Insights into the phylogeny of sporadotrichid ciliates (Protozoa, Ciliophora: Hypotricha) based on genealogical analyses of multiple molecular markers

Chinese Journal of Oceanology and Limnology

Volumn 29, Issue 1, 2011, Pages 96-102

  Hu, Xiaoyan ^a   Hu, Xiaozhong ^a,c   Al Rasheid, Khaled A S ^b   Al Farraj, Saleh A ^b   Song, Weibo ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

^b KING SAUD UNIVERSITY   (Saudi Arabia)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

actin I; alpha tubulin; amino acid sequences; phylogeny; sporadotrichid ciliates; SSrRNA

Indexed keywords

CILIOPHORA; HALTERIA GRANDINELLA; HOLOSTICHA; HYPOTRICHIA; OLIGOTRICHIA; OXYTRICHA; OXYTRICHIDAE; PROTOZOA; SPORADOTRICHIDA; UROLEPTUS; UROSTYLA;

EID: 79955562584     PISSN: 02544059     EISSN: 19935005     Source Type: Journal    
DOI: 10.1007/s00343-011-9008-y     Document Type: Article

References (39)

1. Agatha S, Strüder-Kypke M C. 2007. Phylogeny of the order Choreotrichida (Ciliophora, Spirotricha, Oligotrichea) as inferred from morphology, ultrastructure, ontogenesis, and SSrRNA gene sequences. Eur. J. Protistol., 43: 37-63.
2. Berger H. 1999. Monograph of the Oxytrichidae (Ciliophora, Hypotrichia). Monograph. Biol., 78: 1-1 080.
3. Berger H. 2006. Monograph of the Urostyloidea (Ciliophora, Hypotricha). Monograph. Biol., 85: 1-1 304.
4. Berger H. 2008. Monograph of the Amphisiellidae and Trachelostylidae (Ciliophora, Hypotricha). Monograph. Biol., 88: 1-737.
5. Berger H, Foissner W. 1997. Cladistic relationships and generic characterization of oxytrichid hypotrichs (Protozoa, Ciliophora). Arch. Protistenkd, 148: 125-155.
6. Bernhard D, Stechmann A, Foissner W. 2001. Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences. Mol. Phylogen. Evol., 21: 86-92.
7. Borror A C. 1979. Redefinition of the Urostylidae (Ciliophora, Hypotrichida) on the basis of morphogenetic characters. J. Protozool., 26: 544-550.
8. Chen X, Gao S, Song W, Al-Rasheid K A S, Warren A, Gong J, Lin X. 2010a. 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. Inter. J. Syst. Evol. Microbiol., 60: 234-243.
9. Chen X, Li Z, Hu X, Kutsoka Y. 2010b. Morphology, morphogenesis and gene sequence of a freshwater ciliate, Pseudourostyla cristata (Ciliophora, Urostylida) from the ancient Lake Biwa, Japan. Eur. J. Protistol., 46: 43-60.
10. Croft K E, Dalby A B, Hogan D J, Orr K E, Hewitt E A, Africa R J, DuBois M L, Prescott D M. 2003. Macronuclear molecules encoding actins in spirotrichs. J. Mol. Evol., 56: 341-350.
11. Dimmic M W, Rest J S, Mindell D P, Goldstein D. 2002. RArtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J. Mol. Evol., 55: 65-73.
12. Foissner W, Moon-van der Staay S Y, van der Staay G W, 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.
13. Foissner W, Müller H, Agatha S. 2007. A comparative fine structural and phylogenetic analysis of resting cysts in oligotrich and hypotrich Spirotrichea (Ciliophora). Eur. J. Protistol., 43: 295-314.
14. Foissner W, Stoeck T. 2006. Rigidothrix goiseri nov. gen., nov. spec. (Rigidothrichidae nov. fam.), a new "flagship" ciliate from the Niger floodplain breaks the flexibility-dogma in the classification of stichotrichine spirotrichs (Ciliophora, Spirotrichea). Eur. J. Protistol., 42: 249-267.
15. Gao F, Yi Z, Gong J, Al-Rasheid K A S, Song W. 2010. Molecular phylogeny and species separation of five morphologically similar Holosticha-complex ciliates (Protozoa, Ciliophora) using ARDRA riboprinting and multigene sequence data. Chin. J. Oceanol. Limnol., 28: 542-548.
16. Hu X, Fan X, Lin X, Gong J, Song W. 2009a. The morphology and morphogenesis of a marine ciliate, Epiclintes auricularis rarisetus nov. sspec. (Ciliophora, Epiclintidae), from the Yellow Sea. Eur. J. Protistol., 45: 281-291.
17. Hu X, Hu X, Al-Rasheid K A S, Song W. 2009b. Reconsideration on the phylogenetic position of Epiclintes (ciliophora, stichotrichia) based on SS rRNA gene sequence and morphogenetic data. Acta Protozool., 48: 203-211.
18. Huang J, Yi Z, Al-Farraj S A, Song W. 2010. Phylogenetic positions and taxonomic assignments of the systematically controversial genera, Spirotrachelostyla, Uroleptopsis and Tunicothrix (Protozoa, Ciliophora, Stichotrichia) based on small subunit rRNA gene sequences. Syst. Biodiv., 8: 409-416.
19. Israel R L, Pond S L K, Muse S V, Katz L A. 2002. Evolution of duplicated alpha-tubulin genes in ciliates. Evolution, 56: 1 110-1 022.
20. Li L, Song W, Al-Rasheid K A S, Warren A, Li Z, Xu Y, Shao C. 2010. Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa, Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence. Zool. J. Linn. Soc., 158: 231-243.
21. Li L, Song W, Shin M K, Warren A, Al-Rasheid K A S, Al-Khedhairy A A, Al-Arifi S. 2009a. Reconsideration of the phylogenetic positions of three stichotrichous Genera Holosticha, Anteholosticha and Pseudokeronopsis (Spirotrichea: Ciliophora) inferred from complete SSU rRNA gene sequences. Progr. Nat. Sci., 19: 769-773.
22. Li L, Zhang Q, Hu X, Warren A, Al-Rasheid K A S Al-Khedheiry A A, Jiang J, Song W. 2009b. 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. Eur. J. Protistol., 45: 237-248.
23. 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 an overview of the convergent evolution of midventral complex within the Spirotrichea. Zool. J. Linn. Soc., 158: 697-710.
24. Lynn D H. 2008. The Ciliated Protozoa: Characterization, Classification and Guide to the Literature. Third edn. Springer. 605p.
25. Opperdoes F R. 2003. Phylogenetic analysis using protein sequences. In: Salemi M, Vandamme A M eds. The Phylogenetic Handbook: a Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, New York. p. 207-233.
26. 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. Genet. Mol. Res., 8: 223-246.
27. Schmidt S, Bernhard D, Schlegel M, Foissner W. 2007. Phylogeny of the Stichotrichia (Ciliophora; Spirotrichea) reconstructed with nuclear small subunit rRNA gene sequences: discrepancies and accordances with morphological data. J. Eukaryot. Microbiol., 54: 201-209.
28. Shao C, Song W, Warren A, Al-Rasheid K A S. 2009. Morphogenesis of Kiitricha marina Nozawa, 1941 (Ciliophora, Spirotrichea), a possible model for the ancestor of hypotrichs s. l. Eur. J. Protistol., 45: 292-304.
29. Shao C, Song W, Yi Z, Gong J, Li J, Lin X. 2007. Morphogenesis of the marine spirotrichous ciliate, Trachelostyla pediculiformis (Cohn, 1866) Borror, 1972 (Ciliophora, Stichotrichia), with consideration of its phylogenetic position. Eur. J. Protistol., 43: 255-264.
30. Shao C, Zhang Q, Al-Rasheid K A S, Warren A, Song W. 2010. Ontogenesis and molecular phylogeny of the marine ciliate Diophryopsis hystrix: implications for the systematics of the Diophrys-complex (Ciliophora, Spirotrichea, Euplotida). J. Eukaryot. Microbiol., 57: 33-39.
31. Shen Z, Shao C, Gao S, Lin X, Li J, Hu X, Song W. 2009. Description of the rare marine ciliate, Uronychia multicirrus Song, 1997 (Ciliophora; Euplotida) based on morphology, morphogenesis and SS rRNA gene sequence. J. Eukaryot. Microbiol., 56: 296-304.
32. Snoeyenbos-West O L O, Salcedo T, McManus G B, Katz L A. 2002. Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci. Int. J. Syst. Evol. Microbiol., 52: 1 901-1 913.
33. Song W, Shao C, Yi Z, Li L, Warren A, Al-Rasheid K A S, Yang J. 2009. The morphology, morphogenesis and SSrRNA gene sequence of a new marine ciliate, Diophrys apoligothrix spec. nov. (Ciliophora, Euplotida). Eur. J. Protistol., 45: 38-50.
34. Strüder-Kypke M C, Lynn D H. 2003. Sequence analyses of the small subunit rRNA gene confirm the paraphyly of oligotrich ciliates sensu lato and support the monophyly of the subclasses Oligotrichia and Choreotrichia (Ciliophora, Spirotrichea). J. Zool., 260: 87-97.
35. Tourancheau A B, Villalobo E, Tsao N, Torres A, Pearlman R E. 1998. Protein coding gene trees in ciliates: Comparison with rRNA-Based phylogenies. Mo1. Phy. Evo1., 10: 299-309.
36. Yi Z, Clamp J, Al-Rasheid K A S, Al-Khedhairy A A, Chen Z, Song W. 2009a. Evolutionary relationship and species separation of four morphologically similar stichotrichous ciliates (Protozoa, Ciliophora) inferred from PCR-RFLP patterns, ITS2 region sequence, and ITS2 secondary structures. Progr. Nat. Sci., 19: 581-586.
37. Yi Z, Lin X, Warren A, Al-Rasheid K A S, Song W. 2010. Molecular phylogeny of Nothoholosticha (Protozoa, Ciliophora, Urostylida) and systematic relationships of the Holosticha-complex. Syst. Biodivers., 81: 149-155.
38. Yi Z, Song W, Clamp J C, Chen Z, Gao S, Zhang Q. 2009b. Reconsideration of systematic relationships within the order Euplotida (Protista, Ciliophora) using new sequences of the gene coding for small-subunit rRNA and testing the use of combined data sets to construct phylogenies of the Diophrys-complex. Mol. Phy. Evol., 50: 599-607.
39. Yi Z, Song W, Stoeck T, Al-Rasheid K A S, Al-Khedhairy A. A, Gong J, Ma H, and Chen Z. 2009c. Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylidfamily, based on small subunit rRNA and alpha-tubulin gene sequence information. Zool. J. Linn. Soc., 157: 227-236.