Phylogenetic positions and taxonomic assignments of the systematically controversial genera, Spirotrachelostyla, Uroleptopsis and Tunicothrix (Protozoa, Ciliophora, Stichotrichia) based on small subunit rRNA gene sequences

Systematics and Biodiversity

Volumn 8, Issue 3, 2010, Pages 409-416

  Huang, Jie ^a,b   Yi, Zhenzhen ^a   Al Farraj, Aleh A ^c   Song, Weibo ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

^b SOUTH CHINA NORMAL UNIVERSITY   (China)

^c KING SAUD UNIVERSITY   (Saudi Arabia)

Author keywords

Ciliates; Parabirojimidae; Phylogeny; Pseudokeronopsidae; SSU rRNA gene; Trachelostylidae

Indexed keywords

CILIOPHORA; PROTOZOA; PSEUDOKERONOPSIDAE; PSEUDOKERONOPSIS; STICHOTRICHIA; TRACHELOSTYLA; TRACHELOSTYLIDAE; UROLEPTOPSIS; UROLEPTOPSIS CITRINA;

EID: 78650318598     PISSN: 14772000     EISSN: 14780933     Source Type: Journal    
DOI: 10.1080/14772000.2010.508502     Document Type: Article

References (50)

1. BERGER, H. 1999. Monograph of the Oxytrichidae (Ciliophora, Hypotrichia). Monographiae Biologicae 78, i-xii, 1-1080.
2. BERGER, H. 2004. Uroleptopsis Kahl, 1932 (Ciliophora, Hypotricha): morphology and cell division of type species, redefinition, and phylogenetic relationships. Acta Protozoologica 43, 99-121.
3. BERGER, H. 2006. Monograph of the Urostyloidea (Ciliophora, Hypotricha). Monographie Biologicae 85, 1-1304.
4. BERGER, H. 2008. Monograph of the Amphisiellidae and Trachelostylidae (Ciliophora, Hypotricha). Monographiae Biologicae 88, 1-737.
5. BERGER, H. & FOISSNER, W. 1997. Cladistic relationships and generic characterization of oxytrichid hypotrichs (Protozoa, Ciliophora). Archiv fÜr Protistenkunde 148, 125-155
6. BERNHARD, D., STECHMANN, A., FOISSNER, W., AMMERMANN, D., HEHN, M. & SCHLEGEL, M. 2001. Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences. Molecular Phylogenetics and Evolution 21, 86-92
7. BORROR, A.C. & WICKLOW, B.J. 1983. The suborder Urostylina Jankowski (Ciliophora, Hypotrichida): morphology, systematics and identification of species. Acta Protozoologica 22, 97-126.
8. CALENDINI, F. & MARTIN, J.F. 2005. PaupUP v1.0.3.1. A Free Graphical Frontend for PAUP*Dos Software. http://www. agro-montpellier.fr/sppe/ Recherche/JFM/PaupUp/main.htm (accessed 12 July 2010).
9. CHEN, X., GAO, S., SONG, W., AL-RASHEID, K.A.S., WARREN, A., GONG J. & LIN X. 2010. Parabirojimia multinucleata spec. nov. and Anteholosticha scutellum (Cohn, 1866) Berger, 2003, two marine ciliates (Ciliophora, Hypotrichida) from tropical waters in southern China, with note on their SSU rRNA gene sequences. International Journal of Systematic and Evolutionary Microbiology 60, 234-243.
10. CORLISS, J.O. 1977. Annotated assignment of families and genera to the orders and classes currently comprising the Corlissian scheme of higher classification for the phylum Ciliophora. Transactions of the American Microscopical Society 96, 104-140.
11. CORLISS, J.O. 1979. The Ciliated Protozoa. Characterization, Classification and Guide to the Literature. 2nd edition. Pergamon Press, New York. EDDY, S.R. 2001. HMMER: Profile hidden Markov models for biological sequence analysis. http://hmmer.wustl.edu (accessed 7 July 2010).
12. ELWOOD,H.J.,OLSEN, G.J.&SOGIN,M.L. 1985. The small-subunit ribosomalRNAgene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Molecular Biology and Evolution 2, 399-410.
13. 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. European Journal of Protistology 40, 265-281
14. GAO, S.,GONG, J.,LYNN, D.,LIN, X. & SONG,W. 2009. An updated phylogeny of oligotrich and choreotrich ciliates (Protozoa, Ciliophora, Spirotrichea) with representative taxa collected from Chinese coastal waters. Systematics and Biodiversity 7, 235-242.
15. GONG, J., SONG, W., LI, L., SHAO, C. & CHEN, Z. 2006. A new investigation of the marine ciliate, Trachelostyla pediculiformis (Cohn, 1866) Borror, 1972 (Ciliophora, Hypotrichida), with establishment of a new genus, Spirotrachelostyla nov. gen. European Journal of Protistology 42, 63-73
16. GONG, J., STOECK, T., YI, Z.,MIAO, M., ZHANG, Q., ROBERTS, D., WARREN, A. & SONG, W. 2009. Small subunit rRNA phylogenies show that the class Nassophorea is not monophyletic (Phylum Ciliophora). Journal of Eukaryotic Microbiology 56, 339-347
17. GUINDON, S. & GASCUEL, O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52, 696-704.
18. HALL, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41, 95-98
19. HEWITT, E.A.,MÜLLER, K.M., CANNONE, J.,HOGAN, D.J., GUTELL, R.&PRESCOTT,D.M. 2003. Phylogenetic relationships among 28 spirotrichous ciliates documented by rDNA. Molecular Phylogenetics and Evolution. 29, 258-267.
20. HU, X.,HU, X.,AL-RASHEID, K.A.S. & SONG,W. 2009. Reconsideration on the phylogenetic position of Epiclintes (ciliophora, stichotrichia) based on SS rRNA gene sequence and morphogenetic data. Acta Protozoologica, 48, 203-211
21. HU, X. & SONG, W. 2002. Studies on the ectocommensal ciliate, Trachelostyla tani nov. spec. (Protozoa: Ciliophora: Hypotrichida) from the mantle cavity of the scallop Chlamys farreri. Hydrobiologia 481, 173-179
22. HU, X., SONG, W. & WARREN, A. 2002. Observations on the morphology and morphogenesis of a newmarine hypotrich ciliate, Parabirojimia similes nov. gen., nov. spec. (Ciliophora, Hypotrichida) from China. European Journal of Protistology 38, 351-364
23. JIANG, J. & SONG, W. 2010. Two new Diophrys-like genera and their type species, Apodiophrys ovalis n. g., n. sp. and Heterodiophrys zhui n. g., n. sp. (Ciliophora: Euplotida), with notes on their molecular phylogeny. Journal of Eukaryotic Microbiology 57, 354-361
24. KAHL, A. 1932. Urtiere oder Protozoa I: Wimpertiere oder Ciliata (Infusoria) 3. Spirotricha. Tierwelt Deutschland 25, 399-650
25. LI, L., ZHANG, Q.,HU, X.,WARREN, A.,AL-RASHEID, K.A.S., ALKHEDHEIRY, A.A., JIANG, J. & SONG, W. 2009. A redescription of the marine hypotrichous ciliate, Nothoholosticha fasciola (Kahl, 1932) nov. gen., nov. comb. (Ciliophora: Urostylida) with brief notes on its cellular reorganization and SS rRNA gene sequence. European Journal of Protistology 45, 237-248.
26. LIN, X. & SONG, W. 2004. A new marine ciliate, Erniella wilberti sp. n. (Ciliophora: Hypotrichida), from shrimp culturing waters in north China. Acta Protozoologica 43, 55-60
27. LIU, W., SHAO, C., GONG, J., LI, J., LIN, X. & SONG, W. 2010. Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea. Zoological Journal of the Linnean Society 158, 697-710
28. LYNN, D.H. 2008. The Ciliated Protozoa. Characterization, Classification, and Guide to the Literature. 3rd edition. Springer Verlag, Dordrecht.
29. MEDLIN, L., ELWOOD, H.J., STICKEL, S. & SOGIN, M.L. 1988. The characterization of enzymatically amplified eukaryotic 16Slike rRNA-coding regions. Gene 71, 491-499.
30. MIAO, M., WANG, Y., LI, L., AL-RASHEID, K.A.S. & SONG, W. 2009. Molecular phylogeny of the scuticcociliate, Philaster (Protozoa, Ciliophora), with a description of a new species, P. apodigitiformis sp. nov. Systematics and Biodiversity 7, 381-388.
31. NYLANDER, J.A. 2004. MrModeltest v2. Program. Distributed by the author. Evolutionary Biology Center, Uppsala University
32. PAIVA, T.S., BORGES, B.N., HARADA, M.L. & SILVA-NETO, I.D. 2009. Comparative phylogenetic study of Stichotrichia (Alveolata: Ciliophora: Spirotrichea) based on 18S-rDNA sequences. Genetics and Molecular Research 8, 223-246
33. POSADA, D.&CRANDALL, K.A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
34. RONQUIST, F. & HUELSENBECK, J.P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574
35. SCHLEGEL, M.,ELWOOD, H.J. & SOGIN,M.L. 1991. Molecular evolution in hypotrichous ciliates: sequence of the small subunit ribosomal RNA genes from Onychodromus quadricornutus and Oxytricha granulifera (Oxytrichidae, Hypotrichida, Ciliophora). Journal of Molecular Evolution 32, 64-69.
36. SCHMIDT, S., BERNHARD, D., SCHLEGEL, M. & FOISSNER, W. 2007. Phylogeny of the Stichotrichia (Ciliophora; Spirotrichea) reconstructedwith nuclear small subunit rRNAgene sequences: discrepancies and accordances with morphological data. Journal of Eukaryotic Microbiology 54, 201-209
37. SHIMODAIRA, H. 2002. An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51, 492-508. (Pubitemid 35180700)
38. SHIMODAIRA, H. & HASEGAWA, M. 2001. Consel: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247.
39. SMALL, E.B. & LYNN, D.H. 1985. Phylum Ciliophora Doflein, 1901. In: LEE, J.J., HUTNER, S.H. & BOVEE, E.C. Eds., An Illustrated Guide to the Protozoa. Society of Protozoologists, Lawrence, KS, pp. 393-575
40. SWOFFORD, D.L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and other Methods). Version 4. Sinauer Associates, Sunderland, MA.
41. TAMURA, K., DUDLEY, J., NEI, M. & KUMAR, S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24, 1596-1599.
42. THOMPSON, J.D., HIGGINS, D.G. & GILBSON, 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 Research 22, 4673-4680
43. TUFFRAU, M. 1979. Une nouvelle famille d'hypotriches, Kahliellidae n. fam., et ses consequences dans la repartition des Stichotrichina. Transactions of the American Microscopical Society 98, 521-528.
44. TUFFRAU, M. 1987. Proposition d'une classification nouvelle de l'ordre Hypotrichida (Protozoa, Ciliophora), fondée sur quelques données récentes. Annales des sciences naturelles. Zoologie et Biologie Animale 8, 111-117
45. TUFFRAU, M. & FLEURY, A. 1994. Classe des Hypotrichea Stein, 1859. Traite de Zoologie 2, 83-151
46. WILBERT, N. 1975. Eine verbesserte Technik der Protargolimpr ägnation fÜr Ciliaten. Mikrokosmos 64, 171-179.
47. XU, K., LEI, Y. & CHOI, J. 2006. Tunicothrix rostrata n. g., n. sp., a new urostylid ciliate (Ciliophora, Stichotrichia) from the Yellow Sea. Journal of Eukaryotic Microbiology 53, 485-493
48. YI, Z., SONG, W., SHAO, C., WARREN, A., AL-RASHEID, K.A.S., ROBERTS, D., MIAO, M., AL-QURAISHY, S.A. & CHEN, Z. 2008a. Phylogeny of some systematically uncertain urostyloids-Apokeronopsis, Metaurostylopsis, Thigmokeronopsis (Ciliophora, Stichotrichia) estimated with small subunit rRNA gene sequence information: Discrepancies and agreements with morphological data. European Journal of Protistology 44, 254-262.
49. YI, Z., SONG, W., STOECK, T., AL-RASHEID, K.A.S., ALKHEDHAIRY, A., GONG, J., MA, H. & CHEN, Z. 2009. Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on SSrRNA and alpha-tubulin gene sequence information. Zoological Journal of the Linnean Society 157, 227-236
50. YI, Z., SONG, W.,WARREN, A., ROBERTS, D.,AL-RASHEID, K.A.S., CHEN, Z., AL-FARRAJC, S.A. & HU, X. 2008b. A molecular phylogenetic investigation of Pseudoamphisiella and Parabirojimia (Protozoa, Ciliophora, Spirotrichea), two genera with ambiguous systematic positions. European Journal of Protistology 44, 45-53.