Discussion of Phylogenetic Relationships
Fornicata are traditionally classified into Diplomonadida, Retortamonadida, Carpediemonas, and Dysnectes. Diplomonadida and Retortamonadida have been regarded as closely related and together they constitute the taxon Eopharyngia (the term refers to the extensively developed cytopharynx of diplomonads and retortamonads). The hypothesis of Eopharyngia was supported by molecular-phylogenetic studies which included sequences of Retortamonas and several diplomonad genera.
At first, the studies based on the SSU rRNA gene (Silberman et al. 2002; Kolisko et al. 2005; Keeling and Brugerolle 2006) indicated that diplomonads may not be monophyletic and that Retortamonas may be sister to the Giardiinae diplomonad lineage. However, the analysis based on the hsp90 gene showed that diplomonads are monophyletic and that Retortamonas forms their sister lineage, which was consistent with previous morphology-based hypotheses.
Sequence data of the second retortamonads genus, Chilomastix, have been obtained quite recently (Cepicka et al. 2008). Interestingly, instead of being specifically related to Retortamonas, Chilomastix branched with strong statistical support more basally and formed a sister branch to the Retortamonas , Diplomonadida clade. This means that Retortamonadida may not be monophyletic and that Diplomonadida may be, in fact, an internal lineage of Retortamonadida. In that case, ancestors of Diplomonadida must once have possessed retortamonadid morphological characters, notably the microtubular corset. An unpublished TEM study of Retortamonas suggests that the representatives of the genus for which the sequence data has been obtained lack the microtubular corset which further supports their close relationship with diplomonads. On the other hand, the microtubular corset has been reported from some other Retortamonas species, and it is probable that the genus is not monophyletic.
Former morphological hypotheses always assumed that the unizoic “enteromonads” are either sister to the diplozoic diplomonads, or form a basal paraphyletic grade. Based on the presence or absence of cytostomes, diplozoic diplomonads were divided into Hexamitinae and Giardiinae. While molecular-phylogenetic studies supported the division of diplozoic diplomonads into Hexamitinae and Giardiinae lineages (Keeling and Brugerolle 2006), it turned out that the phylogenetic position of “enteromonads” is rather interesting and was not predicted by any of the former hypotheses. In SSU rRNA and hsp90 trees, unizoic enteromonads form several independent branches within the Hexamitinae lineage (Kolisko et al. 2008). This close relationship is further supported by the use of a non-canonical genetic code (TAA and TAG triplets encode glutamine instead of stop codons) by Hexamitinae and “enteromonads” (Keeling and Doolittle 1996; Kolisko et al. 2008). It indicates that either diplozoic diplomonads arose several times independently from unizoic cells or that unizoic enteromonads arose several times independently from diplozoic diplomonads.
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