Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.

TLDR

All extant organisms are classified into eubacteria, archaebacteria, and eukaryotes, but single‑molecule phylogenetic studies have failed to resolve their exact evolutionary relationships because the tree root cannot be uniquely determined. The study aimed to determine the evolutionary relationship among archaebacteria, eubacteria, and eukaryotes by comparing duplicated genes (elongation factors Tu and G and ATPase alpha and beta subunits) and proposing the resulting tree topology as the general relationship. Composite phylogenetic trees were constructed from each duplicated protein pair, yielding two clusters that uniquely resolved the evolutionary relationships among the primary kingdoms. The composite trees consistently placed archaebacteria closer to eukaryotes than to eubacteria, with bootstrap support of 0.96–1.0, and the authors propose this topology as the general evolutionary relationship among the three kingdoms.

Abstract

All extant organisms are though to be classified into three primary kingdoms, eubacteria, eukaryotes, and archaebacteria. The molecular evolutionary studies on the origin and evolution of archaebacteria to date have been carried out by inferring a molecular phylogenetic tree of the primary kingdoms based on comparison of a single molecule from a variety of extant species. From such comparison, it was not possible to derive the exact evolutionary relationship among the primary kingdoms, because the root of the tree could not be determined uniquely. To overcome this difficulty, we compared a pair of duplicated genes, elongation factors Tu and G, and the alpha and beta subunits of ATPase, which are thought to have diverged by gene duplication before divergence of the primary kingdoms. Using each protein pair, we inferred a composite phylogenetic tree with two clusters corresponding to different proteins, from which the evolutionary relationship of the primary kingdoms is determined uniquely. The inferred composite trees reveal that archaebacteria are more closely related to eukaryotes than to eubacteria for all the cases. By bootstrap resamplings, this relationship is reproduced with probabilities of 0.96, 0.79, 1.0, and 1.0 for elongation factors Tu and G and for ATPase subunits alpha and beta, respectively. There are also several lines of evidence for the close sequence similarity between archaebacteria and eukaryotes. Thus we propose that this tree topology represents the general evolutionary relationship among the three primary kingdoms.