Systematics and Biodiversity 7 (2): 235–242 Issued 26 May 2009 doi:10.1017/S1477200009002989 Printed in the United Kingdom C  The Natural History Museum Shan Gao 1 , Jun Gong 2 , 3 , Denis Lynn 4 , Xiaofeng Lin 2 & Weibo Song 1 * 1 Laboratory of Protozoology, Ocean University of China, Qingdao 266003, China Email: ss19830214@hotmail. com; wsong@ouc.edu.cn 2 Laboratory of Protozoology, South China Normal University, Guangzhou 510631, China Email: j.gong@nhm.ac.uk; xlin@scnu.edu.cn 3 Department of Zoology, Natural History Museum, SW7 5BD, UK 4 Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada Email: ddr@uoguelph.ca submitted October 2008 accepted November 2008 An updated phylogeny of oligotrich and choreotrich ciliates (Protozoa, Ciliophora, Spirotrichea) with representative taxa collected from Chinese coastal waters Abstract Small subunit ribosomal RNA genes of 12 ciliate morphospecies from seven genera (subclasses Oligotrichia and Choreotrichia), Parallelostrombidium, Pseudo- tontonia, Spirostrombidium, Spirotontonia, Tintinnopsis, Favella and Strombidium were sequenced. Phylogenetic trees, constructed using Bayesian inference, max- imum likelihood, maximum parsimony, and after likelihood yielded essentially the same topology. The tail-less Laboea groups with the tail-bearing Spirotontonia and Pseudotontonia, challenging the diagnostic feature of the family Tontoniidae. The three Spirostrombidium species form a monophyletic group, supporting the sep- aration of Spirostrombidium from the morphologically related genus Strombidium. Parallelostrombidium branches off basally to the Spirostrombidium clade, to some extent supporting Agatha’s division of these two similar genera. Under the approxim- ately unbiased (AU) test, topologies constrained for Strombidium monophyly were found not to be significantly worse (P > 0.05) than unconstrained topologies in which Strombidium conicum grouped with non-Strombidium species. Therefore, we can not refute the monophyly of Strombidium. Our analyses also support the previ- ous reports that the genus Tintinnopsis is polyphyletic. Key Words Oligotrichia, SS rRNA, phylogeny, Parallelostrombidium, Spirostrom- bidium, Spirotontonia, Pseudotontonia, ciliate Introduction Oligotrich and choreotrich ciliates usually dominate mar- ine planktonic ciliate communities and greatly contribute to trophic fluxes and nutrient cycling (Pierce & Turner, 1992). They are morphogenetically characterised by an enantiotropic division mode and hypoapokinetal stomatogenesis with de novo-formation of the undulating membranes (Agatha, 2004a). As for the systematics of oligotrich and choreotrich ciliates, there are two slightly different views: (1) that these organ- isms represent two subclasses, Choreotrichia (Tintinnida + Strobilidiida) and Oligotrichia (Oligotrichida + Halteriida), which can be separated by the shape of the membranellar zone (closed vs. C-shaped) (Petz & Foissner, 1992; Agatha, 2004a); and (2) that these organisms represent two subclasses, Choreotrichia and the Oligotrichia, but the latter should ex- clude halteriids, which are viewed as stichotrichs with con- vergent oligotrich features (Lynn, 2008). We will follow the taxonomy proposed by Lynn (2008). ∗ Corresponding author. Email: wsong@ouc.edu.cn There are a few reports reconstructing the phylogeny of oligotrichs and choreotrichs, using either morphological characters and/or small subunit (SS) rRNA gene sequences (Snoeyenbos-West et al., 2002; Str ¨ uder-Kypke & Lynn, 2003; Agatha, 2004a, b; Agatha & Str¨ uder-Kypke, 2007). Agatha (2004b) assumed the contractile tail evolved only once in the Family Tontoniidae Agatha, 2004, and proposed several new families (i.e. Cyrtostrombidiidae; Pelagostrombidiidae) and new genera (i.e. Omegastrombidium, Pseudotontonia, Spirotontonia, Parallelostrombidium), primarily rationalised by variations in the somatic kinety patterns. However, the number of taxa with SS rRNA sequence information avail- able from GenBank is low, compared with the large number of described morphospecies, which now includes many new taxa (see Agatha, 2004a, b for review of literature). Thus, molecu- lar genetic information from additional key taxa would deepen our understanding and interpretation of the phylogenetic rela- tionships now proposed for these ciliates. We have identified some oligotrichs, including Spirostrombidium, Spirotontonia, and Parallelostrombidium, Pseudotontonia, whose sequences have hitherto not been 235