Universal Tree of Life


The first tree of life based on the comparison of ribosomal RNA (ribonucleic acid) allowed classifying all ribosome‐encoding organisms into three domains: Archaea, Bacteria and Eukarya. Phylogenomics analyses later on show that these domains probably emerged from a last universal common ancestor (LUCA) simpler than modern organisms. Different results are however still obtained regarding the relationships between Archaea and Eukarya when relying on concatenations of universal proteins. Recent analyses have revealed that the topology obtained in these studies is strongly dependent on the universal proteins and species data sets. On the basis of this observation, our recent phylogenetic analyses presently support the sisterhood of Archaea and Eukarya. Viruses, defined as virion‐encoding organisms, cannot be formally located in the tree of life but populate it entirely from its trunk to the leaves.

Key Concepts

  • Ribosome‐encoding organisms have been classified into three domains based on their 16S ribosomal RNA sequences.
  • The last universal common ancestor (LUCA) was probably much simpler than modern organisms.
  • The tree of life can be theoretically determined from the phylogenetic analysis of universal proteins.
  • Different universal proteins strongly favour opposite scenarios for the origin of eukaryotes.
  • The addition of fast‐evolving organisms to species data sets favours the branching of eukaryotes within archaea.
  • Phylogenies of RNA polymerases, the largest universal proteins, support the monophyly of the three domains and the sisterhood of Archaea and Eukarya.
  • Viruses cannot be formally located in the universal tree of life, but infect the universal tree from the trunk to the leaves.

Keywords: tree of life; LUCA; Archaea; Bacteria; origin of eukaryotes; virus evolution

Figure 1. (a) Venn diagram representing the number of shared or specific ribosomal subunits in the ribosomes of the three domains. (b) Hypothesis of distribution of the r‐proteins along the evolution of the ribosomes, from LUCA to the three cellular domains.
Figure 2. Some specific molecular features that originated in the different branches of the universal tree of life.
Figure 3. (a) Schematic representation of an eocyte tree of life. (b) Schematic representation of a Woese tree of life.


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Further Reading

Forterre P (2016) Microbes from Hell. Chicago, IL: University of Chicago Press.

Sapp J and Fox GE (2013) The singular quest for a universal tree of life. Microbiology and Molecular Biology Reviews 77 (4): 541–550.

The Evomobil Project (2017) Archaea of the Putative Asgard Superphylum do not Close the Debate about the Universal Tree of Life Topology. https://www.the‐evomobil‐project.com/single‐post/2017/08/22/Archaea‐of‐the‐putative‐Asgard‐superphylum‐do‐not‐close‐the‐debate‐about‐the‐universal‐tree‐of‐life‐topology

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Forterre, Patrick, Da Cunha, Violette, and Gaïa, Morgan(Jun 2018) Universal Tree of Life. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001525.pub3]