Termite gut flagellates belong to three distinct taxa: trichomonads, hypermas-tigids, and oxymonads (Yamin 1979). Originally, all were considered primitive, primarily amitochondriate eukaryotes, but recent molecular data proved that they represent two separate eukaryotic lineages.

Phylogenetic analyses of the termite gut flagellates by various groups (reviewed by Ohkuma 2003; Gerbod et al. 2004), mainly based on 18S rRNA gene sequence analysis, confirmed the presence of two classes of the phylum Parabasalia, the Trichomonadea and Hypermastigea (Cavalier-Smith 2002), the latter representing the most basal lineage.

The phylogeny of Oxymonadea was long in the dark. Comparative sequence analysis revealed that they are a sister taxon to the excavate protists (Moriya et al. 1998, 2001, 2003; Dacks et al. 2001; Stingl and Brune 2003); they are now classified in the phylum Loukozoa (Cavalier-Smith 2002).

While Hypermastigea consist exclusively of termite gut symbionts, the Oxymonadea and the Trichomonadea comprise also species occurring in other habitats, such as the intestinal tract or body cavities of other animals, including humans.

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