Phylogenetic position of the ciliates Phacodinium (Order Phacodiniida) and Protocruzia (Subclass Protocruziidia) and systematics of the spirotrich ciliates examined by small subunit ribosomal RNA gene sequences

The small subunit rRNA (SSrRNA) genes were sequenced for Protocruzia sp2, Phacodinium metchnicoffi, Holosticha multistylata, and Halteria grandinella. All four genera are placed within the Class Spirotrichea with strong bootstrap support in both distance matrix and parsimony tree construction methods and by maximum likelihood analysis using quartet puzzling. Protocruzia sp2 groups with Protocruzia sp1 with 100% bootstrap support, and the 5.6% genetic difference between them strongly argues that they are different species although they are morphologically quite similar. The Protocruzia species branch first in the spirotrich clade at a deep level, supporting their recognition as a Subclass Protocruziidia. Phacodinium branches after Euplotes at a deep level, confirming the conclusion that others have reached that this genus is related to the hypotrich and stichotrich spirotrichs. Phacodinium is assigned to its own family and order, and we conclude that the deep branching within the spirotrichs argues for its own subclass, the Subclass Phacodiniidia. Consistent with the partial SSrRNA sequences and with the sequence of a polymerase gene, Halteria groups within the stichotrich clade, supporting the argument that the oligotrichs are not monophyletic as currently conceived. Finally, Holosticha, which has been assigned to the Order Urostylida, groups outside the stichotrichs with parsimony analysis, which is consistent with this ordinal assignment. However, it is associated with Halteria and Oxytricha granulifera in the other analyses. Additional stichotrich sequences obviously are required before we can confidently begin revision of the Subclass Stichotrichia.