Reconsideration of the phylogenetic positions of five peritrich genera, Vorticella, Pseudovorticella, Zoothamnopsis, Zoothamnium, and Epicarchesium (Ciliophora, Peritrichia, Sessilida), based on small subunit rRNA gene sequences

Journal of Eukaryotic Microbiology

Volumn 55, Issue 5, 2008, Pages 448-456

  Li, Lifang ^a,b   Song, Weibo ^a   Warren, Alan ^c   Shin, Mann Kyoon ^b   Chen, Zigui ^a   Ji, Daode ^a   Sun, Ping ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

^b University of Ulsan   (South Korea)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

Molecular systematics; Peritrichia; Phylogeny; Secondary structure; SSU rRNA

Indexed keywords

PROTOZOAL DNA; RIBOSOME DNA; RNA 18S;

CILIATE; DIVERGENCE; EVOLUTION; GENETIC ANALYSIS; MORPHOLOGY; PHYLOGENY; RNA; TAXONOMY;

ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; CYTOLOGY; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OLIGOHYMENOPHOREA; PHYLOGENY; RNA GENE;

ANIMALS; DNA, PROTOZOAN; DNA, RIBOSOMAL; GENES, RRNA; MOLECULAR SEQUENCE DATA; OLIGOHYMENOPHOREA; PHYLOGENY; RNA, RIBOSOMAL, 18S; SEQUENCE ANALYSIS, DNA;

ASTYLOZOON; CILIOPHORA; EPICARCHESIUM; OPISTHONECTA; PERITRICHIA (CILIATES); PSEUDOVORTICELLA; SESSILIDA; VORTICELLA; VORTICELLA MICROSTOMA; VORTICELLIDAE; ZOOTHAMNIIDAE; ZOOTHAMNIUM; ZOOTHAMNOPSIS; ZOOTHAMNOPSIS SINICA;

EID: 54249136756     PISSN: 10665234     EISSN: 15507408     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2008.00351.x     Document Type: Article

References (64)

1. Bardele, C. F. 1981. Functional and phylogenetic aspects of the ciliary membrane: a comparative freeze-fracture study. Biosystems, 14 : 403 421.
2. Chen, Z. Song, W. 2002. Phylogenetic positions of Aspidisca steini and Euplotes vannus within the order Euplotida (Hypotrichia: Ciliophora) inferred from complete small subunit ribosomal RNA gene sequences. Acta Protozool., 41 : 1 9.
3. Clamp, J. C. Williams, D. 2006. A molecular phylogenetic investigation of Zoothamnium (Ciliophora, Peritrichia, Sessilida). J. Eukaryot. Microbiol., 53 : 494 498.
4. Corliss, J. O. 2002. A salute to Antony van Leeuwenhoek of Delft, most versatile 17th century founding father of Protistology. Protist, 153 : 177 190.
5. Corliss, J. O. 1979. The Ciliated Protozoa: Characterization, Classification and Guide to the Literature. 2nd ed. Pergamon Press, New York.
6. De Peer, Y. V. De Wachter, R. 1997. Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA. J. Mol. Evol., 45 : 619 630.
7. De Rijk, P. De Wachter, R. 1997. RNAViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res., 25 : 4679 4684.
8. Dobell, C. 1932. Antony van Leeuwenhoek and His "Little Animals". Bale, Sone and Danielsson, London.
9. Ehrenberg, C. G. 1838. Die Infusionsthierchen als Volkommene Organismen. Leopold Voss, Leipzig. 612 p.
10. Elwood, H. J., Olsen, G. J. Sogin, M. L. 1985. The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol. Evol., 2 : 399 410.
11. Foissner, W. 1979. Peritriche Ciliaten (Protozoa: Ciliophora) aus alpinen Kleingewässern. Zool. Jb. Syst., 106 : 529 558.
12. Foissner, W. Schiffmann, H. 1974. Vergleichende Studien an argyrophilen Strukturen von vierzehn peritrichen Ciliaten. Protistologica, 10 : 489 508.
13. Foissner, W., Berger, H. Kohmann, F. 1992. Taxonomische und Ökologische Revision der ciliaten des saprobiensystems-Band II: Peritrichia, Heterotrichida, Odontostomatida. Bayerisches Landesamt fûr Wasserwirtschaft. 5/92, p. 1 502.
14. Foissner, W., Moon-van der Staay, S. Y., van der Staay, G. W. M., Hackstein, J. H. P., Krautgartner, W.-D. Berger, H. 2004. Reconciling classical and molecular phylogenies in the stichotrichines (Ciliophora, Spirotrichea), including new sequences from some rare species. Eur. J. Protistol., 40 : 265 281.
15. Gong, Y., Yu, Y., Polo, E. V., Zhu, F. Miao, W. 2006. Reevaluation of the phylogenetic relationship between mobilid and sessilid peritrichs (Ciliophora, Oligohymenophorea) based on small subunit rRNA genes sequences. J. Eukaryot. Microbiol., 53 : 397 403.
16. Greenwood, S. J., Sogin, M. L. Lynn, D. H. 1991. Phylogenetic relationships within the class Oligohymenophorea, phylum Ciliophora, inferred from the complete small subunit rRNA gene sequences of Colpidium campylum, Glaucoma chattoni, and Opisthonecta henneguyi. J. Mol. Evol., 33 : 163 174.
17. Jankowski, A. W. 1985. Life cycles and taxonomy of generic groups Scyphidia, Heteropolaria, Zoothamnium and Cothurnia (class Peritricha). Trudy Zool. Inst., Leningr., 12 : 74 100. (in Russian)
18. Ji, D. Song, W. 2004. Notes on a new marine peritrichous ciliate (Ciliophora: Peritrichida), Zoothamnopsis sinica n. sp. from north China, with reconsideration of Zoothamnium maximum Song, 1986. Acta Protozool., 43 : 61 71.
19. Ji, D., Song, W. AL-Rasheid, K. A. S. 2003. Description of a marine peritrichous ciliate, Pseudovorticella sinensis n. sp. (Ciliophora, Peritrichia) from China. J. Eukaryot. Microbiol., 50 : 360 365.
20. Ji, D., Song, W. Clamp, J. 2006. Pseudovorticella zhengae n. sp., P. difficilis (Kahl, 1933) Jankowski, 1976, and P. punctata (Dons, 1918) Warren, 1987, three marine peritrichous ciliates from north China. Eur. J. Protistol., 42 : 269 279.
21. Ji, D., Song, W. Warren, A. 2005. Two new marine sessile peritrichous ciliates (Protozoa, Ciliophora). Acta Zool. Sin., 30 : 702 705.
22. Ji, D., Song, W. Warren, A. 2004a. Pseudovorticella paracratera n. sp., a new marine peritrich ciliate (Ciliophora: Peritrichida) from north China. Hydrobiologia, 515 : 49 57.
23. Ji, D., Song, W. Warren, A. 2004b. Rediscovery and redescription of the marine peritrichous ciliate Epicarchesium abrae (Precht, 1935) nov. comb. (Protozoa, Ciliophora, Peritrichia). Eur. J. Protistol., 40 : 219 224.
24. Ji, D., Song, W. Warren, A. 2006. Redescriptions of three marine peritrichous ciliates, Zoothamnium alternans Claparède et Lachmann, 1859, Z. sinense Song, 1991 and Z. commune Kahl, 1933 (Ciliophora: Peritrichia), from north China. Acta Protozool., 45 : 27 39.
25. Ji, D., Song, W., AL-Rasheid, K. A. S. Li, L. 2005b. Taxonomic characterization of two marine peritrichous ciliates, Pseudovorticella clampi n. sp. and Zoothamnium pararbuscula n. sp. (Ciliophora: Peritrichia), from north China. J. Eukaryot. Microbiol., 52 : 159 169.
26. Ji, D., Song, W., AL-Rasheid, K. A. S. Sun, P. 2005a. Description of Zoothamnium foissneri n. sp. and redescriptions of Z. duplicatum Kahl, 1933 and Z. mucedo Entz, 1884, three species of marine, peritrichous ciliates. Eur. J. Protistol., 41 : 45 56.
27. Kahl, A. 1933. Ciliata librae et ectocommensalia. In : Grimpe, G. Wagler, E. (ed.), Die Tierwelt der Nord-und Ostsee, Lief. 23 (Teil, II, c3), Leipzig. p. 147 183.
28. Kumar, S., Tamura, K. Nei, M. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinf., 5 : 150 163.
29. Leitner, A. R. Foissner, W. 1997. Taxonomic characterization of Epicarchesium granulatum (Kellicott, 1887) Jankowski, 1985 and Pseudovorticella elongata (Fromentel, 1876) nov. comb., two peritrichs (Protozoa, Ciliophora) from activated sludge. Eur. J. Protistol., 33 : 13 29.
30. Li, L. Song, W. 2006. Phylogenetic position of the marine ciliate, Certesia quadrinucleata (Ciliophora; Hypotrichia; Hypotrichida) inferred from the complete small subunit ribosomal RNA gene sequence. Eur. J. Protistol., 42 : 55 61.
31. Li, L., Song, W., Warren, A., Wang, Y., Ma, H., Hu, X. Chen, Z. 2006. Phylogenetic position of the marine ciliate, Cardiostomatella vermiforme (Kahl, 1928) Corliss, 1960 inferred from the complete SS rRNA gene sequence, with establishment of a new order Loxocephalida n. ord. (Ciliophora, Oligohymenophorea). Eur. J. Protistol., 42 : 107 114.
32. Lynn, D. H. 1979. Changes in the classification of several major taxa of Ciliophora on the basis of a numerical phenetic analysis. J. Protozool., 26 : 359 366.
33. Lynn, D. H. 1981. The organization and evolution of microtubular organelles in ciliated protozoa. Biol. Rev., 56 : 243 292.
34. Lynn, D. H. 2003. Morphology or molecules: how we identify the major lineages of ciliates (Phylum Ciliophora)? Eur. J. Protistol., 39 : 356 364.
35. Lynn, D. H. Small, E. B. 2002. Phylum Ciliophora Doflein, 1901. In : Lee, J. J., Bradbury, P. C. Leedale, G. F. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Lawrence, Kansas. p. 371 656.
36. Lynn, D. H. Sogin, M. L. 1988. Assessment of phylogenetic relationships among ciliated protists using partial ribosomal RNA sequences derived from reverse transcripts. Biosystems, 21 : 249 254.
37. 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.
38. Miao, W., Yu, Y. Shen, Y. 2001. Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) with emphasis on the genus Epistylis, inferred from small subunit rRNA gene sequences. J. Eukaryot. Microbiol., 48 : 583 587.
39. Miao, W., Fen, W., Yu, Y., Zhang, X. Shen, Y. 2004. Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences. J. Eukaryot. Microbiol., 51 : 180 186.
40. Neefs, J. M., Van de Peer, Y., De Rijk, P., Chapelle, S. De Wachter, R. 1993. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res., 21 : 3025 3049.
41. Nixon, K. C. 1999. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics, 15 : 407 414.
42. Noland, L. E. Finley, H. E. 1931. Studies on the taxonomy of the genus Vorticella. Trans. Am. Microsc. Soc., 50 : 81 123.
43. Nylander, J. A. A. 2004. MrModeltest v. Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
44. Pätsch, B. 1974. Die Aufwuchsciliaten des Naturlehrparks Haus Wildenrath. Diss. Bonn University, Bonn, Germany, 78 p.
45. Posada, D. Crandall, K. A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics, 14 : 817 818.
46. Ragan, M. A., Cawthorn, R. J., Despres, B., Murphy, C. A., Singh, R. K., Loughlin, M. B. Bayer, R. C. 1996. The lobster parasite Anophryoides haemophila (Scuticociliatida: Orchitophryidae): nuclear 18S rDNA sequence, phylogeny and detection using oligonucleotide primers. J. Eukaryot. Microbiol., 43 : 341 346.
47. Ronquist, F. Huelsenbeck, J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19 : 1572 1574.
48. Sikes, D. S. Lewis, P. O. 2001. Beta Software, Version 1. PAUPRat: PAUP Implementation of the Parsimony Ratchet. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs.
49. Sogin, M. Elwood, H. J. 1986. Primary structure of the Paramecium tetraurelia small-subunit rRNA coding region: phylogenetic relationships within the Ciliophora. J. Mol. Evol., 23 : 53 60.
50. Sommer, G. 1951. Die peritrichen Ciliaten des groben Plöner Sees. Arch Hydrobiol., 44 : 349 440.
51. Song, W. 1997. A new genus and two new species of marine peritrichous ciliates (Protozoa, Ciliophora, Peritrichida) from Qingdao, China. Ophelia, 47 : 203 214.
52. Song, W. Warren, A. 2000. A redescription of Pseudovorticella patellina (O. F. Muller, 1776) nov. comb. a peritrichous ciliate (Protozoa: Ciliophora: Peritrichida) isolated from mariculture biotopes in north China. Acta Protozool., 39 : 43 50.
53. Song, W., AL-Rasheid, K. A. S. Hu, X. 2002. Notes on the poorly-known marine peritrichous ciliate, Zoothamnium plumula Kahl, 1933 (Protozoa: Ciliophora), an ectocommensal organism from cultured scallops in Qingdao, China. Acta Protozool., 41 : 163 168.
54. Stoeck, T., Przybos, E. Schmidt, H. J. 1998. A combination of genetics with inter-and intra-strain crosses and RAPD-fingerprints reveals different population structures within the Paramecium aurelia species complex. Eur. J. Protistol., 34 : 348 355.
55. Strüder-Kypke, M. C., Wright, A.-G., Fokin, S. I. Lynn, D. H. 2000. Phylogenetic relationships of the subclass Peniculia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences. J. Eukaryot. Microbiol., 47 : 419 429.
56. Sun, P., Song, W., Clamp, J. C. AL-Rasheid, K. 2006. Taxonomic characterization of Vorticella fusca Precht, 1935 and Vorticella parapulchella n. sp., two marine peritrichs (Ciliophora, Oligohymenophorea) from China. J. Eukaryot. Microbiol., 53 : 348 357.
57. *and Other Methods). Version 4. Sinauer Associates, Sunderland, MA.
58. Thompson, J. D., Higgins, D. G. Gibson, T. J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22 : 4673 4680.
59. Utz, L. R. P. Eizirik, E. 2007. Molecular phylogenetics of subclass Peritrichia (Ciliophora Oligohymenophorea) based on expanded analyses of 18S rRNA sequences. J. Eukaryot. Microbiol., 54 : 303 305.
60. Van de Peer, Y., Baleauf, S. L., Doodlittle, W. F. Meyer, A. 2000. An updated and comprehensive rRNA phylogeny of (Crown) eukaryotes based on rate-calibrated evolutionary distances. J. Mol. Evol., 51 : 565 576.
61. Vos, R. A. 2003. Accelerated likelihood surface exploration: the likelihood ratchet. Syst. Biol., 52 : 368 373.
62. Warren, A. 1986. A revision of the genus Vorticella (Ciliophora: Peritrichida). Bull. Br. Mus. Nat. Hist. (Zool.), 50 : 1 57.
63. Warren, A. 1987. A revision of the genus Pseudovorticella Foissner & Schiffmann, 1974 (Ciliophora: Peritrichida). Bull. Br. Mus. Nat. Hist. (Zool.), 52 : 1 12.
64. Williams, D. Clamp, J. C. 2007. A molecular phylogenetic investigation of Opisthonecta and related genera. (Ciliophora, Peritrichia, Sessilida). J. Eukaryot. Microbiol., 54 : 317 323.