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Published January 25, 2022 | Version v1
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Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis

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Xu, Wenxin, Ma, Jiyang, Li, Yuan, Bourland, William A., Petroni, Giulio, Luo, Xiaotian, Song, Weibo (2022): Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis. Zoological Journal of the Linnean Society 196: 88-104, DOI: 10.1093/zoolinnean/zlab102, URL: https://doi.org/10.1093/zoolinnean/zlab102

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URL
https://www.checklistbank.org/dataset/296638
LSID
urn:lsid:zoobank.org:pub:C7008A79-ABF6-403A-9366-2C68AE7C405C
LSID
urn:lsid:plazi.org:pub:045BFFCAFFF4FF9FFF871404FFC4AF63
URL
http://publication.plazi.org/id/045BFFCAFFF4FF9FFF871404FFC4AF63

Has part
Taxonomic treatment: 10.5281/zenodo.11242963 (DOI)
Taxonomic treatment: urn:lsid:zoobank.org:act:B1A4ED11-078E-4E66-9146-3207F69962A9 (LSID)
Taxonomic treatment: http://treatment.plazi.org/id/F86287B2FFF0FF9BFED71602FE3DAC7B (URL)
Taxonomic treatment: 10.5281/zenodo.11242965 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/F86287B2FFF0FF9BFEE5177FFD84AA22 (URL)
Taxonomic treatment: 10.5281/zenodo.11242967 (DOI)
Taxonomic treatment: urn:lsid:zoobank.org:act:894A94B9-FD7C-4E85-AB08-EC470D2DE78F (LSID)
Taxonomic treatment: http://treatment.plazi.org/id/F86287B2FFF0FF96FEC611A3FE4FAA8E (URL)
Figure: 10.5281/zenodo.7034932 (DOI)
Figure: 10.5281/zenodo.7034936 (DOI)
Figure: 10.5281/zenodo.7034938 (DOI)
Figure: 10.5281/zenodo.7034940 (DOI)
Dataset: 10.5281/zenodo.15142665 (DOI)
Figure: 10.5281/zenodo.7034942 (DOI)
Figure: 10.5281/zenodo.7034944 (DOI)
Figure: 10.5281/zenodo.7034947 (DOI)
Is source of
Dataset: https://www.gbif.org/dataset/6af74839-d318-4eee-9001-0a570a953c6b (URL)

References

  • Alfaro M. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic Confidence. Molecular Biology and Evolution 20: 255-266.
  • Asghar U, Chi Y, Gao Y, Lu B, Jiang Y, Gong R, Ma H, Al-RasheidKAS, GaoF. 2021. Morphogenesis of the ciliature during sexual process of conjugation in the ciliated protist Euplotes raikovi. Frontiers in Marine Science 7: 615377.
  • Bai Y, Wang R, Song W, Suzuki T, Hu X. 2020. Redescription of five tintinnine ciliates (Alveolata: Ciliophora: Oligotrichea) from coastal waters of Qingdao, China. Marine Life Science & Technology 2: 209-221.
  • Berger H. 1999. Monograph of the Oxytrichidae (Ciliophora, Hypotrichia). Monographiae Biologicae 78: 1-1080.
  • Berger H. 2003. Redefinition of Holosticha Wrzesniowski, 1877 (Ciliophora: Hypotricha). European Journal of Protistology 39: 373-379.
  • Berger H. 2006. Monograph of the Urostyloidea (Ciliophora, Hypotricha). Monographiae Biologicae 85: 1-1304.
  • Berger H. 2008. Monograph of the Amphisiellidae and Trachelostylidae (Ciliophora, Hypotricha). Monographiae Biologicae 88: 1-737.
  • Berger H. 2011. Monograph of the Gonostomatidae and Kahliellidae (Ciliophora, Hypotricha). Monographiae Biologicae 90: 1-741.
  • Chen X, Dong J, Lin X, Al-Rasheid KAS. 2011. Morphology and phylogeny of a new urostylid ciliate, Monocoronella carnea nov. gen., nov. spec. (Ciliophora, Hypotricha) from Daya Bay, southern China. Journal of Eukaryotic Microbiology 58: 497-503.
  • Chen X, Shao C, Liu X, Huang J, Al-Rasheid KAS. 2013. Morphology and phylogenies of two hypotrichous brackishwater ciliates from China, Neourostylopsis orientalis nov. spec. and Protogastrostyla sterkii (Wallengren, 1900) n. comb., with establishment of a new genus Neourostylopsis n. gen. (Protista, Ciliophora, Hypotrichia). International Journal of Systematic and Evolutionary Microbiology 63: 1197-1209.
  • Corliss JO. 1979. The ciliated Protozoa. Characterization, classification and guide to the literature, 2nd edn. Oxford: Pergamon Press.
  • Deng Y, Lu X, Li J, Ba S, Paiva TS. 2018. Morphology of two Eschaneustyla species (Ciliophora, Urostylida), with notes on morphogenesis of Eschaneustyla lugeri. Acta Protozoologica 57: 69-78.
  • EhrenbergCG. 1830. Beitrage zur Kenntniss der Organisation der Infusorien und ihrer geographischen Verbreitung, besonders in Sibirien. Berlin: Akademie der Wissenschaften.
  • Fan Y, Hu X, Gao F, Al-Farraj SA, Al-Rasheid KAS. 2014. Morphology, ontogenetic features and SSU rRNA gene-based phylogeny of a soil ciliate, Bistichella cystiformans spec. nov. (Protista, Ciliophora, Stichotrichia). International Journal of Systematic and Evolutionary Microbiology 64: 4049-4060.
  • Fernandes NM, Schrago CG. 2019. A multigene timescale and diversification dynamics of Ciliophora evolution. Molecular Phylogenetics and Evolution 139: 106521.
  • Foissner W. 2016. Terrestrial and semiterrestrial ciliates (Protozoa, Ciliophora) from Venezuela and Galapagos. Denisia 35: 1-912.
  • Foissner W. 2021. Taxonomy of soil ciliates (Ciliophora) from Australia and some other parts of the world. Series Monographiae Ciliophorae 5: 55-345.
  • Foissner W, Agatha S, Berger H. 2002. Soil ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa), with emphasis on two contrasting environments, the Etosha region and the Namib desert. Part I: text and line drawings. Part II: photographs. Denisia 5: 1-1459.
  • Foissner W, Van der Staay SYM, Van der Staay GWM, Hackstein JHP, 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.
  • Foissner W, Chao A, Katz LA. 2008a. Diversity and geographic distribution of ciliates (Protista: Ciliophora). Biodiversity and Conservation 17: 345-363.
  • Foissner W, Quintela-Alonso P, Al-Rasheid K. 2008b. Soil ciliates from Saudi Arabia, including descriptions of two new genera and six new species. Acta Protozoologica 47: 317-352.
  • Gao F, Huang J, Zhao Y, Li L, Liu W, Miao M, Zhang Q, Li J, Yi Z, El-Serehy H, Warren A, Song WB. 2017. Systematic studies on ciliates (Alveolata, Ciliophora) in China: progress and achievements based on molecular information. European Journal of Protistology 61: 409-423.
  • Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT.Nucleic Acids Symposium Series 41: 95-98.
  • Hillis D, Bull J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42: 182-192.
  • Hu X, Fan X, Lin X, Gong J, Song WB. 2009. The morphology and morphogenesis of a marine ciliate, Epiclintes auricularis rarisetus nov. sspec. (Ciliophora, Epiclintidae), from the Yellow Sea. European Journal of Protistology 45: 281-291.
  • Hu X, Lin X, Song WB. 2019. Ciliates atlas: species found in the South China Sea. Beijing: Science Press.
  • Huang J, Chen Z, Song W, Berger H. 2014. Threegene based phylogeny of the Urostyloidea (Protista, Ciliophora, Hypotricha), with notes on classification of some core taxa. Molecular Phylogenetics and Evolution 70: 337-347.
  • JankowskiAW. 1979. Revision of the order Hypotrichida Stein, 1859 (Protozoa, Ciliophora). Generic catalogue, phylogeny, taxonomy. Trudy Zoologischeski Institute Leningrad 86: 48-85 [in Russian with English summary].
  • Jung JH, Berger H. 2019. Monographic treatment of Paraholosticha muscicola (Ciliophora, Keronopsidae), including morphological and molecular biological characterization of a brackish water population from Korea. European Journal of Protistology 68: 48-67.
  • Jung JH, Park KM, Min GS, Berger H, Kim S. 2015. Morphology and molecular phylogeny of an Antarctic population of Paraholosticha muscicola (Kahl, 1932) Wenzel, 1953 (Ciliophora, Hypotricha). Polar Science 9: 374-381.
  • Jung JH, Omar A, Park MH, Nguyen TV, Jung YH, Yang HM, Min GS. 2021. Anteholosticha foissneri n. sp. a marine hypotrich ciliate (Ciliophora: Spirotrichea) from Vietnam: morphology, morphogenesis, and molecular phylogeny. European Journal of Protistology 78: 125768.
  • KahlA. 1931. Urtiere oder Protozoa I: Wimpertiere oder Ciliata (Infusoria) 2. Holotricha. Die Tierwelt und der angrenzenden Meeresteile 21: 181-398.
  • Kaur H, Shashi RK, Kamra K. 2019. Morphological and molecular characterization of Neogastrostyla aqua nov. gen., nov. spec. (Ciliophora, Hypotrichia) from River Yamuna, Delhi; comparison with Gastrostyla -like genera. European Journal of Protistology 68: 68-79.
  • Kim JH, Min GS. 2015. New record of two soil ciliates (Ciliophora: Stichotrichia) from Korea. Korean Journal of Environmental Biology 33: 383-389.
  • Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870-1874.
  • Liu W, Shao C, Gong J, Li J, Lin X, Song WB. 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.
  • Lu X, Wang YY, Al-Farraj SA, El-Serehy H, Huang J, Shao C. 2020. The insights into the systematic relationship of Gastrostyla -affinitive genera, with report on a new saline soil ciliate genus and new species (Protozoa, Ciliophora). BMC Evolutionary Biology 20: 1-14.
  • Luo X, Gao F, Al-Rasheid KAS, Warren A, Hu X, Song W. 2015. Redefinition of the hypotrichous ciliate Uncinata, with descriptions of the morphology and phylogeny of three urostylids (Protista, Ciliophora). Systematics and Biodiversity 13: 455-471.
  • Luo X, Bourland W, Song WB, Huang J. 2021. New contributions to the taxonomy of urostylid ciliates (Ciliophora, Hypotrichia), with establishment of a new genus and new species. European Journal of Protistology 80: 125810.
  • Lynn D. 2008. The ciliated Protozoa: characterization, classification, and guide to the literature, 3rd edn. New York: Springer.
  • Lyu Z, Wang J, Huang J, WarrenA , Shao C. 2018. Multigene based phylogeny of Urostylida (Ciliophora, Hypotrichia), with establishment of a novel family. Zoologica Scripta 47: 243-254.
  • Medlin L, Elwood HJ, Stickel S, Sogin ML. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491-499.
  • Miao W, Song L, Ba S, Zhang L, Guan G, Zhang Z, Ning K. 2020. Protist 10,000 genomes project. The Innovation 1: 100058.
  • Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Proceedings of the 2010 Gateway Computing Environments Workshop (GCE). New Orleans: Institute of Electrical and Electronics Engineers, 1-8.
  • Nylander JAA. 2004. MrModeltest, v.2. Uppsala: Evolutionary Biology Centre, Uppsala University.
  • Omar A, Moon JH, Jung JH. 2021. Molecular phylogeny of a new gonostomatid ciliate revealing a discrepancy between interphasic and cell divisional patterns (Ciliophora, Hypotricha). European Journal of Protistology 79: 125794.
  • Paiva TDS. 2020. Systematic redefinition of the Hypotricha (Alveolata, Ciliophora) based on combined analyses of morphological and molecular characters. Protist 171: 125755.
  • Pan X, Bourland WA, Song WB. 2013. Protargol synthesis: an in-house protocol. Journal of Eukaryotic Microbiology 60: 609-614.
  • Pan X, Fan Y, Gao F, Qiu Z, Alfarraj SA, Warren A, Shao C. 2016. Morphology and systematics of two freshwater urostylid ciliates, with description of a new species (Protista, Ciliophora, Hypotrichia). European Journal of Protistology 52: 73-84.
  • Park KM, Chae N, Jung JH, Min GS, Kim S, Berger H. 2017. Redescription of Keronopsis helluo Penard, 1922 from Antarctica and Paraholosticha pannonica Gellert and Tamas, 1959 from Alaska (Ciliophora, Hypotricha). European Journal of Protistology 60: 102-118.
  • Park KM, Jung JH, Jeong HK, Min GS, Kim S. 2020. Morphology, morphogenesis, and molecular phylogeny of a new freshwater ciliate, Gonostomum jangbogoensis nov. spec. (Ciliophora, Hypotricha), from Victoria Land, Antarctica. European Journal of Protistology 73: 125669.
  • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542.
  • SelaI, AshkenazyH, KatohK, PupkoT. 2015. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Research 43: W7-W14.
  • Shao C, Hu X, Warren A, Al-Rasheid KAS, Al-Qurashy SA, Song WB. 2007. Morphogenesis in the marine spirotrichous ciliate Apokeronopsis crassa (Claparede & Lachmann, 1858) nov. comb. (Ciliophora: Stichotrichia), with the establishment of a new genus, Apokeronopsis nov. gen. and redefinition of the genus Thigmokeronopsis. Journal of Eukaryotic Microbiology 54: 392-401.
  • Shao C, Gao Q, Warren A, Wang J. 2021. Morphology, morphogenesis, and molecular phylogeny of a new freshwater ciliate, Quadristicha subtropica n. sp. (Ciliophora, Hypotrichia). Frontiers in Microbiology 12: 705826.
  • Song WB, Shao C. 2017. Ontogenetic patterns of hypotrich ciliates. Beijing: Science Press (in Chinese).
  • SongWB ,WarrenA. 1996. A redescription of the marine ciliates Uroleptus retractilis (Claparede and Lachmann, 1858) comb. n. and Epiclintes ambiguus (Muller, 1786) Butschli, 1889 (Ciliophora, Hypotrichida). Acta Protozoologica 35: 227-234.
  • Song WB, Petz W, Warren A. 2001. Morphology and morphogenesis of the poorly-known marine urostylid ciliate, Metaurostylopsis marina (Kahl, 1932) nov. gen., nov. comb. (Protozoa, Ciliophora, Hypotrichida). European Journal of Protistology 37: 63-76.
  • Song WB, Warren A, Hu X. 2009. Free-living ciliates in the Bohai and Yellow Seas, China. Beijing: Science Press.
  • Song Y, Liu YQ, Pan B, Luo X, Song WB, Warren A. 2019. Morphological studies on four brackish water ciliates of the class Spirotrichea (Protista, Ciliophora). Journal of Ocean University of China 18: 663-674.
  • Song WY, Zhang TY, Zhang X, Warren A, Song WB, Zhao Y , Luo X. 2021. Taxonomy, ontogenesis and evolutionary phylogeny of the algae-bearing ciliate Bourlandella viridis (Kahl, 1932) comb. nov., with establishment of a new genus and new family (Protista, Ciliophora, Hypotrichia). Frontiers in Microbiology 11: 560915.
  • Stamatakis A. 2014. RAxML, v.8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
  • Stein F. 1863. Neue Infusorienformen in der Ostsee. Amtliche Bericht Deutscher Naturforscher und AErzte in Karlsbad 37: 161-162, 165-166.
  • Stokes AC. 1886. Some new hypotrichous infusoria. Proceedings of the American Philosophical Society 23: 21-30.
  • Vdacny P, Foissner W. 2021. Morphology and ontogenesis of two new Hemiholosticha species (Ciliophora, Hypotrichia, Hemiholostichidae nov. fam.). European Journal of Protistology 77: 125763.
  • WangYG , Hu X, Huang J, Al-Rasheid KAS, WarrenA. 2011. Characterization of two urostylid ciliates, Metaurostylopsis flavicana spec. nov. and Tunicothrix wilberti (Lin & Song, 2004) Xu et al., 2006 (Ciliophora, Stichotrichia), from a mangrove nature protection area in China. International Journal of Systematic and Evolutionary Microbiology 61: 1740-1750.
  • Wang J, Li J, Shao C. 2020a. Morphology, morphogenesis, and molecular phylogeny of a novel saline soil ciliate, Heterourosomoida sinica nov. spec. (Ciliophora, Hypotrichia). European Journal of Protistology 73: 125666.
  • Wang J, ZhaoY, Lu X, Lyu Z, WarrenA , Shao C. 2020b. Does the Gonostomum -patterned oral apparatus in Hypotrichia carry a phylogenetic signal? Evidence from morphological and molecular data based on extended taxon sampling using three nuclear genes (Ciliophora, Spirotrichea). Science China Life Sciences 64: 311-322.
  • Wang J, Zhang T, Li F, Warren A, Li Y, Shao C. 2021. A new hypotrich ciliate, Oxytricha xianica sp. nov., with notes on the morphology and phylogeny of a Chinese population of Oxytricha auripunctata Blatterer & Foissner, 1988 (Ciliophora, Oxytrichidae). Marine Life Science & Technology 3: 303-312.
  • Wicklow BJ. 1981. Evolution within Hypotrichida (Ciliophora, Protozoa): ultrastructure and morphogenesis of Thigmokeronopsis jahodai (n. gen., n. sp.); phylogeny in the Urostylina (Jankowski, 1979). Protistologica 17: 331-351.
  • Wicklow BJ, Borror AC. 1990. Ultrastructure and morphogenesis of the marine epibenthic ciliate Epiclintes ambiguus (Epiclintidae, nov. fam.; Ciliophora). European Journal of Protistology 26: 182-194.
  • Wilbert N. 1975. Eine verbesserte Technik der Protargol impragnation fur Ciliaten. Mikrokosmos 64: 171-179.
  • Xu W, Wang YR , Cheng T , Yu Y , El-Serehy H , Al-Farraj SA, Bourland WA, Luo X. 2020. Reevaluation of the 'well-known' Paraurostyla weissei complex, with notes on the ontogenesis of a new Paraurostyla species (Ciliophora, Hypotrichia). European Journal of Protistology 73: 125672.
  • Zhang TY, Dong J, Cheng T, Duan L, Shao C. 2020a. Reconsideration of the taxonomy of the marine ciliate Neobakuella aenigmatica Moon et al., 2019 (Protozoa, Ciliophora, Hypotrichia). Marine Life Science & Technology 2: 97-108.
  • Zhang TY, Wang YR, Cheng T, Ma J, Vd'acny P, Song WB, Shao C. 2020b. Systematics and multi-gene phylogeny of the subfamily Nothoholostichinae (Ciliophora, Hypotrichia), with integrative description of a new marine species Nothoholosticha luporinii n. sp. Frontiers in Marine Science 7: 610886.