Further insights into the phylogeny of two ciliate classes Nassophorea and Prostomatea (Protista, Ciliophora)

Molecular Phylogenetics and Evolution

Volumn 70, Issue 1, 2014, Pages 162-170

  Zhang, Qianqian ^a,b   Yi, Zhenzhen ^c   Fan, Xinpeng ^d   Warren, Alan ^e   Gong, Jun ^a,c   Song, Weibo ^b  

^a YANTAI INSTITUTE OF COASTAL ZONE RESEARCH   (China)

^b OCEAN UNIVERSITY OF CHINA   (China)

^c SOUTH CHINA NORMAL UNIVERSITY   (China)

^d EAST CHINA NORMAL UNIVERSITY   (China)

^e DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

18S rRNA; 28S rRNA; Ciliophora; Nassophorea; Phylogeny; Prostomatea

Indexed keywords

CILIOPHORA; CRYPTOCARYON IRRITANS; FURGASONIA; HOLOPHRYIDAE; INTRAMACRONUCLEATA; MICROTHORACIDAE; NASSOPHOREA; NASSULIDA; OLIGOHYMENOPHOREA; PARAFURGASONIA; PARANASSULA; PENICULIA; PENICULIDA; PHYLLOPHARYNGEA; PLACUS; PRORODONTIDA; PROSTOMATEA; PROTISTA; UROTRICHIDAE;

RIBOSOME RNA; RNA 18S; RNA 28S;

ARTICLE; CHEMISTRY; CILIATE; CONFORMATION; DNA SEQUENCE; GENETICS; NASSOPHOREA; NUCLEOTIDE SEQUENCE; OLIGOHYMENOPHOREA; PHYLOGENY; PROSTOMATEA; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

18S RRNA; 28S RRNA; CILIOPHORA; NASSOPHOREA; PHYLOGENY; PROSTOMATEA;

BASE SEQUENCE; LIKELIHOOD FUNCTIONS; NUCLEIC ACID CONFORMATION; OLIGOHYMENOPHOREA; PHYLOGENY; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84885514564     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.09.015     Document Type: Article

References (59)

1. Adl S.M., Simpson A.G.B., Lane C.E., Lukes J., Bass D., Bowser S.S., Brown M.W., Burki F., Dunthorn M., Hampl V., Heiss A., Hoppenrath M., Lara E., Gall L.L., Lynn D.H., McManus H., Mitchell E.A.D., Mozley-Stanridge S.E., Parfrey L.W., Pawlowski J., Rueckert S., Shadwick L., Schoch C.L., Smirnov A., Spiegel F.W. The revised classification of eukaryotes. J. Eukaryot. Microbiol. 2012, 59:429-493.
2. Bardele C.F. Ultrastructure, morphogenetics, and a discussion of the phylogeny of the prostome ciliate Balanion planctonicum. Eur. J. Protistol. 1999, 35:17-33.
3. Baroin-Tourancheau A., Delgado P., Perasso R., Adoutte A. A broad molecular phylogeny of ciliates: identification of major evolutionary trends and radiations within the phylum. Proc. Natl. Acad. Sci. USA 1992, 89:9764-9768.
4. Borror A.C. Tidal marsh ciliates (Protozoa): morphology, ecology, systematics. Acta Protozool. 1972, 31:29-73.
5. Breiner H., Foissner W., Stoeck T. The search finds and end: colpodidiids belong to the class Nassophorea (Ciliophora). J. Eukaryot. Microbiol. 2008, 55:100-102.
6. Carey P.G. Marine Interstitial Ciliates. An Illustrated Key 1992, Chapman and Hall, London.
7. Corliss J.O. The Ciliated Protozoa: Characterization, Classification and Guide to the Literature 1979, Pergamon Press, Oxford, New York.
8. Darriba D., Taboada G.L., Doallo R., Posada D. JModelTest 2: more models, new heuristics and parallel computing. Nat. Meth. 2012, 9:772.
9. de Puytorac, P., 1994. Phylum Ciliophora Doflein, 1901. In: de Puytorac, P. (Ed.), Traité de Zoologie, Tome II, Infusoires Ciliés, Fasc. 2, Systématique. Masson, Paris, pp. 1-15.
10. De Rijk P., De Wachter R. RnaViz, a program for the visualisation of RNA secondary structure. Nucl. Acids Res. 1997, 25:4679-4684.
11. Dragesco J., Iftode F., Fryd-Versavel G. Contribution à la connaissance de quelques ciliés holotriches rhabdophores; I. Prostomiens. Protistologica 1974, 10:59-75.
12. Dunthorn M., Foissner W., Katz L.A. Molecular phylogenetic analysis of class Colpodea (phylum Ciliophora) using broad taxon sampling. Mol. Phylogenet. Evol. 2008, 46:316-327.
13. Eisler K. Electron microscopical observations on the ciliate Furgasonia blochmanni Fauré-Fremiet, 1967: Part I: An update on morphology. Eur. J. Protistol. 1988, 24:75-93.
14. Fleury A., Delgado P., Iftode F., Adoutte A. Molecular phylogeny of ciliates: what does it tell us about the evolution of the cytoskeleton and of developmental strategies?. Dev. Genet. 1992, 13:247-254.
15. Foissner W. Infraciliature and systematic position of the marine interstitial ciliates (Protozoa, Ciliophora) Lopezoterenia torpens (Kahl, 1931) nov. gen., nov. comb., Discotricha papillifera Tuffrau, 1954, and Paraspathidium fuscum (Kahl, 1928) Fjeld, 1955. Rev. Soc. Mex. Hist Nat. 1997, 47:41-63.
16. Foissner W. A compilation of soil and moss ciliates (Protozoa, Ciliophora) from Germany, with new records and descriptions of new and insufficiently known species. Eur. J. Protistol. 2000, 36:253-283.
17. Foissner W., Berger H., Kohmann F. Taxonomische und ökologische Revision der Ciliaten des Saprobiensystems - Band III: Hymenostomata, Prostomatida, Nassulida. Informationsberichte Bayer. Landesamt. Wasserwirtschaft 1994, 1(94):1-548.
18. Foissner W., Kusuoka Y., Shimano S. Morphology and gene sequence of Levicoleps biwae n. gen., n. sp. (Ciliophora, Prostomatida), a proposed endemic from the ancient Lake Biwa, Japan. J. Eukaryot. Microbiol. 2008, 55:185-200.
19. Gao S., Huang J., Li J., Song W. Molecular phylogeny of the cyrtophorid ciliates (Protozoa, Ciliophora, Phyllopharyngea). PLoS ONE 2012, 7:e33198.
20. Gao F., Katz L.A., Song W. Multigene-based analyses on evolutionary phylogeny of two controversial ciliate orders: Pleuronematida and Loxocephalida (Protista, Ciliophora, Oligohymenophorea). Mol. Phylogenet. Evol. 2013, 68:55-63.
21. Gong J., Kim S., Kim S., Min G., Roberts D., Warren A., Choi J. Taxonomic redescriptions of two ciliates, Protogastrostyla pulchra n. g., n. comb. and Hemigastrostyla enigmatica (Ciliophora: Spirotrichea: Stichotrichia), with phylogenetic analyses based on 18S and 28S rRNA gene sequences. J. Eukaryot. Microbiol. 2007, 54:306-316.
22. Gong J., Song W., Warren A. Nassophorea. Free-living Ciliates in the Bohai and Yellow Seas, China 2009, Science Press, Beijing. W. Song, A. Warren, X. Hu (Eds.).
23. Gong J., Stoeck T., Yi Z., Miao M., Zhang Q., Roberts D.M., Warren A., Song W. Small subunit rRNA phylogenies show that the class Nassophorea is not monophyletic (Phylum Ciliophora). J. Eukaryot. Microbiol. 2009, 56:339-347.
24. Gong J., Dong J., Liu X., Massana R. Extremely high copy numbers and polymorphisms of the rDNA operon estimated from single cell analysis of oligotrich and peritrich ciliates. Protist 2013, 164:369-379.
25. Gouy M., Guindon S., Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 2010, 27:221-224.
26. Guindon S., Gascuel O. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
27. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 1999, 41:95-98.
28. Hiller S. Bursellopsis spaniopogon (Ciliophora: Prostomatida). II: Stomatogenesis as revealed by light microscopy and scanning electron microscopy and some phylogenetic implications concerning prostome ciliates. Eur. J. Protistol. 1992, 28:102-119.
29. Hiller S. Ultrastructure of Prorodon (Ciliophora, Prostomatida) I. Somatic cortex and some implications concerning kinetid evolution in prostomatid and colpodid ciliates. J. Eukaryot. Microbiol. 1993, 40:467-486.
30. Kim J.S., Jeong H.J., Lynn D., Park J.Y., Lim Y.W., Shin W. Balanion masanensis n. sp. (Ciliophora: Prostomatea) from the coastal waters of Korea: morphology and small subunit ribosomal RNA gene sequence. J. Eukaryot. Microbiol. 2007, 54:482-494.
31. Kivimaki K.L., Bowditch B.M., Riordan G.P., Lipscomb D.L. Phylogeny and systematic position of Zosterodasys (Ciliophora, Synhymeniida): a combined analysis of ciliate relationships using morphological and molecular data. J. Eukaryot. Microbiol. 2009, 56:323-338.
32. Lipscomb D.L., Bowditch B.M., Riordan G.P., Lipscomb D.L. A molecular and ultrastructural description of Spathidiopsis buddenbrocki and the phylogenetic position of the family Placidae (Ciliophora). J. Eukaryot. Microbiol. 2012, 59:67-79.
33. Lynn D. Morphology or molecules: how do we identify the major lineages of ciliates (Phylum Ciliophora)?. Eur. J. Protistol. 2003, 39:356-364.
34. Lynn D.H. The Ciliated Protozoa: Characterization, Classification and Guide to the Literature 2008, Springer, Dordrecht.
35. Lynn D.H., Small E.B. Phylum Ciliophora Doflein, 1901. An Illustrated Guide to the Protozoa 2002, 371-656. Society of Protozoologists, Lawrence, Kansas. J.J. Lee, G.F. Leedale, P. Bradbury (Eds.).
36. Medlin L., Elwood H.J., Stickel S., Sogin M.L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 1988, 71:491-499.
37. Moreira D., von der Heyden S., Bass D., López-Garcia P., Chao E., Cavalier-Smith T. Global eukaryote phylogeny: combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Mol. Phylogenet. Evol. 2007, 44:255-266.
38. Noland L. Observations on marine ciliates of the gulf coast of Florida. Trans. Am. Micros. Soc. 1937, 56:160-171.
39. Nylander, J.A., 2004. MrModeltest v2. Evolutionary Biology Centre. Uppsala University, Uppsala.
40. Orsi W., Edgcomb V., Faria J., Foissner W., Fowle W.H., Hohmann T., Suarez P., Taylor C., Taylor G.T., Vd'ačný P., Epstein S.S. Class Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela. Int. J. Syst. Evol. Microbiol. 2011, 62:1425-1433.
41. Ronquist F., Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
42. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 2002, 51:492-508.
43. Shimodaira H., Hasegawa M. Consel: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.
44. Small E.B., Lynn D.H. Phylum Ciliophora Doflein, 1901. An Illustrated Guide to the Protozoa. Soc. Protozool. Special Publ. 1985, 393-575. Allen Press, Lawrence, Kansas. J.J. Lee, S.H. Hutner, E.D. Bovee (Eds.).
45. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
46. Stechmann A., Schlegel M., Lynn D.H. Phylogenetic relationships between prostome and colpodean ciliates tested by small subunit rRNA sequences. Mol. Phylogenet. Evol. 1998, 9:48-54.
47. Strüder-Kypke M.C., Wright A.D., Foissner W., Chatzinotas A., Lynn D.H. Molecular phylogeny of litostome ciliates (Ciliophora, Litostomatea) with emphasis on free-living haptorian genera. Protist 2006, 157:261-278.
48. Tuffrau M. Discotricha papillifera, n. g., n. sp. cilié psammobie de la famille des Trichopelmidae. J. Protozool. 1954, 1:183-186.
49. Van de Peer Y., De Rijk P., Wuyts J., Winkelmans T., De Wachter R. The European small subunit ribosomal RNA database. Nucl. Acids Res. 2000, 28:175-176.
50. Vd'ačný P., Tirjaková E. Taxonomic revision and neotypification of Zosterodasys transversus (Kahl, 1928), with description of a mirror-image doublet (Ciliophora, Phyllopharyngea, Synhymeniida). Acta Protozool. 2012, 51:39-54.
51. Vd'ačný P., Tirjaková E. Taxonomic revision of the ciliate genus Zosterodasys Deroux, 1978 (Protista: Ciliophora: Synhymeniida). Zootaxa 2012, 3345:34-58.
52. Vd'ačný P., Bourland W.A., Orsi W., Epstein S.S., Foissner W. Phylogeny and classification of the Litostomatea (Protista, Ciliophora), with emphasis on free-living taxa and the 18S rRNA gene. Mol. Phylogenet. Evol. 2011, 59:510-522.
53. Wicklow B.J., Borror A.C. Discotricha papillifera: structure and morphogenesis of a marine interstitial ciliate. J. Protozool. 1977, 24:99-108.
54. Wilbert N. Eine verbesserte Technik der Protargolimprägnation für Ciliaten. Mikrokosmos 1975, 64:171-179.
55. Wright A.D., Colorni A. Taxonomic re-assignment of Cryptocaryon irritans, a marine fish parasite. Eur. J. Protistol. 2002, 37:375-378.
56. Xu D., Song W., Hu X. Notes on two marine ciliates from the Yellow Sea, China: Placus salinus and Strombidium apolatum (Protozoa, Ciliophora). J. Ocean. Univ. Chin. 2005, 4:144-197.
57. Yi Z., Dunthorn M., Song W., Stoeck T. Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea). Mol. Phylogenet. Evol. 2012, 57:937-941.
58. Zhang Q., Simpson A.G.B., Song W. Insights into the phylogeny of systematically controversial haptorian ciliates (Ciliophora, Litostomatea) based on multigene analyses. Proc. Roy. Soc. B - Biol. Sci. 2012, 279:2625-2635.
59. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res. 2003, 31:3406-3415.