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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 tree of the archaeal domain. The alternative proposed roots are from : I (Brochier-Armanet et al., 2008a), II (Petitjean et al., 2014), III (Raymann et al., 2015). Thin blue arrow: emergence of pseudomurein; large green arrow, introduction of DNA gyrase from Bacteria (Raymann et al., 2014), pale blue ovals emphasize poorly resolved, controversial nodes.
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Figure 6: Schematic tree of the archaeal domain. The alternative proposed roots are from : I (Brochier-Armanet et al., 2008a), II (Petitjean et al., 2014), III (Raymann et al., 2015). Thin blue arrow: emergence of pseudomurein; large green arrow, introduction of DNA gyrase from Bacteria (Raymann et al., 2014), pale blue ovals emphasize poorly resolved, controversial nodes.

Mentions: Figure 6 illustrates a rather detailed, but schematic, archaeal tree as a tribute to this issue devoted to Archaea. This tree has been adapted from the ribosomal protein tree of Brochier-Armanet et al. (2011) and from a recent phylogeny based on the concatenation of 273 proteins conserved in at least 119 archaeal species out of 129 (Petitjean et al., 2015; thereafter called the archaeal protein tree). I also include the recently described candidate phylum “Lokiarchaeota” (corresponding to the DSAG clade) considering its importance for the discussions about the origin of Eukarya. The various roots that have been proposed for the domain Archaea are indicated by orange circles.


The universal tree of life: an update.

Forterre P - Front Microbiol (2015)

Schematic tree of the archaeal domain. The alternative proposed roots are from : I (Brochier-Armanet et al., 2008a), II (Petitjean et al., 2014), III (Raymann et al., 2015). Thin blue arrow: emergence of pseudomurein; large green arrow, introduction of DNA gyrase from Bacteria (Raymann et al., 2014), pale blue ovals emphasize poorly resolved, controversial nodes.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 6: Schematic tree of the archaeal domain. The alternative proposed roots are from : I (Brochier-Armanet et al., 2008a), II (Petitjean et al., 2014), III (Raymann et al., 2015). Thin blue arrow: emergence of pseudomurein; large green arrow, introduction of DNA gyrase from Bacteria (Raymann et al., 2014), pale blue ovals emphasize poorly resolved, controversial nodes.
Mentions: Figure 6 illustrates a rather detailed, but schematic, archaeal tree as a tribute to this issue devoted to Archaea. This tree has been adapted from the ribosomal protein tree of Brochier-Armanet et al. (2011) and from a recent phylogeny based on the concatenation of 273 proteins conserved in at least 119 archaeal species out of 129 (Petitjean et al., 2015; thereafter called the archaeal protein tree). I also include the recently described candidate phylum “Lokiarchaeota” (corresponding to the DSAG clade) considering its importance for the discussions about the origin of Eukarya. The various roots that have been proposed for the domain Archaea are indicated by orange circles.

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