Not the most basal eukaryotes: challenges and pitfalls affecting the placement of Giardia and Trichomonas

Abstract

Diplomonads (including Giardia) and parabasalids (including Trichomonas) have traditionally been seen as the deepest‐branching eukaryotes, on the evidence of apparently simple ultrastructural morphology, and small subunit ribosomal RNA trees. However, this position does not appear to be well supported, especially in the light of the discoveries of apparent mitochondrial remnants in Giardia and Trichomonas. We systematically re‐analysed protein data, and show here that their traditional placement may be due to a combination of factors acting on data sets (narrow taxon sampling) and on genes (rate heterogeneity and compositional heterogeneity, mutational saturation). Our data found no consistent support for either Giardia or Trichomonas being basal eukaryotes.