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Diplomonads, such as Giardia, and their close relatives retortamonads have been proposed as early-branching eukaryotes that diverged before the acquisition/retention of mitochondria. We have turned our attention to studies of eukaryotes that on morphological grounds appear to be related to diplomonads. These so-called excavates include the taxon Carpediemonas. Our analyses of small subunit ribosomal ribonucleic acid (RNA) genes, α-tubulin, βtubulin, and combined α + β-tubulin, all scatter the various excavate taxa across the diversity of eukaryotes. However, all phylogenies place the excavate taxon Carpediemonas as the closest relative of diplomonads (and, where data are available, retortamonads). This novel relationship is recovered across phylogenetic methods and across various taxon-deletion experiments. Statistical support is strongest under maximum likelihood (when among-site rate variation is modelled) and when the most divergent diplomonad sequences are excluded, suggesting a true relationship rather than an artifact of long-branch attraction. While diplomonads and retortamonads lack any mitochondria-like organelle, Carpediemonas contains double membrane-bounded structures physically resembling hydrogenosomes.

Pelobionts represent another group of eukaryotes that has been identified as a potentially deep-branching eukaryotic lineage on the basis of ultrastructure and certain molecular phylogenies. Pelobionts inhabit micro-oxic and anoxic environments. Because they lack stacked dictyosomes, mitochondria, and outer dynein arms in their flagellar apparatus, pelobionts might represent early diverging eukaryotic lineages. In contrast to molecular analyses of DNA-dependent RNA polymerase II that show the putative pelobiont Mastigamoeba invertens diverged early, our analyses of SSU (small subunit) ribosomal RNAs from several new pelobiont taxa position them near the eukaryotic “crown groups,” but they are not specifically related to M. invertens. Based upon re-examination of the M. invertens structure and its failure to converge with other pelobionts in molecular analyses, we conclude that this organism was not correctly identified. Futhermore, we determined that Pelobionts are specifically related to Entamoebidae and they do not represent one of the earliest branching eukaryotic lineages.