Protist, Vol. 156, 215—224, August 2005 http://www.elsevier.de/protis Published online date 11 July 2005 ORIGINAL PAPER 18S Ribosomal RNA Gene Sequences of Cochliopodium (Himatismenida) and the Phylogeny of Amoebozoa Alexander Kudryavtsev a,1 , Detlef Bernhard b , Martin Schlegel b , Ema E-Y Chao c , and Thomas Cavalier-Smith c a Department of Invertebrate Zoology, Faculty of Biology and Soil Science, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia b Laboratory of Molecular Evolution and Animal Systematics, University of Leipzig, Leipzig, D-04103, Germany c Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK Submitted December 24, 2004; Accepted March 28, 2005 Monitoring Editor: Michael Melkonian Cochliopodium is a very distinctive genus of discoid amoebae covered by a dorsal tectum of carbohydrate microscales. Its phylogenetic position is unclear, since although sharing many features with naked ‘‘gymnamoebae’’, the tectum sets it apart. We sequenced 18S ribosomal RNA genes from three Cochliopodium species (minus, spiniferum and Cochliopodium sp., a new species resembling C. minutum). Phylogenetic analysis shows Cochliopodium as robustly holophyletic and within Amoebozoa, in full accord with morphological data. Cochliopodium is always one of the basal branches within Amoebozoa but its precise position is unstable. In Bayesian analysis it is sister to holophyletic Glycostylida, but distance trees mostly place it between Dermamoeba and a possibly artifactual long-branch cluster including Thecamoeba. These positions are poorly supported and basal amoebozoan branching ill-resolved, making it unclear whether Discosea (Glycostylida, Himatismenida, Dermamoebida) is holophyletic; however, Thecamoeba seems not specifically related to Dermamoeba. We also sequenced the small-subunit rRNA gene of Vannella persistens, which constantly grouped with other Vannella species, and two Hartmannella strains. Our trees suggest that Vexilliferidae, Variosea and Hartmannella are polyphyletic, confirming the existence of two very distinct Hartmannella clades: that comprising H. cantabrigiensis and another divergent species is sister to Glaeseria, whilst Hartmannella vermiformis branches more deeply. & 2005 Elsevier GmbH. All rights reserved. Key words: Amoebozoa; Cochliopodium; Hartmannella; Vannella; molecular phylogeny; rRNA sequences. Introduction The genus Cochliopodium Hertwig et Lesser, 1874 comprises lens-shaped amoebae covered by the tectum, a flexible layer of carbohydrate scales, which covers the dorsal surface only of the ARTICLE IN PRESS 1 Corresponding author; fax 7 812 3289703 e-mail aak@ak14261.spb.edu (A. Kudryavtsev) & 2005 Elsevier GmbH. All rights reserved. doi:10.1016/j.protis.2005.03.003