Expanding character sampling for the molecular phylogeny of euplotid ciliates (Protozoa, Ciliophora) using three markers, with a focus on the family Uronychiidae

Although euplotida ciliates are widely used as model organisms in multiple fields of biology, details of their phylogenetic relationships remain unresolved despite a rich history of investigation with small subunit (SSU) rDNA sequences and other characters. Here, six genera in Diophrys-like complex and three other euplotid genera are sampled for SSU-rDNA, ITS1-5.8S-ITS2 and LSU-rDNA, and their phylogenies were inferred with unconstrained and constrained analyses. In general, the concatenated analyses infer more reliable, less ambiguous phylogenies with higher node support values. The following conclusions can be made: (1) four well-supported clades are consistently detected in the family Uronychiidae, forming into two subgroups, which challenge the traditional arrangement based on morphological similarities; (2) the subfamily Diophryinae is paraphyletic; (3) the monophyly of Paradiophrys and the establishment of Apodiophrys and Diophryopsis is fully supported by concatenated data; (4) Apodiophrys and Paradiophrys form independent lineages, at the subfamily level, from other Diophrys-like genera; and (5) the highly specialized Pseudodiophrys nests within Diophrys.

Figure optionsDownload as PowerPoint slideHighlights
► The monophyly of Paradiophrys and the establishment of Apodiophrys are well supported by multi-gene combined data.
► Three-gene analyses support separating Diophryopsis from the well-known Diophrys.
► Internal branches within Uronychiidae receive stronger support in the three-gene combined analyses.
► Nine new SSU-rDNA sequences and 39 new sequences from the ITS1-5.8S-ITS2 and LSU-rDNA loci for 24 taxa are supplied.