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The universal tree of life: an update.

Forterre P - Front Microbiol (2015)

Bottom Line: This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway.Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase.These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

View Article: PubMed Central - PubMed

Affiliation: Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur , Paris, France ; Institut de Biologie Intégrative de la cellule, Université Paris-Saclay , Paris, France.

ABSTRACT
Biologists used to draw schematic "universal" trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese's universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

No MeSH data available.


Related in: MedlinePlus

Schematic simplified universal tree updated from Woese et al. (1990). Abbreviations are the same as in Figure 3.
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Figure 4: Schematic simplified universal tree updated from Woese et al. (1990). Abbreviations are the same as in Figure 3.

Mentions: Since all rooting indicated in the tree of Figure 3, as well as most internal nodes within domains, are controversial, I present a second tree (Figure 4), in which the information is limited to only that accepted by consensus. Accordingly, each one of the three domains is shown in a radial form without roots and only a few nodes within domains that seem supported by strong phylogenetic analyses are indicated (Brochier-Armanet et al., 2008a; He et al., 2014; Kamke et al., 2014; Ramulu et al., 2014; Spang et al., 2015).


The universal tree of life: an update.

Forterre P - Front Microbiol (2015)

Schematic simplified universal tree updated from Woese et al. (1990). Abbreviations are the same as in Figure 3.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508532&req=5

Figure 4: Schematic simplified universal tree updated from Woese et al. (1990). Abbreviations are the same as in Figure 3.
Mentions: Since all rooting indicated in the tree of Figure 3, as well as most internal nodes within domains, are controversial, I present a second tree (Figure 4), in which the information is limited to only that accepted by consensus. Accordingly, each one of the three domains is shown in a radial form without roots and only a few nodes within domains that seem supported by strong phylogenetic analyses are indicated (Brochier-Armanet et al., 2008a; He et al., 2014; Kamke et al., 2014; Ramulu et al., 2014; Spang et al., 2015).

Bottom Line: This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway.Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase.These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

View Article: PubMed Central - PubMed

Affiliation: Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur , Paris, France ; Institut de Biologie Intégrative de la cellule, Université Paris-Saclay , Paris, France.

ABSTRACT
Biologists used to draw schematic "universal" trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese's universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

No MeSH data available.


Related in: MedlinePlus