stechmann, A. & Cavalier-Smith, T. (2003). The root of the eukaryote tree pinpointed. Curr Biol 13, R665-R666.
43. Swofford, D. L. (1998). PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). Sunderland, MA: Sinauer Associates.
44. Walker, G., Simpson, A. G. B., Edgcomb, V., Sogin, M. L. & Patterson, D. J. (2001). Ultrastructural identities of Mastigamoeba punctachora, Mastigamoeba simplex and Mastigella commutans and assessment of hypotheses of relatedness of the pelobionts (Protista). Eur J Protistol 37, 25-49.
45. Walker, G., Dacks, J. B. & Embley, T. M. (2006). Ultrastructural description of Breviata anathema, n. gen., n. sp., the organism previously studied as Mastigamoeba invertens. J Eukaryot Microbiol 53, 65-78.
46. Wuyts, J., Van de Peer, Y. & De Wachter, R. (2001). Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res 29, 5017-5028.
47. Zuker, M., Mathews, D. H. & Turner, D. H. (1999). Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In RNA Biochemistry and Biotechnology, pp. 11-43. Edited by J. Barciszewski & B. F. C. Clark. Dordtrecht: Kluwer.