Figure 2: Two contrasting phylogenies of the same universal protein. Schematic representation of two published phylogenies of a universal protein known under different names (YgjD, YeaZ, Kae1/OSGEP, and Qri7/OSGEP L) which is involved in the biosynthesis of the universal tRNA modified base t6A [54]. These simplified phylogenies are adapted from Figure S46 in [55] (left panel) and from Figure S1 in [56] (right panel). Squares indicate unresolved nodes, whereas triangles indicate resolve nodes. The tree on the right is congruent with firmly established biological knowledge such as the monophyly of bacteria and eukarya, the bacterial origin of mitochondria. It favours the classical three-domain tree of Woese and colleagues. The tree on the left, which is not resolved, with aberrant paraphyly of archaea (see for instance the position of Nanoarchaeum equitans) was nevertheless used by the authors to support the “eocyte tree”. Comparison of these trees clearly reveals that the methodology (data sampling and/or algorithm for tree reconstruction) used by Cox and co-workers [55] for phylogenetic analyses cannot recover correct phylogenies for universal proteins.