Pelobionts (Archamoebae sensu Cavalier-Smith 1991) lack mitochondria and are mostly free-living, heterotrophic, amoeboid, flagellated protists that inhabit organically enriched, microoxic, or anoxic freshwater and marine environments (Schulze 1877; Penard 1921; Brugerolle 1993). Because of their ultrastructural simplicity and the basal position of many amitochondriate parasitic portists in ribosomal RNA phylogenies (Sogin 1997), pelobionts were hypothesized to represent one of the earliest diverging eukaryotic lineages (Margulis 1970; Whatley 1976; Griffin 1979; Cavalier-Smith 1983; Griffin 1988; Whatley & Chapman-Andresen 1990; Cavalier-Smith 1991; Brugerolle 1993; Patterson 1994). However, molecular data support conflicting hypotheses about the monophyly and phylogenetic placement of pelobionts. Early analyses of small subunit rRNAs (SSU rRNA) (Hinkle et al. 1994) and partial sequences of large subunit rRNAs (LSU rRNA) (Morin & Mignot 1995) show that the pelobiont Mastigamoeba balamuthi (= Phreatoamoeba balamuthi [Simpson et al. 1977]) diverged relatively late among eukaryotes. In contrast, a phylogenetic analysis of DNA-dependent RNA polymerase II (RPB1) genes (Stiller, Duffield & Hall 1998) placed a sequence from an organism identified as M. invertens as one of the most basal eukaryotes.
Discrepancies between inferences from cytology and RPB1 versus LSU rRNA and SSU rRNA data prompted Stiller and Hall (1999) to examine the position of M. invertens in SSU rRNA trees. Their initial maxium likelihood (ML)-based analysis did not cluster M. invertens with the other pelobiont sequences, nor were they basal to other eukaryotes. Stiller and Hall hypothesized that long-branch attractions (LBA) or skewed base compostions in rRNAs account for conflicting phylogenies of SSU rRNAs and RNA polymerases. When the rapidly evolving lineages were removed from that anylsis, the two pelobionts formed a monophyletic group basal to other eukaryotes, but the GC content of half of the basal branches was not aberrant and was unlikely to impact the analysis.