This discovery has resulted in the establishment of a new terminology to identify the major distinct groups of microbes namely, the eubacteria (the traditional or "true" bacteria) and the archaea, bacteria that diverged from other bacteria at an early stage of evolution and are distinct from the eubacteria), and eukarya (the eukaryotes).
Although Aquifex aeolicus is considered to be among the earliest-diverging bacteria on the basis of 16S rDNA phylogeny, phylogenomic analyses have identified a number of alternative partner lineages, including the Epsilon-proteobacteria and various Archaeal lineages [ 5, 24].
Apparently, many domain architectures are shared among early diverging plants, bacteria, fungi and primitive marine animals (Additional file 5, Table S5).
This inference follows from accepting the proposal that bacteria diverged first, followed by the divergence between archaea and eukaryotes [ 40].
However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.
If, we suppose, bacteria diverged first from the root, followed by the branching of archaea and eukaryotes, then the derived origin of the domain is located in the common ancestor of archaea and eukaryotes, and the bacteria never contained this domain.
Subsequently, as bacteria diverged, so did GlnRS, but it could be retained only by some bacterial phyla.
Moreover the authors favour eukaryogenesis by fusion between an Archaeon and a Bacterium, perhaps because if they assumed a common ancestor for all three Domains, their hypothesis would imply that Archaea and Bacteria diverged from a line already distinct from LUCA; this would not be in keeping with the well documented view that Archaea and Eukarya share an ancestor distinct from that of Bacteria.
For example, if rRNA doesn't perfectly track organismal history (and so is not faithful), it can still be a reliable basis for some broad generalizations (e.g. LGT is more common between groups X and Y than between X and Z, archaea and bacteria diverged very deeply in the past, etc).
By the late 1980s, we had come generally to believe in a rooted three-domain tree, with archaea and eukaryotes sisters, and bacteria more deeply diverging.
