Further consideration on the phylogeny of the Ciliophora: Analyses using both mitochondrial and nuclear data with focus on the extremely confused class Phyllopharyngea

Abstract

Most ciliate phylogenetic analyses have largely relied on the nuclear small subunit ribosome DNA (nSSU-rDNA) locus. However, single locus or multi-loci from the same genome or chromosome may not be sufficient enough to elucidate phylogenetic relationships among ciliate taxa. Therefore, in addition to nSSU-rDNA, the mitochondrial small subunit ribosome DNA (mtSSU-rDNA) was applied in this study. We expanded the taxon sampling especially within the class Phyllopharyngea. Phylogenetic analyses based on nSSU-rDNA and mtSSU-rDNA, independently, as well as concatenated were performed and revealed the following: (1) mtSSU-rDNA is more variable than nSSU-rDNA, and is better at elucidating relationships at lower levels, e.g. intra-/inter-specific or generic relationships; (2) the validity of the two genera Mirodysteria and Spirodysteria is challenged based on their similar morphology with Dysteria and the analyses from both mtSSU-rDNA and nSSU-rDNA; (3) Brooklynella is confirmed to be an intermediate taxon between Dysteriidae and Hartmannulidae, and may represent a distinct family; (4) Trithigmostoma should remain in Chilodonellidae; (5) the separation of Paraspathidium from Litostomatea is supported and it groups with prostomateans and plagiopyleans. In summary, results from mtSSU-rDNA corroborated those of nSSU-rDNA for highly supported clades, and the mtSSU-rDNA tree with its secondary structure gave topologies that could be explained by the morphology; therefore it can be useful in some cases towards better resolution of robust phylogenies.