The Rooting of the Universal Tree of Life Is Not Reliable

Darwin provided a great unifying theory for biology; its visual expression is the universal tree of life. The tree concept is challenged by the occurrence of horizontal gene transfer and—as summarized in this review—by the omission of viruses. Microbial ecologists have demonstrated that viruses are the most numerous biological entities on earth, outnumbering cells by a factor of 10. Viral genomics have revealed an unexpected size and distinctness of the viral DNA sequence space. Comparative genomics has shown elements of vertical evolution in some groups of viruses. Furthermore, structural biology has demonstrated links between viruses infecting the three domains of life pointing to a very ancient origin of viruses. However, presently viruses do not find a place on the universal tree of life, which is thus only a tree of cellular life. In view of the polythetic nature of current life definitions, viruses cannot be dismissed as non-living material. On earth we have therefore at least two large DNA sequence spaces, one represented by capsid-encoding viruses and another by ribosome-encoding cells. Despite their probable distinct evolutionary origin, both spheres were and are connected by intensive two-way gene transfers.

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Asgard archaea do not close the debate about the universal tree of life topology

PLoS Genetics ◽

10.1371/journal.pgen.1007215 ◽

2018 ◽

Vol 14 (3) ◽

pp. e1007215 ◽

Cited By ~ 49

Author(s):

Violette Da Cunha ◽

Morgan Gaia ◽

Arshan Nasir ◽

Patrick Forterre

Keyword(s):

Tree Of Life ◽

Universal Tree

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Archaea and the prokaryote-to-eukaryote transition

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.61.4.456-502.1997 ◽

1997 ◽

Vol 61 (4) ◽

pp. 456-502

Author(s):

J R Brown ◽

W F Doolittle

Keyword(s):

Gene Evolution ◽

Phylogenetic Analyses ◽

General Pattern ◽

Tree Of Life ◽

Gene Trees ◽

Universal Tree ◽

The Status ◽

Molecular Phylogenetic ◽

Domains Of Life ◽

Cumulative Knowledge

Since the late 1970s, determining the phylogenetic relationships among the contemporary domains of life, the Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes), has been central to the study of early cellular evolution. The two salient issues surrounding the universal tree of life are whether all three domains are monophyletic (i.e., all equivalent in taxanomic rank) and where the root of the universal tree lies. Evaluation of the status of the Archaea has become key to answering these questions. This review considers our cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya. Particular attention is paid to the recent use of molecular phylogenetic approaches to reconstructing the tree of life. In this regard, the phylogenetic analyses of more than 60 proteins are reviewed and presented in the context of their participation in major biochemical pathways. Although many gene trees are incongruent, the majority do suggest a sisterhood between Archaea and Eucarya. Altering this general pattern of gene evolution are two kinds of potential interdomain gene transferrals. One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis.

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