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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., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Taxon sampling for molecular phylogenetic inferences of microbial eukaryotes is limited because of the difficulties in finding specific taxa and culturing them. By contrast, unidentified sequences are easily collected during environmental diversity surveys. Here taxon sampling within prorodontid ciliates is increased using identified cultured isolates, and complemented with unidentified environmental sequences, with the nuclear small subunit rDNA locus. With identified cultured isolates there is support for the morphologically-circumscribed Colepidae. Increasing taxon sampling with unidentified environmental sequences is shown to change both topology and node support in clades that have low sampling for identified cultured isolates. This approach to increasing taxon sampling using unidentified environmental sequences can be used in other ciliate clades in which there is also low taxon sampling., (Copyright © 2010 Elsevier Inc. All rights reserved.)

The ciliate class Colpodea provides a powerful case in which a molecular genealogy can be compared to a detailed morphological taxonomy of a microbial group. Previous analyses of the class using the small-subunit rDNA are based on sparse taxon sampling, and are therefore of limited use in comparisons with morphologically-based classifications. Taxon sampling is increased here to include all orders within the class, and more species within previously sampled orders and in the species rich genus Colpoda. Results indicate that the Colpodea may be paraphyletic, although there is no support for deep nodes. The orders Bursariomorphida, Grossglockneriida, and Sorogenida are monophyletic. The orders Bryometopida, Colpodida, and Cyrtolophosidida, and the genus Colpoda, are not monophyletic. Although congruent in many aspects, the conflict between some nodes on this single gene genealogy and morphology-based taxonomy suggests the need for additional markers as well as a reassessment of the Colpodea taxonomy.