Phylogeny of Heteromita, Cercomonas and Thaumatomonas based on SSU rDNA sequences, including the description of Neocercomonas jutlandica sp. nov., gen. nov.

European Journal of Protistology

Volumn 40, Issue 2, 2004, Pages 119-135

  Ekelund, Flemming ^a   Daugbjerg, Niels ^a   Fredslund, Line ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Cercomonas; Heteromita; Neocercomonas gen. nov.; Phylogeny; SSU rDNA sequences; Thaumatomonas

Indexed keywords

CERCOMONAS; CHLORARACHNIOPHYCEAE; CRYOTHECOMONAS; EUGLYPHIDA; HAPLOSPORIDIA; HETEROMITA; MASSISTERIA; MASTIGOPHORA (FLAGELLATES); NEOCERCOMONAS JUTLANDICA; PLASMODIOPHORIDAE; THAUMATOMONAS;

EID: 3843101351     PISSN: 09324739     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejop.2003.12.002     Document Type: Article

References (67)

1. Atkins M.S., Teske A.P., Anderson O.R. A survey of flagellate diversity at four deep-sea hydrothermal vents in the Eastern Pacific Ocean using structural and molecular approaches. J. Eukaryot. Microbiol. 47:2000;400-411
2. Bhattacharya D., Helmchen T., Melkonian M. Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent rhizopod lineage containing the Euglyphina and the Chlorarachniophyta. J. Eukaryot. Microbiol. 42:1995;65-69
3. Burki F., Berney C., Pawlowski J. Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist. 153:2002;251-260
4. Castlebury L.A., Domier L.L. Small subunit ribosomal RNA gene phylogeny of Plasmodiophora brassicae. Mycologia. 90:1998;102-107
5. Cavalier-Smith T. Amoeboflagellates and mitochondrial cristae in eukaryote evolution. megasystematics of the new protozoan subkingdoms Eozoa and Neozoa Arch. Protistenkd. 147:1996/97;237-258
6. Cavalier-Smith T. Neomonada and the origin of animals and fungi. Coombs G.H., Vickerman K., Sleigh M.A., Warren A. Evolutionary Relationships Among Protozoa. 1998;375-407 Kluwer Academic Publishers, Dordrecht, The Netherlands
7. Cavalier-Smith T. A revised six-kingdom system of life. Biol. Rev. 73:1998;203-266
8. Cavalier-Smith T. Zooflagellate phylogeny and the systematics of Protozoa. Biol. Bull. 196:1999;393-396
9. Cavalier-Smith T., Chao E.E. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch. Protistenkd. 147:1996/97;227-236
10. Cavalier-Smith T., Chao E.E. Phylogeny and classification of phylum Cercozoa (Protozoa). Protist. 154:2003;341-358
11. De Saedeleer H. Notes de Protistologie IV.-Thaumatomonas lauterborni n.g., n. sp. flagellé nouveau. Recl Inst. zool. Torley-Rousseau. 3:1931;89-103
12. Ekelund F., Patterson D.J. Some heterotrophic flagellates from a cultivated soil in Australia. Arch. Protistenkd. 148:1997;461-478
13. Ekelund F., Rønn R., Griffiths B.S. Quantitative estimation of flagellate community structure and diversity in soil samples. Protist. 152:2001;301-314
14. Felsenstein J. Evolutionary trees from DNA sequences. a maximum likelihood approach J. Mol. Evol. 17:1981;368-376
15. Felsenstein J. Confidence limits on phylogenies. an approach using the bootstrap Evolution. 39:1985;783-791
16. Felsenstein J., Kishino H. Is there something wrong with the bootstrap on phylogenies? A reply. Syst. Biol. 42:1993;193-200
17. Foissner W. Diversity and ecology of soil flagellates. Patterson D.J., Larsen J. The Biology of Free-Living Heterotrophic Flagellates. Vol. 45:1991;93-112 Systematics Association, Clarendon Press, Oxford
18. Foissner W. Neotypification of protists, especially ciliates (Protozoa, Ciliophora). Bull. Zool. Nom. 59:2002;165-169
19. Gargas A., Depriest P.T., Tailor J.W. Positions of multiple insertions in SSU rDNA of lichen-forming fungi. Mol. Biol. Evol. 12:1995;208-218
20. Hall T.A. BioEdit. a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucl. Acids. Symp. Ser. 41:1999;95-98
21. Hillis D.M., Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:1993;182-192
22. Hillis D.M., Huelsenbeck J.P., Cunningham C.W. Application and accuracy of molecular phylogenies. Science. 264:1994;671-677
23. Ishida K., Green B.R., Cavalier-Smith T. Diversification of a chimeric algal group, the chlorarachniophytes. phylogeny of nuclear and nucleomorph small-subunit rRNA genes Mol. Biol. Evol. 16:1999;321-331
24. Johnsen K., Enger Ø., Jacobsen C.S., Thirup L., Torsvik V. Quantitative selective PCR of 16S ribosomal DNA correlates well with selective agar plating in describing population dynamics of indigenous Pseudomonas spp. in soil hot spots. Appl. Environ. Microbiol. 65:1999;1786-1789
25. Johansen S., Johansen T., Haugli F. Structure and evolution of myxomycete nuclear group I introns. a model for horizontal transfer by intron homing Curr. Genet. 22:1992;297-304
26. Karpov S.A., Ekelund F., Moestrup Ø. Katabia gromovi nov. gen., nov sp. - a new soil flagellate with affinities to Heteromita (Cercomonadida). Protistology. 3:2004;30-41
27. Keeling P.J., Deane J.A., McFadden G.I. The phylogenetic position of alpha- and beta-tubulins from the Chlorarachnion host and Cercomonas (Cercozoa). J. Eukaryot. Microbiol. 45:1998;561-570
28. Knoll A.H. The early evolution of eukaryotes. a geological perspective Science. 256:1992;622-628
29. Kumar S., Rzhetsky A. Evolutionary relationships of eukaryotic kingdoms. J. Mol. Evol. 42:1996;183-193
30. Logsdon J.M. Jr., Tyshenko M.G., Dixon C., Jafari J.D., Walker V.K., Palmer J.D. Seven newly discovered intron positions in the triose-phosphate isomerase gene. evidence for the introns-late theory Proc. Natl. Acad. Sci. USA. 92:1995;8507-8511
31. MacDonald C.M., Darbyshire J.F., Ogden C.G. The morphology of a common soil flagellate, Heteromita globosa Stein (Mastigophorea: Protozoa). Bull. Br. Mus. Nat. Hist. (Zool.). 31:1977;255-264
32. McFadden G.I., Gilson P., Hofmann C.J.B., Adcock G.A., Maier U.G. Evidence that an amoeba acquired photosynthesis by retaining parts of an engulfed eukaryotic alga. Proc. Natl. Acad. Sci. USA. 91:1994;3690-3694
33. Mylnikov A.P. New species of colourless flagellate Cercomonas minimus. Inf. Byull. Bot. Vnutrennich Vod. 66:1985;17-18. (in Russian)
34. Mylnikov A.P., Karpov S.A. A new representative of colourless flagellates, Thaumatomonas seravini sp. n. (Thaumatomonadida, Protista). Zool. Zh. 73:1993;5-10. (in Russian)
35. Nielsen T.H., Christophersen C., Anthoni U., Sørensen J. Viscosinamide, a new cyclic depsipeptide with surfactant and antifungal properties produced by Pseudomonas fluorescens DR54. J. Appl. Microbiol. 86:1999;80-90
36. Page F.C. A New Key to Freshwater and Soil Gymnoamoebae. 1988;Freshwater Biological Association, Ambleside, UK
37. Patterson D.J. The diversity of eukaryotes. Am. Nat. 154:1999;96-124
38. Patterson D.J., Zölffel M. Heterotrophic flagellates of uncertain taxonomic position. Patterson D.J., Larsen J. The Biology of Free-Living Heterotrophic Flagellates. 1991;427-475 Clarendon Press, Oxford
39. Philippe H., Adoutte A. The molecular phylogeny of eukaryota. solid facts and uncertainties Coombs G.H., Vickerman K., Sleigh M.A., Warren A. Evolutionary Relationships Among Protozoa. 1998;25-56 Kluwer Academic Publishers, Dordrecht, The Netherlands
40. Robertson M. Notes on Heteromita (Protozoa, Flagellata). Parasitology. 20:1928;10-24
41. Rosenberg M.S., Kumar S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA. 98:2001;10751-10756
42. Rzhetsky A., Nei M. Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. J. Mol. Biol. 38:1994;295-299
43. Saitou N., Nei M. The neighbor-joining method. a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4:1987;406-425
44. Sandon H. The Composition and Distribution of the Protozoan Fauna of the Soil. 1927;Oliver and Boyd, Edinburgh and London
45. Sogin M.L. Evolution of eukaryotic microorganisms and their small subunit ribosomal RNAs. Am. Zool. 29:1989;487-499
46. Sogin M.L., Hinkle G. Common measures for studies of biodiversity. molecular phylogeny in the eukaryotic microbial world Reaka-Kudla M.L., Wilson D.E., Wilson E.O. Biodiversity, II. Understanding and Protecting Our Biological Resources. 1997;109-122 Joseph Henry Press, Washington, DC
47. Stoltzfus A., Logsdon J.M. Jr., Palmer J.D., Doolittle W.F. Intron "sliding" and the diversity of intron positions. Proc. Natl. Acad. Sci. USA. 94:1997;10739-10744
48. Sullivan J., Holsinger K.E., Simon C. The effect of topology on estimates of among-site rate variation. J. Mol. Evol. 42:1996;308-312
49. Swofford D.L. PAUP. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4:2003;Sinauer Associates, Sunderland, London
50. Swofford D.L., Olsen G.J., Waddell P.J., Hillis D.M. Phylogenetic inference. Hillis D.M., Moritz C., Mable B.K. Molecular Systematics. 1996;407-514 Sinauer, Sunderland, London
51. Van de Peer Y., De Wachter R. TREECON for Windows. a software package for the construction and drawing of evolutionary trees for the Microsoft windows environment Comput. Appl. Biosci. 10:1994;569-570
52. Van de Peer Y., De Wachter R. Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site variation in 18S rRNA. J. Mol. Evol. 45:1997;619-630
53. Van de Peer Y., Neefs J.-M., De Rijk P., De Wachter R. Evolution of eukaryotes as deduced from small ribosomal subunit RNA sequences. Biochem. Syst. Ecol. 21:1993;43-55
54. Van de Peer Y., Neefs J.-M., De Rijk P., De Wachter R. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences. calibration of the molecular clock J. Mol. Evol. 37:1993;221-232
55. Van de Peer Y., Rensing S.A., Maier U.-G., De Wachter R. Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. Proc. Natl. Acad. Sci. 93:1996;7732-7736
56. Van de Peer Y., Van der Auwera G., De Wachter R. The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. J. Mol. Evol. 42:1996;201-210
57. Van de Peer Y., Jansen J., De Rijk P., De Wachter R. Database on the structure of small ribosomal subunit RNA. Nucl. Acids Res. 25:1997;111-116
58. Van de Peer Y., De Rijk P., Wuyts J., Winkelmans T., De Wachter R. The European small subunit ribosomal RNA database. Nucl. Acids Res. 28:2000;175-176
59. Van der Auwera G., De Wachter R. Complete large subunit ribosomal RNA sequences from the heterokont algae Ochromonas danica, Nannochloropsis salina, and Tribonema aequale, and phylogenetic analysis. J. Mol. Evol. 45:1997;84-90
60. Vickerman K. Revolution among the protozoa. Coombs G.H., Vickerman K., Sleigh M.A., Warren A. Evolutionary Relationships Among Protozoa. 1998;1-24 Kluwer Academic Publishers, Dordrecht, The Netherlands
61. Vickerman K., Le Ray D., Hoef-Emden K., De Jonckheere J. The soil flagellate Proleptomonas faecicola. cell organisation and phylogeny suggest that the only described free-living trypanosomatid is not a kinetoplastid but has cercomonad affinities Protist. 153:2002;9-24
62. Wainwright P.O., Hinkle G., Sogin M.L., Stickel S.K. Monophyletic origins of the Metazoa. An evolutionary link with the fungi Science. 260:1993;340-342
63. Willerslev E., Hansen A.J., Christensen B., Steffensen J.P., Arctander P. Diversity of Holocene life forms in fossil glacier ice. Proc. Natl. Acad. Sci. USA. 96:1999;8017-8021
64. Wylezich C., Meisterfeld R., Meisterfeld S., Schlegel M. Phylogenetic analyses of small subunit ribosomal RNA coding regions reveal a monophyletic lineage of euglyphid testate amoebae (order Euglyphida). J. Eukaryot. Microbiol. 49:2002;108-118
65. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. TREE. 11:1996;367-372
66. Yang Z., Roberts D. On the use of nucleic acid sequences to infer early branching in the tree of life. Mol. Biol. Evol. 12:1995;451-458
67. Zaman V., Zaki M., Howe J., Ng M., Leipe D.D., Sogin M.L., Silberman J.D. Hyperamoeba isolated from human feces. description and phylogenetic affinity Eur. J. Protistol. 35:1999;197-207