Oxymonads are closely related to the excavate taxon Trimastix

Despite intensive study in recent years, large-scale eukaryote phylogeny re mains poorly resolved. This is particularly problematic among the groups co nsidered to be potential early branches. In many recent systematic schemes for early eukaryotic evolution, the amitochondriate protists oxymonads and Trimastix have figured prominently, having been suggested as members of man y of the putative deep-branching higher taxa. However, they have never befo re been proposed as close relatives of each other. We amplified, cloned, an d sequenced small-subunit ribosomal RNA genes from the oxymonad Pyrsonympha and from several Trimastix isolates. Rigorous phylogenetic analyses indica te that these two protist groups are sister taxa and are not clearly relate d to any currently established eukaryotic lineages. This surprising result has important implications for our understanding of cellular evolution and high-level eukaryotic phylogeny. Given that Trimastix contains small, elect ron-dense bodies strongly suspected to be derived mitochondria, this study constitutes the best evidence to date that oxymonads are not primitively am itochondriate. Instead, Trimastix and oxymonads may be useful organisms for investigations into the evolution of the secondary amitochondriate conditi on. All higher taxa involving either oxymonads or Trimastix may require mod ification or abandonment. Affected groups include four contemporary taxa gi ven the rank of phylum (Metamonada. Loukozoa, Trichozoa, Percolozoa), and t he informal excavate taxa. A new "phylum-level" taxon may be warranted for oxymonads and Trimastix.