Molecular phylogenetic analysis places Percolomonas cosmopolitus within heterolobosea: Evolutionary implications

Journal of Eukaryotic Microbiology

Volumn 51, Issue 5, 2004, Pages 575-581

  Nikolaev, Sergey I ^a   Mylnikov, Alexandre P ^b   Berney, Cedric ^c   Fahrni, Jose ^c   Pawlowski, Jan ^c   Aleshin, Vladimir V ^a   Petrov, Nikolay B ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

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

^c UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

Helix 17; Heterolobosea; Phylogeny; SSU rRNA; V3 region

Indexed keywords

PHYLOGENETICS;

HETEROLOBOSEA; MASTIGOPHORA (FLAGELLATES); PERCOLOMONAS COSMOPOLITUS; PROTOZOA; VAHLKAMPFIIDAE;

EID: 5344277575     PISSN: 10665234     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2004.tb00294.x     Document Type: Article

References (46)

1. Arisue, N., Hashimot, T., Lee, J. A., Moore, D. V., Gordon, P., Sensen, C. W., Gaasterland, T., Hasegawa, M. & Müller, M. 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.
2. Broers, C. A. M., Stumm, C. K., Vogels, G. D. & Brugerolle, G. 1990. Psalteriomonas lanterna gen. nov., spec, nov., a free-living amoeboflagellate isolated from freshwater anaerobic sediments. Eur. J. Protozool., 25:369-380.
3. Brown, S. & De Jonckheere, J. F. 1999. A reevaluation of the amoeba genus Vahlkampfia based on SSU rDNA sequences. Eur. J. Protistol., 35:49-54.
4. Brugerolle, G. & Simpson, A. G. B. 2004. The flagellar apparatus of Heteroloboseans. J. Eukaryot. Microbiol., 51:96-107.
5. Cavalier-Smith, T. 1993. Percolozoa and the symbiotic origin of the metakaryote cell. In: Ishikawa, H., Ishida, M. & Sato, S. (ed.), Endocytobiology. Tübingen University Press, Tübingen. 5:399-406.
6. Cavalier-Smith, T. 1995. Zooflagellate phylogeny and classification. Tsitologyia, 37:1010-1029.
7. Cavalier-Smith, T. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol., 52:297-354.
8. Cavalier-Smith, T. 2004. 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., 53:1741-1758.
9. De Jonckheere, J. F. & Brown, S. 1999. SSU rDNA analysis reveals the existence of a second Naegleria sp. with dividing flagellates: N. robinsoni sp. nov. Eur. J. Protistol., 35:264-266.
10. De Rijk, P. & De Wachter, R. 1997. RnaViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res., 25:4679-4684.
11. Edgcomb, V. P., Simpson, A. G. B., Amaral Zeltler, 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.
12. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17:368-376.
13. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39:783-791.
14. Felsenstein, J. 1993. PHYLIP: phylogeny inference package, version 3.5. University of Washington, Seattle.
15. Fenchel, T. & Patterson, D. J. 1986. Percolomonas cosmopolitus (Ruinen) n. gen., a new type of filter-feeding flagellate from marine plankton. J. Mar. Biol. Ass. U.K., 66:465-482.
16. Jones, D. T., Taylor, W. R. & Thornton, J. M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8:275-282.
17. Huelsenbeck, J. P. & Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17:754-755.
18. Kishino, H. & Hasegawa, M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the Hominoidea. J. Mol. Evol., 29:170-179.
19. Lanave, C., Preparata, G., Saccone, C. & Serio, G. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol., 20:86-93.
20. Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene, 71:491-499.
21. O'Kelly, C. J., Silberman, J. D., Amaral Zettler, L. A., Nerad, T. A., & Sogin, M. L. 2003. Monopylocystis visvesvarai n. gen., n. sp. and Sawyeria marylandensis n. gen., n. sp.: two new amitochondrial heterolobosean amoebae from anoxic environments. Protist, 154:281-290.
22. Page, C. 1987. Transfer of Stachyamoeba lipophora to the class Heterolobosea. Arch. Protistenkd., 133:191-197.
23. Page, F. C. & Blanton, R. L. 1985. The Heterolobosea (Sarcodina: Rhizopoda), a new class uniting the Schizopyrenida and the Acrasidae (Acrasida). Protistologica, 21:121-132.
24. Petrov, N. B. & Aleshin, V. V. 2002. Conditionally neutral phylogenetic markers of major taxa: a new aspect of the evolution of macromolecules. Russ. J. Genet., 38:877-894.
25. Philippe, H. & Germot, A. 2000. Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol. Biol. Evol., 17:830-834.
26. Posada, D. & Crandall, K. A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics, 14:817-818.
27. Rodriguez, F., Oliver, J. L., Marin, A. & Medina, J. R. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol., 142:485-501.
28. Rokas, A. & Holland, P. W. 2000. Rare genomic changes as a tool for phylogenetics Trends Ecol. Evol., 15:454-459.
29. Ruinen, J. 1938. Notizen uber Salzflagellaten. II. Uber die Verbreitung der Salzflagellaten. Arch. Protistenkd., 90:210-258.
30. Saitou, N. & Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4:406-425.
31. Seravin, L. N. 1992. Eukaryotes devoid of the most important cellular organelles (flagella, Golgi apparatus, mitochondria) and the main task of organellology. Tsitologyia, 34:3-33.
32. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol., 51:492-508.
33. Shimodaira, H. & Hasegawa, M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol., 16:1114-116.
34. Shimodaira, H. & Hasegawa, M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics, 17:1246-47.
35. Silberman, J. D., Simpson, A. G. B., Kulda, J., Cepicka, I., Hampl, V., Johnson, P. J. & Roger, A. J. 2002. Retortamonad flagellates are closely related to diplomonads - implications for the history of mitochondrial function in eukaryote evolution. Mol. Biol. Evol., 19: 777-86.
36. Simpson, A. G. B. 1997. The identity and composition of the Euglenozoa. Arch. Protistenkd., 148:318-328.
37. Simpson, A. G. B. 2003. Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). Int. J. Syst. Evol. Microbiol., 53:1759-1777.
38. Simpson, A. G. B. & Patterson, D. J. 1999. The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the excavate hypothesis. Europ. J. Protistol., 35:357-370.
39. Sogin, M. L., Silberman, J. D., Hinkle, G. & Morrison, H. G. 1996. Problems with molecular diversity in the Eukarya. In: Roberts, D. M., Sharp, P., Alderson, G. & Collins, M. A. (ed.), Society of General Microbiology Symposium: Evolution of Microbial Life. Cambridge University Press, Cambridge. p. 167-184.
40. Stechmann, A. & Cavalier-Smith, T. 2002. Rooting the eukaryote tree by using a derived gene fusion. Science, 297:89-91.
41. Swofford, D. L. 1998. PAUP *: phylogenetic analysis using parsimony (* and other methods). Sinauer Associates, Sunderland, Massachusetts.
42. Van de Peer, Y., De Rijk, P., Wuyts, J., Winkelmans, T. & De Wachter, R. 2000. The European small subunit ribosomal RNA database. Nucleic Acids Res., 28:175-176.
43. Voncken, F., Boxma, B., Tjaden, J., Akhmanova, A., Huynen, M., Verbeek, F., Tielens, A. G. M., Haferkamp, I., Neuhaus, H. E., Vogels, G., Veenhuis, M. & Hackstein, J. H. P. 2002. Multiple origins of hydrogenosomes: functional and phylogenetic evidence from the ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp. Mol. Microbiol., 44:1441-1454.
44. Weekers, P. H. H., Kleyn, J. & Vogels, G. D. 1997. Phylogenetic position of Psalteriomonas lanterna deduced from the SSU rDNA sequence. J. Eukaryot. Microbiol., 44:467-470.
45. 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.
46. Zuker, M., Mathews, D. H. & Turner, D. H. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In: Barciszewski, J. & Clark, B. F. C. (ed.), RNA Biochemistry and Biotechnology. NATO ASI Series, Kluwer Academic Publishers. p. 11-43.