Phylogeny of Lobose Amoebae Based on Actin and Small-Subunit Ribosomal RNA Genes

Molecular Biology and Evolution

Volumn 20, Issue 11, 2003, Pages 1881-1886

  Fahrni, José F ^a   Bolivar, Ignacio ^a   Berney, Cédric ^a   Nassonova, Elena ^b   Smirnov, Alexey ^c   Pawlowski, Jan ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b INSTITUTE OF CYTOLOGY   (Russian Federation)

^c ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

Author keywords

Actin; Amoebozoa; Lobosea; Molecular phylogeny; Small subunit ribosomal RNA

Indexed keywords

ACTIN; SMALL SUBUNIT RIBOSOMAL RNA;

AMOEBA; ARTICLE; ENTAMOEBA; EVOLUTION; GENE SEQUENCE; MOLECULAR PHYLOGENY; MOULD; NONHUMAN; NUCLEOTIDE SEQUENCE; SARCODINA; TAXONOMY;

ACTINS; AMOEBA; ANIMALS; EVOLUTION, MOLECULAR; GENES, RRNA; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL; SEQUENCE ANALYSIS, DNA;

AMOEBOZOA; ARCHAMOEBAE; ARCHEZOA; ENTAMOEBA; ENTAMOEBIDAE; GYMNAMOEBIA; LOBOSEA; MYCETOZOA; MYXOGASTRIA; PELOBIONTIDA; PROTISTA; PROTOZOA; SARCODINA;

EID: 0242497850     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg201     Document Type: Article

References (60)

1. Adachi, J., and M. Hasegawa. 1996. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1-150.
2. Amaral Zettler, L. A., T. A. Nerad, C. J. O'Kelly, M. T. Peglar, P. M. Gillevet, J. D. Silberman, and M. L. Sogin. 2000. A molecular reassessment of the leptomyxid amoebae. Protist 151:275-282.
3. Anderson, O. 1997. Annual abundances, diversity and growth potential of gymnamoebae in a shallow freshwater pond. J. Eukaryot. Microbiol. 44:393-398.
4. Arisue, N., T. Hashimoto, J. A. Lee, D. V. Moore, P. Gordon, C. W. Sensen, T. Gaasterland, M. Hasegawa, and M. Müller. 2002. The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2. J. Eukaryot. Microbiol. 49:1-10.
5. Bakker-Grunwald, T., and C. Wöstmann. 1993. Entamoeba histolytica as a model for the primitive eukaryotic cell. Parasitol. Today 9:27-31.
6. Baldauf, S. L., and J. D. Palmer. 1993. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA 90:11558-11562.
7. Baldauf, S. L., A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
8. Bapteste, E., H. Brinkmann, J. A. Lee et al. (11 co-authors). 2002. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 99:1414-1419.
9. Bhattacharya, D., and K. Weber. 1997. The actin gene of the glaucocystophyte Cyanophora paradoxa: analysis of the coding region and introns, and an actin phylogeny of eukaryotes. Curr. Genet. 31:439-446.
10. Bolivar, I., J. F. Fahmi, A. Smirnov, and J. Pawlowski. 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.
11. Bovee, E. 1985. Class Lobosea Carpenter 1861. Pp. 158-211 in J. Lee, S. Hutner, and E. Bovee, eds. An illustrated guide to the Protozoa. Society of Protozoologists, Lawrence, Kansas.
12. Butler, H., and A. Rogerson. 2000. Naked amoebae from benthic sediments in the Clyde Sea area, Scotland. Ophelia 53:37-54.
13. Cavalier-Smith, T. 1987. Eukaryotes with no mitochondria. Nature 326:332-333.
14. -. 1993. Kingdom Protozoa and its 18 phyla. Microbiol. Rev. 57:953-994.
15. -. 1998. A revised six-kingdom system of life. Biol. Rev. Camb. Philos. Soc. 73:203-266.
16. -. 2000. Flagellate megaevolution: the basis for eukaryote diverification. Pp. 361-390 in J. R. Green and B. S. C. Leadbeater, eds. The flagellates: unity, diversity and evolution. Taylor and Francis, London.
17. Cavalier-Smith, T., and E. E. Chao. 1996. Molecular phylogeny of the free-living archezoan Trepomonas agilis and the nature of the first Eukaryote. J. Mol. Evol. 43:551-562.
18. Chomczynski, P., and N. Sacchi. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:156-159.
19. Clark, C. G., and G. A. Cross. 1988. Small-subunit ribosomal RNA sequence from Naegleria gruberi supports the polyphyletic origin of amoebas. Mol. Biol. Evol. 5:512-518.
20. Clark, C. G., and A. Roger. 1995. Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proc. Natl. Acad. Sci. USA 92:6518-6521.
21. Corliss, J. O. 1994. An interim utilitarian ('user friendly') hierarchical classification and characterization of the protists. Acta Protozool. 33:1-51.
22. Edgcomb, V. P., A. G. B. Simpson, L. Amaral Zettler, T. A. Nerad, D. J. Patterson, M. E. Holder, and M. L. Sogin. 2002. Pelobionts are degenerate protists: insights from molecules and morphology. Mol. Biol. Evol. 19:978-982.
23. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
24. -. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
25. -. 2002. PHYLIP (phylogeny inference package). Version 3.6a3. Distributed by the author, Department of Genetics, University of Washington, Seattle.
26. Finlay, B. J., H. I. J. Black, S. Brown, K. J. Clarke, G. F. Esteban, R. M. Hindle, J. L. Olmo, A. Rollett, and K. Vickerman. 2000. Estimating the growth potential of the soil protozoan community. Protist 151:69-80.
27. Forget, L., J. Ustinova, Z. Wang, V. A. R. Huss, and B. F. Lang. 2002. Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi. Mol. Biol. Evol. 19:310-319.
28. Galtier, N., M. Gouy, and C. Gautier. 1996. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12:543-548.
29. Hasegawa, M., and H. Kishino. 1994. Accuracies of the simple methods for estimating the bootstrap probability of a maximum likelihood tree. Mol. Biol. Evol. 11:142-145.
30. Hausmann, K., and N. Hülsmann. 1996. Protozoology. Georg Thieme Verlag, Stuttgart, Germany.
31. Hinkle, G., D. D. Leipe, T. A. Nerad, and M. L. Sogin. 1994. The unusually long small subunit ribosomal RNA of Phreatamoeba balamuthi. Nucleic Acids Res. 22:465-469.
32. Hinkle, G., and M. L. Sogin. 1993. The evolution of the Vahlkampfiidae as deduced from 16S-like ribosomal RNA analysis. J. Eukaryot. Microbiol. 40:599-603.
33. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
34. Kelleher, J. F., S. J. Atkinson, and T. D. Pollard. 1995. Sequences, structural models, and cellular localization of the actin-related proteins Arp2 and Arp3 from Acanthamoeba. J. Cell. Biol. 131:385-397.
35. Kishino, H., T. Miyata, and M. Hasegawa. 1990. Maximum likelihood inference of protein phylogeny, and the origin of chloroplasts. J. Mol. Evol. 31:151-160.
36. Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93.
37. Larsen, N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L. Marsh, and C. R. Woese. 1993. The ribosomal database project. Nucleic Acids Res. 21:3021-3023.
38. Lee, J. J., G. F. Leedale, and P. Bradbury. 2000. An illustrated guide to the Protozoa. 2nd edition. Society of Protozoologists, Lawrence, Kansas.
39. Levine, N. D., J. O. Corliss, F. E. Cox et al. (16 co-authors). 1980. A newly revised classification of the Protozoa. J. Protozool. 27:37-58.
40. Margulis, L. 1974. Five-kingdom classification and the origin and evolution of cells. Evol. Biol. 7:45-78.
41. Margulis, L., J. Corliss, M. Melkonian, and D. Chapman. 1990. Handbook of Protoctista. Jones and Bartlett, Boston.
42. Milyutina, I. A., V. V. Aleshin, K. A. Mikrjukov, O. S. Kedrova, and N. B. Petrov. 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.
43. Neefs, J. M., Y. Van de Peer, P. De Rijk, S. Chapelle, and R. De Wachter. 1993. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21:3025-3049.
44. Page, F. 1987. The classification of 'naked' amoebae (phylum Rhizopoda). Arch. Protistenk. 133:199-217.
45. Page, F., and L. Blanton. 1985. The Heterolobosea (Sarcodina: Rhizopoda), a new class uniting the Schizopyrenida and the Acrasidae (Acrasida). Protistologica 21:121-132.
46. Pawlowski, J., I. Bolivar, J. F. Fahmi, C. De Vargas, and S. S. Bowser. 1999. Molecular evidence that Reticulomyxa filosa is a freshwater naked foraminifer. J. Eukaryot. Microbiol. 46:612-617.
47. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
48. Rodriguez, F., J. L. Oliver, A. Marin, and J. R. Medina. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
49. Saitou, N., and M. Nei. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
50. Schafer, D. A., and T. A. Schroer. 1999. Actin-related proteins. Annu. Rev. Cell. Dev. Biol. 15:341-363.
51. Silberman, J. D., C. G. Clark, L. S. Diamond, and M. L. Sogin. 1999. Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences. Mol. Biol. Evol. 16:1740-1751.
52. Sims, G. P., A. Rogerson, and R. Aitken. 1999. Primary and secondary structure of the small-subunit ribosomal RNA of the naked, marine amoeba Vannella anglica: phylogenetic implications. J. Mol. Evol. 48:740-749.
53. Smimov, A. 2001. Vannella ebro n. sp. (Lobosea, Gymnamoebia), isolated from cyanobacterial mats in Spain. Europ. J. Protistol. 37:147-153.
54. Sogin, M. L. 1991. Early evolution and the origin of eukaryotes. Curr. Opin. Genet. Dev. 1:457-63.
55. Stechmann, A., and T. Cavalier-Smith. 2002. Rooting the eukaryote tree by using a derived gene fusion. Science 297:89-91.
56. Strimmer, K., and A. Von Haeseler. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
57. Swofford, D. L. 1998. PAUP*: phylogenetic analyses using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
58. Szenasi, Z., T. Endo, K. Yagita, and E. Nagy. 1998. Isolation, identification and increasing importance of 'free-living' amoebae causing human disease. J. Med. Microbiol. 47:5-16.
59. Wang, H., M. Qi, and A. J. Cutler. 1993. A simple method of preparing plant samples for PCR. Nucleic Acids Res. 21:4153-4154.
60. Wuyts, J., P. De Rijk, Y. Van de Peer, G. Pison, P. Rousseeuw, and R. De Wachter. 2000. 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. 28:4698-4708.