Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the well-known genus Zoothamnium (Ciliophora, Peritrichia)

Lifang Li; Honggang Ma; Khaled A. S. Al-Rasheid

doi:10.1007/s00343-015-4083-0

Your Location：

Home >

Browse articles >

Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the well-known genus Zoothamnium (Ciliophora, Peritrichia)

Updated：2023-05-16

- Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the well-known genus Zoothamnium (Ciliophora, Peritrichia)
- Journal of Oceanology and Limnology Vol. 33, Issue 2, Pages: 490-499(2015)
- Affiliations：
  
  1. Marine College Shandong University
  2. Institute of Evolution & Marine Biodiversity Ocean University of China
  3. Zoology Department King Saud University
- Author bio：
- Funds：
- DOI：10.1007/s00343-015-4083-0
  CLC：
- Online First：10 December 2014，
  
  Published：2015
- Accepted：
Scan QR Code
Li, L., Ma, H. & Al-Rasheid, K.A.S. Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the well-known genus Zoothamnium (Ciliophora, Peritrichia)., Chin. J. Ocean. Limnol. 33, 490–499 (2015). https://doi.org/10.1007/s00343-015-4083-0
DOI：

Li, L., Ma, H. & Al-Rasheid, K.A.S. Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the well-known genus Zoothamnium (Ciliophora, Peritrichia)., Chin. J. Ocean. Limnol. 33, 490–499 (2015). https://doi.org/10.1007/s00343-015-4083-0 DOI：

摘要

Abstract

In this paper

we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence

for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless

Zoothamnium exhibits higher genetic diversity than the gross morphology of its species. Here

we used all available genetic information for the small subunit of ribosomal RNA (SSU rRNA) and internal transcribed spacer region (ITS1-5.8S-ITS2) for this genus to reconstruct phylogenies for four datasets (SSU rRNA

ITS1

ITS2

and ITS1-5.8S-ITS2) and a combined dataset (SSU rRNA+ITS1-5.8SITS2) using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic

and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly

as with some other groups of ciliates

to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies

covering additional Zoothamnium spp. and members of closely related genera (e.g. Zoothamnopsis

Myoschiston

and Epistylis).

关键词

Keywords

references

Bauer-Nebelsick M, Bardele C F, Ott J A. 1996. Redescription of Zoothamnium niveum (Hemprich & Ehrenberg, 1831) Ehrenberg, 1838 (Oligohymenophora, Peritrichida), a ciliate with ectosymbiotic, chemoautotrophic bacteria. European Journal of Protistology, 32: 18–30.

Clamp J, Williams D. 2006. A molecular phylogenetic investigation of Zoothamnium (Ciliophora, Peritrichia, Sessilida). Journal of Eukaryotic Microbiology, 53: 494–498.

Corliss J O. 1979. The Ciliated Protozoa: Characterization, Classification and Guide to the Literature. 2nd Edition. Pergamon Press. New York.

Dunthorn M, Foissner W, Katz L A. 2008. Molecular phylogenetic analysis of class Colpodea (phylum Ciliophora) using broad taxon sampling. Molecular Phylogenetics and Evolution, 46: 316–327.

Ehrenberg C G. 1838. Die Infusionsthierchen als Volkommene Organismen. Leipzig. 612p.

Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

Fitch W M, Margoliash E. 1967. Construction of phylogenetic trees. Science, 155: 279–284.

Foissner W, Blake N, Wolf K, Breiner H W, Stoeck T. 2010. Morphological and molecular characterization of some peritrichs (Ciliophora: Peritrichida) from tank bromeliads, including two new genera: Orborhabdostyla and Vorticellides. Acta Protozoologica, 48: 291–319.

Foissner W, Berger H, Kohmann F. 1992. Taxonomische und ökologische Revision der Ciliaten des Saprobiensystems—Band II: Peritrichida, Heterotrichida, Odontostomtida. Informationsberichte des Bayerischen. Landesamtes für Wasserwirtschaft, 5: 1–502.

Foissner W, Schiffmann H. 1974. Vergleichende Studien an argyrophilen Strukturen von vierzehn peritrichen Ciliaten. Protistologica, 10: 489–508.

Gao F, Katz L A. 2014. Phylogenomic analyses support the bifurcation of ciliates into two major clades that differ in properties of nuclear division. Molecular Phylogenetics and Evolution, 70: 240–243.

Gao F, Katz L A, Song W. 2013. Multigene-based analyses on evolutionary phylogeny of two controversial ciliate orders: Pleuronematida and Loxocephalida (Protista, Ciliophora, Oligohymenophorea). Molecular Phylogenetics and Evolution, 68: 55–63.

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.

Ji D, Kusuoka Y. 2009. A description of Apocarchesium rosettum n. gen., n. sp. and a redescription of Ophrydium eichornii Ehrenberg, 1838, two freshwater peritrichous ciliates from Japan. European Journal of Protistology, 45: 21–28.

Ji D, Xu H, Choi J K, Warren A, Song W. 2009. Taxonomic characterization of three marine peritrichous ciliates from China: Zoothamnium alrasheidi spec. nov., Z. marinum Kahl, 1933 and Z. vermicola Precht, 1935 (Ciliophora: Peritrichia). Acta Protozoologica, 48: 171–183.

Ji D, Song W, Al-Rasheid K A S, Li L. 2005. Taxonomic characterization of two new narine peritrichous ciliates, Pseudovorticella clampi n. sp. and Zoothamnium pararbuscula n. sp. (Protozoa: Ciliophora: Peritrichida) from North China. Journal of Eukaryotic Microbiology, 52: 159–169.

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 Protozoologica, 45: 27–39.

Kahl A. 1933. Ciliata librae et ectocommensalia. In: Grimpe G, Wagler E eds. Die Tierwelt der Nord- und Ostsee. Lieferung. 23, Leipzig. p.147–183.

Kimura M. 1980. A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16: 111–120.

Li J M, Liu W, Gao S, Warren A, Song W. 2013. Multigene-based analyses of the phylogenetic evolution of oligotrich ciliates, with consideration of the internal transcribed spacer 2 secondary structure of three systematically ambiguous genera. Eukaryotic Cell, 12: 430–437.

Li L, Song W, Warren A, Shin M K, Chen Z, Ji D, Sun P. 2008a. 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, 55: 448–456.

Li Z, Chen Z, Yi Z, Miao M, Li L, Zhu M, Ma H, Hu X, Wang M, Song W. 2008b. Molecular phylogenetic investigation on Vorticellidae and Zoothamniidae inferred from ITS1-5.8S-ITS2 sequences. Acta Hydrobiologica Sinica, 32: 8–13. (in Chinese with English abstract)

Lynn D H, Small E B. 2002. Phylum Ciliophora Doflein, 1901. In: Lee J J, Bradbury P C, Leedale G F eds. An Illustrated Guide to the Protozoa. 2nd Ed. Allen Press incorporated, Lawrence, Kansas. p.371–656.

Lynn D H. 2008. The Ciliated Protozoa. Characterization, Classification, and Guide to the Literature, 3rd edn. Springer, Dordrecht.

Lynn D H, Wright A D G, Fokin S I, Foissner W. 1999. Phylogenetic relationships of orders within the class Colpodea (Phylum Ciliophora) inferred from small subunit rRNA gene sequences. Journal of Molecular Evolution, 48: 605–614.

Miao W, Fen W S, Yu Y H, Zhang X Y, Shen Y F. 2004. Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences. Journal of Eukaryotic Microbiology, 51: 180–186.

Miller M A, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA. p.1–8.

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 Research, 21: 3 025–3 049.

Nylander J A A. 2004. MrModeltest v2. Evolutionary Biology Centre, Uppsala University.

Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T. 2010a. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Research, 38: W23–W28, http://dx.doi.org/10.1093/nar/gkq443.

Penn O, Privman E, Landan G, Graur D, Pupko T. 2010b. An alignment confidence score capturing robustness to guidetree uncertainty. Molecular Biology and Evolution, 27: 1 759–1 767.

Ronquist F, Huelsenbeck J P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1 572–1 574.

Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4: 406–425.

Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Systematic Biology, 51: 492–508.

Shimodaira H, Hasegawa M. 2001. Consel: For assessing the confidence of phylogenetic tree selection. Bioinformatics, 17: 1 246–1 247.

Siebert S, Backofen R. 2005. MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics, 21: 3 352–3 359.

Sommer G. 1951. Die peritrichen Ciliaten des groben Plöner Sees. Archiv für Hydrobiologie, 44: 349–440.

Song W. 1997. A new genus and two new species of marine peritrichous ciliates (Protozoa, Ciliophora, Peritrichida) from Qingdao, China. Ophelia, 47: 203–214.

Song W, Al-Rasheid K A S, Hu X. 2002. Notes on the poorlyknown marine peritrichous ciliate, Zoothamnium plumula Kahl, 1933 (Protozoa: Ciliophora), an ectocommensal organism from cultured scallops in Qingdao, China. Acta Protozoologica, 41: 163–168.

Song W, Warren A, Hu X. 2009. Free-Living Ciliates in Bohai and Yellow Sea, China. Science Press, Beijing.

Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22: 2 688–2 690.

Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology, 57: 758–771.

Stiller J. 1971. Szájkoszorús Csillósok-Peritricha. Fauna Hung., 105: 1–245.

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. Journal of Eukaryotic Microbiology, 47: 419–429.

Sun P, Clamp J C, Xu D, Kusuoka Y, Miao W. 2012a. Vorticella Linnaeus, 1767 (Ciliophora, Oligohymenophora, Peritrichia) is a grade not a clade: redefinition of Vorticella and the families Vorticellidae and Astylozoidae using molecular characters derived from the gene coding for small subunit ribosomal RNA. Protist, 163: 129–142.

Sun P, Xu D, Clamp J C, Shin M K. 2012b. Molecular and morphological characterization of a poorly known marine ciliate, Myoschiston duplicatum precht 1935: implications for phylogenetic relationships between three morphologically similar genera—Zoothamnium, Myoschiston, and Zoothamnopsis (Ciliophora, Peritrichia, Zoothamniidae). Journal of Eukaryotic Microbiology, 59: 163–170.

Sun P, Ma H, Shin M, Al-Rasheid K A S. 2013. Morphology of two new marine peritrich ciliates from Yellow Sea, Pseudovorticella dingi nov. spec. and P. wangi nov. spec., with supplementary descriptions of P. plicata, P. banatica and P. anomala (Ciliophora, Peritrichia). European Journal of Protistology, 49: 467–476.

Swofford D L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.

Utz L R P, Eizirik E. 2007. Molecular phylogenetics of subclass Peritrichia (Ciliophora: Oligohymenophorea) based on expanded analyses of 18S rRNA sequences. Journal of Eukaryotic Microbiology, 54: 303–305.

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. Journal of Molecular Evolution, 51: 565–576.

Zhan Z, Xu K, Dunthorn M. 2013. Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships within the Mobilida (Ciliophora, Oligohymenophorea). Zoologica Scripta, 42: 213–226.

Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31: 3 406–3 415.

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

Phylogeny of subclass Scuticociliatia (Protozoa, Ciliophora) using combined data inferred from genetic, morphological, and morphogenetic evidence

Parametric Model of Lubricant Particle Trajectory inAnnulus Inter-Spools

Influence of Structural Parameters of Diversion Cone on Smooth Effect of Gas Ejection Bottom Pressure Impact

Investigation on Interaction Mechanism Between Rim Sealing Flow and Mainstream Flow in High-Pressure Turbine

Numerical Studies on Effects of V-Shaped Leading Edge on Incident Shock Wave Boundary Layer Interaction

Related Author

Zhenzhen Yi

Yangang Wang

Xiaofeng Lin

Weibo Song

Yunlu XIAO

Ning XIAO

Xiaoqi ZENG

Related Institution

Laboratory of Protozoology Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education South China Normal University

Laboratory of Protozoology Ocean University of China

Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences

Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Science

University of Chinese Academy of Science

Address：Editorial Office of JOL, 88 Haijun Rd. Qingdao, 266000, China
Tel：+86-532-82898754 Email：jol@qdio.ac.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备09064830号-19 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰