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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

Evolution of the ribosome proteins content. The universal tree is rooted in the bacterial branch (left) or in the eukaryotic branch (right). In each case, the most parsimonious scenarios for the evolution of ribosomal proteins content are presented. The numbers of proteins present at each evolutionary steps are deduced from the distribution of homologous ribosomal proteins in the three domains of life, Archaea (A), Bacteria (B), and Eukarya (E) (adapted from the data of Lecompte et al., 2002).
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Figure 1: Evolution of the ribosome proteins content. The universal tree is rooted in the bacterial branch (left) or in the eukaryotic branch (right). In each case, the most parsimonious scenarios for the evolution of ribosomal proteins content are presented. The numbers of proteins present at each evolutionary steps are deduced from the distribution of homologous ribosomal proteins in the three domains of life, Archaea (A), Bacteria (B), and Eukarya (E) (adapted from the data of Lecompte et al., 2002).

Mentions: This is well illustrated by the case of Plantae. The endosymbiosis of a Cyanobacterium that created this eukaryotic megagroup don’t prevent evolutionists to draw a tree of Eukarya in which Plantae are represented as one branch of the tree, and not as the product of a ring (He et al., 2014). The tree of any particular taxonomic unit is indeed not affected by the presence (or absence) of endosymbionts in some of its branches! Thus, a universal tree of life depicting the three domains as three separate entities does not contradict the fusion/endosymbiotic hypotheses at the origin of Eukarya, as long as this event had no effect on the eukaryotic ribosome itself. This is not the case, because the eukaryotic ribosome is not a mixture of archaeal and bacterial ribosomes; it shares 33 proteins with archaeal ribosomes that are not present in Bacteria, but none with the bacterial ribosome that are not present in Archaea (Lecompte et al., 2002; Figure 1).


The universal tree of life: an update.

Forterre P - Front Microbiol (2015)

Evolution of the ribosome proteins content. The universal tree is rooted in the bacterial branch (left) or in the eukaryotic branch (right). In each case, the most parsimonious scenarios for the evolution of ribosomal proteins content are presented. The numbers of proteins present at each evolutionary steps are deduced from the distribution of homologous ribosomal proteins in the three domains of life, Archaea (A), Bacteria (B), and Eukarya (E) (adapted from the data of Lecompte et al., 2002).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Evolution of the ribosome proteins content. The universal tree is rooted in the bacterial branch (left) or in the eukaryotic branch (right). In each case, the most parsimonious scenarios for the evolution of ribosomal proteins content are presented. The numbers of proteins present at each evolutionary steps are deduced from the distribution of homologous ribosomal proteins in the three domains of life, Archaea (A), Bacteria (B), and Eukarya (E) (adapted from the data of Lecompte et al., 2002).
Mentions: This is well illustrated by the case of Plantae. The endosymbiosis of a Cyanobacterium that created this eukaryotic megagroup don’t prevent evolutionists to draw a tree of Eukarya in which Plantae are represented as one branch of the tree, and not as the product of a ring (He et al., 2014). The tree of any particular taxonomic unit is indeed not affected by the presence (or absence) of endosymbionts in some of its branches! Thus, a universal tree of life depicting the three domains as three separate entities does not contradict the fusion/endosymbiotic hypotheses at the origin of Eukarya, as long as this event had no effect on the eukaryotic ribosome itself. This is not the case, because the eukaryotic ribosome is not a mixture of archaeal and bacterial ribosomes; it shares 33 proteins with archaeal ribosomes that are not present in Bacteria, but none with the bacterial ribosome that are not present in Archaea (Lecompte et al., 2002; Figure 1).

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