Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies

International Journal of Systematic and Evolutionary Microbiology

Volumn 53, Issue 6, 2003, Pages 1735-1739

  Longet, David ^a   Archibald, John M ^b   Keeling, Patrick J ^b   Pawlowski, Jan ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; PROTOZOAL DNA; RIBOSOME DNA; RNA POLYMERASE II; SMALL SUBUNIT RIBOSOMAL RNA; UBIQUITIN;

AMINO ACID SEQUENCE; ARTICLE; CERCOZOA; CONTROLLED STUDY; EUKARYOTE; EUKARYOTE EVOLUTION; FORAMINIFER; GENE SEQUENCE; GENETIC ANALYSIS; GROMIA OVIFORMIS; HYPOTHESIS; NEW GENUS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTOZOAL GENETICS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

ANIMALS; CLASSIFICATION; DNA, RIBOSOMAL; EUKARYOTIC CELLS; PHYLOGENY; RNA POLYMERASE II;

CERCOZOA; EUKARYOTA; FILOSEA; FORAMINIFERA; GROMIA; GROMIA OVIFORMIS; PROTISTA; PROTOZOA;

EID: 0344897110     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.02597-0     Document Type: Article

References (39)

1. Archibald, J. M., Longet, D., Pawlowski, J. & Keeling, P. J. (2003). A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic Supergroup. Mol Biol Evol 20, 62-66.
2. Arnold, Z. M. (1972). Observations on the biology of the protozoan Gromia oviformis Dujardin. Univ Calif Publ Zool 100.
3. Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. & Doolittle, W. F. (2000). A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972-977.
4. Berney, C. & Pawlowski, J. (2003). Revised small subunit rRNA analysis provides further evidence that Foraminifera are related to Cercozoa. J Mol Evol 57, 1-8.
5. Bhattacharya, D., Helmchen, T. & Melkonian, M. (1995). Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent rhizopod lineage containing the Euglyphina and the Chlorarachniophyta. J Eukaryot Microbiol 42, 65-69.
6. Bovee, E. C. (1985). Class Filosea Leidy, 1879. In An Illustrated Guide to the Protozoa, pp. 228-245. Edited by J. J. Lee, S. H. Hutner & E. C. Bovee. Lawrence, KS: Society of Protozoologists.
7. Bruno, W. J., Socci, N. D. & Halpern, A. L. (2000). Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 17, 189-197.
8. Bulman, S. R., Kühn, S. F., Marshall, J. W. & Schnepf, E. (2001). A phylogenetic analysis of the SSU rDNA from members of the Plasmodiophorida and Phagomyxida. Protist 152, 43-51.
9. Burki, F., Berney, C. & Pawlowski, J. (2002). Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist 153, 251-260.
10. Cavalier-Smith, T. (1998). A revised six-kingdom 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 B. S. C. Leadbeater & J. C. Green. London: Taylor & Francis.
12. Cavalier-Smith, T. & Chao, E. E. (1996/7). Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid Amoebae. Arch Protistenkd 147, 227-236.
13. Cramer, P., Bushnell, D. A. & Kornberg, R. D. (2001). Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863-1876.
14. Dacks, J. B., Marinets, A., Ford Doolittle, W., Cavalier-Smith, T. & Logsdon, J. M., Jr (2002). Analyses of RNA polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang. Mol Biol Evol 19, 830-840.
15. Fast, N. M., Kissinger, J. C., Roos, D. S. & Keeling, P. J. (2001). Nuclear-encoded, plastid-targeted genes suggest a common origin for apicomplexa and dinoflagellates plastids. Mol Biol Evol 18, 418-426.
16. Felsenstein, J. (1993). PHYLIP (Phylogeny Inference Package). Department of Genetics, University of Washington, Seattle, USA.
17. Harper, J. T. & Keeling, P. J. (2003). Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol MBE Advance Access, http://dx.doi.org/10.1093/molbev/msg195
18. Hedley, R. H. (1958). Confusion between Gromia oviformis and Allogromia ovoidea. Nature 182, 1391-1392.
19. Hirt, R. P., Logsdon, J. M., Jr, Healy, B., Dorey, M. W., Doolittle, W. F. & Embley, T. M. (1999). Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci U S A 96, 580-585.
20. Keeling, P. J. (2001). Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Mol Biol Evol 18, 1551-1557.
21. Keeling, P. J. & Fast, N. M. (2002). Microsporidia: biology and evolution of highly reduced intracellular parasites. Annu Rev Microbiol 56, 93-116.
22. Keeling, P. J., Deane, J. A. & McFadden, G. I. (1998). The phylogenetic position of alpha- and beta-tubulins from the Chlorarachnion host and Cercomonas (Cercozoa). J Eukaryot Microbiol 45, 561-570.
23. Keeling, P. J., Deane, J. A., Hink-Schauer, C., Douglas, S. E., Maier, U.-G. & McFadden, G. I. (1999). The secondary endosymbiont of the cryptomonad Guillardia theta contains alpha-, beta-, and gammatubulin genes. Mol Biol Evol 16, 1308-1313.
24. Klenk, H.-P., Zillig, W., Lanzendörfer, M., Grampp, B. & Palm, P. (1995). Location of protist lineages in a phylogenetic tree inferred from sequences of DNA-dependent RNA polymerases. Arch Protistenkd 145, 221-230.
25. Kühn, S., Lange, M. & Medlin, L. K. (2000). Phylogenetic position of Cryothecomonas inferred from nuclear-encoded small subunit ribosomal RNA. Protist 151, 337-345.
26. Meisterfeld, R., Holzmann, M. & Pawlowski, J. (2001). Morphological and molecular characterization of a new terrestrial allogromiid species: Edaphoallogromia australica gen. et spec. nov. (Foraminifera) from Northern Queensland (Australia). Protist 152, 185-192.
27. Patterson, D. J., Simpson, A. G. B. & Rogerson, A. (2000). Amoebae of uncertain affinities. In An Illustrated Guide to the Protozoa, 2nd edn, pp. 804-827. Edited by J. J. Lee, G. F. Leedale & P. Bradbury. Lawrence, KS: Society of Protozoologists.
28. Pawlowski, J., Bolivar, I., Guiard-Maffia, J. & Gouy, M. (1994). Phylogenetic position of the Foraminifera inferred from LSU rRNA gene sequences. Mol Biol Evol 11, 929-938.
29. Pawlowski, I., Bolivar, I., Fahrni, J. F., Cavalier-Smith, T. & Gouy, M. (1996). Early origin of Foraminifera suggested by SSU rRNA gene sequences. Mol Biol Evol 13, 445-450.
30. Pawlowski, J., Bolivar, I., Fahrni, J. F., de Vargas, C., Gouy, M. & Zaninetti, L. (1997). Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Mol Biol Evol 14, 498-505.
31. Pawlowski, J., Bolivar, I., Fahrni, J. F., de Vargas, C. & Bowser, S. S. (1999). Molecular evidence that Reticulomyxa filosa is a freshwater naked foraminifer. J Eukaryot Microbiol 46, 612-617.
32. Philippe, H. & Adoutte, A. (1998). The molecular phylogeny of eukaryotes: solid facts and uncertainties. In Evolutionary Relationships Among Protozoa, pp 25-56. Edited by H. Coombs, K. Vickerman, M. A. Sleigh & A. Warren. London: Chapman & Hall.
33. Sogin, M. (1997). History assignment: when was the mitochondrion founded? Curr Opin Genet Dev 7, 792-799.
34. Stiller, J. W. & Hall, B. D. (1997). The origin of red algae: implications for plastid evolution. Proc Natl Acad Sci U S A 94, 4520-4525.
35. Stiller, J. W. & Hall, B. D. (2002). Evolution of the RNA polymerase II C-terminal domain. Proc Natl Acad Sci U S A 99, 6091-6096.
36. Stiller, J. W., Riley, J. & Hall, B. D. (2001). Are red algae plants? A critical evaluation of three key molecular data sets. J Mol Evol 52, 527-539.
37. Strimmer, K. & von Haeseler, A. (1996). Quartet puzzling: a quartet maxinium-likelihood method for reconstructing tree topologies. Mol Biol Evol 13, 964-969.
38. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
39. Wylezich, C., Meisterfeld, R., Meisterfeld, S. & Schlegel, M. (2002). Phylogenetic analyses of small subunit ribosomal RNA coding regions reveal a monophyletic lineage of euglyphid testate amoebae (Order Euglyphida). J Eukaryot Microbiol 49, 108-118.