Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea).

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.