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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 universal tree updated from Woese et al. (1990) and modified according to the “eocyte” hypothesis. Abbreviations are the same as in Figure 3. In this configuration, Archaea is no more a valid taxon since “Archaea” are paraphyletic (LACA is also an ancestor of Eukarya) suggesting using the suffix karyota for the various “archaeal” phyla. Together with Eukarya, these phyla became various phyla of Arkarya.
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Figure 5: Schematic universal tree updated from Woese et al. (1990) and modified according to the “eocyte” hypothesis. Abbreviations are the same as in Figure 3. In this configuration, Archaea is no more a valid taxon since “Archaea” are paraphyletic (LACA is also an ancestor of Eukarya) suggesting using the suffix karyota for the various “archaeal” phyla. Together with Eukarya, these phyla became various phyla of Arkarya.

Mentions: The rooting of the universal tree in the so-called “bacterial branch” (Figures 3–5) has been often interpreted as suggesting a “prokaryotic phenotype” for LUCA. This is a misleading interpretation that again confuses the phenotypes at the tip and base of a branch. The rooting between a lineage leading to Bacteria and a lineage leading to Archaea and Eukarya is compatible with diverse types of LUCA, including a LUCA with some “eukaryotic-like features” that were lost in Archaea and Bacteria (Forterre, 2013a).


The universal tree of life: an update.

Forterre P - Front Microbiol (2015)

Schematic universal tree updated from Woese et al. (1990) and modified according to the “eocyte” hypothesis. Abbreviations are the same as in Figure 3. In this configuration, Archaea is no more a valid taxon since “Archaea” are paraphyletic (LACA is also an ancestor of Eukarya) suggesting using the suffix karyota for the various “archaeal” phyla. Together with Eukarya, these phyla became various phyla of Arkarya.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Schematic universal tree updated from Woese et al. (1990) and modified according to the “eocyte” hypothesis. Abbreviations are the same as in Figure 3. In this configuration, Archaea is no more a valid taxon since “Archaea” are paraphyletic (LACA is also an ancestor of Eukarya) suggesting using the suffix karyota for the various “archaeal” phyla. Together with Eukarya, these phyla became various phyla of Arkarya.
Mentions: The rooting of the universal tree in the so-called “bacterial branch” (Figures 3–5) has been often interpreted as suggesting a “prokaryotic phenotype” for LUCA. This is a misleading interpretation that again confuses the phenotypes at the tip and base of a branch. The rooting between a lineage leading to Bacteria and a lineage leading to Archaea and Eukarya is compatible with diverse types of LUCA, including a LUCA with some “eukaryotic-like features” that were lost in Archaea and Bacteria (Forterre, 2013a).

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