The two-domain tree of life is linked to a new root for the Archaea

TLDR

Recent evidence suggests an archaeal origin of eukaryotes, yet this conclusion has largely relied on universal tree reconstructions. The authors employ an alternative approach using markers shared between Archaea–eukaryotes and Archaea–Bacteria, avoiding issues inherent in simultaneous three‑domain analyses. Phylogenetic comparison of these marker sets reveals eukaryotes as sister to a Thaumarchaeota/Crenarchaeota/Korarchaeota lineage and identifies a new Archaea root that reshapes our understanding of early life and Earth evolution.

Abstract

Significance An archaeal origin for eukaryotes is an exciting recent finding. Nevertheless, it has been based largely on the reconstruction of universal trees. The use of an alternative strategy based on markers shared between Archaea and eukaryotes and Archaea and Bacteria bypasses potential problems linked to the analysis of the three domains simultaneously. Comparison of the phylogenies obtained by these two complementary sets of markers supports a sister relationship between eukaryotes and the Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Crenarchaeota/Korarchaeota lineage but also robustly indicates a root of the tree of Archaea that challenges the traditional topology of this domain. This sensibly changes our perspective of the ancient evolution of the Archaea, early life, and Earth.