Phylogeny of the families Zoothamniidae and Epistylididae (Protozoa: Ciliophora: Peritrichia) based on analyses of three rRNA-coding regions

Abdallah, 2011, First record of an epibiont protozoan Epistylis sp. (Ciliophora, Peritrichia) attached to Amplexibranchius bryconis Thatcher & Paredes, 1985 (Copepoda, Ergasilidae) from Peixe’s River, state of Sāo Paulo, Brazil, Crustaceana, 84, 1139, 10.1163/001121611X584352 Crites, 1977, The occurrence of Epistylis niagarae (Ciliophora: Peritrichida) on fishes from the island region of western Lake Erie, Ohio J. Sci., 77, 193 Ehrenberg, C.G., 1838. Die Infusionsthierchen als vollkommene Organismen. 2 vols., Leipzig. Foissner, 1976, Erfahrungen mit einer trockenen Silberimprägnationsmethode zur Darstellung argyrophiler Strukturen bei Protisten, Verh. Zool.-Bot. Ges. Wien., 115, 68 Gao, 2014, Phylogenetic analyses of cyclidiids (Protista, Ciliophora, Scuticociliatia) based on multiple genes suggest their close relationship with thigmotrichids, Mol. Phylogenet. Evol., 75, 219, 10.1016/j.ympev.2014.01.032 Gao, 2016, Multi-gene-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups: Cyrtostrombidiids and strombidiids (Protozoa, Ciliophora), Mol. Phylogenet. Evol., 105, 241, 10.1016/j.ympev.2016.08.019 Gentekaki, 2010, Evidence for cryptic speciation in Carchesium polypinum Linnaeus, 1758 (Ciliophora: Peritrichia) inferred from mitochondrial, nuclear, and morphological markers, J. Eukaryot. Microbiol., 57, 508, 10.1111/j.1550-7408.2010.00505.x Gentekaki, 2014, Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages, Mol. Phylogenet. Evol., 78, 36, 10.1016/j.ympev.2014.04.020 Gouy, 2010, SeaView version 4: a multiplatform graphical user interface 355 for sequence alignment and phylogenetic tree building, Mol. Biol. Evol., 27, 221, 10.1093/molbev/msp259 Guindon, 2010, New algorithms and methods to estimate maximum-likelihood, Syst. Biol., 59, 307, 10.1093/sysbio/syq010 Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucl. Acids Symp. Ser., 41, 95 Huang, 2014, Three-gene based phylogeny of the Urostyloidea (Protista, Ciliophora, Hypotricha), with notes on classification of some core taxa, Mol. Phylogenet. Evol., 70, 337, 10.1016/j.ympev.2013.10.005 Huang, 2016, Multigene-based phylogeny of the ciliate families Amphisiellidae and Trachelostylidae (Protozoa: Ciliophora: Hypotrichia), Mol. Phylogenet. Evol., 101, 101, 10.1016/j.ympev.2016.05.007 Jankowski, 1985, Life cycles and taxonomy of generic groups Scyphidia, Heteropolaria, Zoothamnium and Cothurnia (class Peritricha), Tr. Zool. Inst. Leningrad., 129, 74 Jankowski, A.W., 2007. Phylum Ciliophora Doflein, 1901. In: Alimov, A.F. (Ed.), Protista. Part 2. Handbook on Zoology. St. Petersburg: Russian Academy of Science, Zoological Institute, pp. 415–993 (in Russian with English summary). Ji, 2004, Notes on a new marine peritrichous cilicate (Ciliophora: Peritrichida), Zoothamnopsis sinica n. sp. from north China, with reconsideration of Zoothamnium maximum Song, 1986, Acta Protozool., 43, 61 Ji, 2005, Description of three marine peritrichous ciliates, Zoothamnium foissneri n. sp., Z. duplicatum Kahl, 1933 and Z. mucedo Entz, 1884 (Ciliophora: Peritrichia), Europ. J. Protistol., 41, 45, 10.1016/j.ejop.2004.09.003 Ji, 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 Protozool., 48, 171 Ji, 2015, Two new species of Zoothamnium (Ciliophora, Peritrichia) from Korea, with new observations of Z. parahentscheli Sun et al., 2009, J. Eukaryot. Microbiol., 62, 505, 10.1111/jeu.12205 Kahl, 1935, Urtiere order Protozoa I: Wimpertiere order Ciliata (Infusoria) 4, Peritricha und Chonotricha. Tierwelt Dtl., 30, 651 Li, 2015, Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the well known genus Zoothamnium (Ciliophora, Peritrichia), Chin. J. Oceanol. Limnol., 33, 490, 10.1007/s00343-015-4083-0 Li, 2008, 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, J. Eukaryot. Microbiol., 55, 448, 10.1111/j.1550-7408.2008.00351.x Lynn, 2008 Medlin, 1988, The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions, Gene, 71, 491, 10.1016/0378-1119(88)90066-2 Posada, 2004, Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests, Syst. Biol., 53, 793, 10.1080/10635150490522304 Rajabunizal, 2011, Presence of an epibiont Epistylis niagarae (Protozoa, Ciliophora) on Mesocjzclops aspericomis in Velachery Lake, Chennai, India. J. Biol. Sci., 11, 189, 10.3923/jbs.2011.189.195 Ronquist, 2003, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180 Shen, 1980, Descriptions of six new species of periphytic protozoa in Donghu Lake of Wuhan, Acta Hydrobiol. Sin., 7, 245 Shimodaira, 2002, An approximately unbiased test of phylogenetic tree selection, Syst. Biol., 51, 492, 10.1080/10635150290069913 Shimodaira, 2001, Consel: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246, 10.1093/bioinformatics/17.12.1246 Sommer, 1951, Die peritrichen Ciliaten des groben Plöner Sees, Arch. Hydrobiol., 44, 349 Song, 1986, Descriptions of seven new species of peritrichs on Penaeus orientalis (Peritricha: Zoothamnidae, Epistylididae), Acta Zootaxon. Sin., 11, 225 Song, 2003, Chapter 1: Ectocommensal peritrichs on the cultured shrimps, 13 Sun, 2012, 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, 10.1016/j.protis.2011.06.005 Sun, 2012, J. Eukaryot. Microbiol., 59, 163, 10.1111/j.1550-7408.2011.00609.x Sun, P. Clamp, J., Xu, D., Huang, B., Shin, M.K., 2016. An integrative approach to phylogeny reveals patterns of environmental distribution and novel evolutionary relationships in a major group of ciliates. Sci. Rep. 6, 21695, doi:https://doi.org/10.1038/srep21695. Swofford, D.L., 2002. PAUP∗. Phylogenetic Analysis Using Parsimony (∗And Other Methods). Version 4. Sunderland, MA. Utz, 2007, Molecular phylogenetics of subclass Peritrichia (Ciliophora: Oligohymenophorea) based on expanded analyses of 18S rRNA sequences, J. Eukaryot. Microbiol., 54, 303, 10.1111/j.1550-7408.2007.00260.x Utz, 2010, Expanded phylogenetic representation of genera Opercularia and Epistylis sheds light on the evolution and higher-level taxonomy of peritrich ciliates (Ciliophora: Peritrichia), J. Eukaryot. Microbiol., 57, 415, 10.1111/j.1550-7408.2010.00497.x Visse, 2007, Detrimental effect of peritrich ciliates (Epistylis sp.) as epibionts on the survival of the copepod Acartia bifilosa, Esto. J. Ecol., 56, 173, 10.3176/eco.2007.3.01 Wilbert, 1975, Eine verbesserte Technik der Protargolimprägnation für Ciliaten, Mikrokosmos., 64, 171 Yi, 2009, Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information, Zool. J. Linn. Soc., 157, 227, 10.1111/j.1096-3642.2008.00524.x Yi, 2009, 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. Phylogenet. Evol., 50, 599, 10.1016/j.ympev.2008.12.006 Yi, 2011, Evolution of the order Urostylida (Protozoa, Ciliophora): new hypotheses based on multi-gene information and identification of localized incongruence, PLoS ONE, 6, e17471, 10.1371/journal.pone.0017471 Zhuang, 2016, A new peritrich ciliate from a hypersaline habitat in northern China, Zootaxa., 4169, 179, 10.11646/zootaxa.4169.1.10