The ring of life provides evidence for a genome fusion origin of eukaryotes

@article{Rivera2004TheRO,
  title={The ring of life provides evidence for a genome fusion origin of eukaryotes},
  author={Maria C. Rivera and James Alan Lake},
  journal={Nature},
  year={2004},
  volume={431},
  pages={152-155}
}
Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our… 
Decoding the genomic tree of life
TLDR
A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved the prospects for reconstructing prokaryotic evolution and is able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote.
Comprehensive analysis of the origin of eukaryotic genomes.
TLDR
The results suggest the eukaryotic nuclear genome descends from an archaea that was neither euryarchaeota nor cren archaeota and that the mitochondrial genome descending from alpha-proteobacteria.
Supertrees disentangle the chimerical origin of eukaryotic genomes.
TLDR
A novel supertree-based phylogenetic signal-stripping method is used to recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes and rejects all but two of the current hypotheses for the origin of eukaryotes.
Genomic Analyses and the Origin of the Eukaryotes
TLDR
CR is the first phylogenetic‐reconstruction method to provide precise evidence about the origin of the eukaryotes, and a cycle graph or ‘ring’ rather than a ‘tree’ is a better representation of the evolutionary relationships between prokaryotes and eukARYotes.
Genome beginnings: rooting the tree of life
TLDR
A new root of life obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets is introduced, implying that the last common ancestor was not hyperthermophilic, although moderate thermophily cannot be excluded.
The tree of life viewed through the contents of genomes.
  • C. House
  • Biology
    Methods in molecular biology
  • 2009
TLDR
Genomic trees and geologic evidence together suggest that the vertical descent of genes and the horizontal transfer of genes between genetically similar lineages ultimately results in a core Tree of Life with at least some lineages that have phenotypic characteristics recognizable for billions of years.
Does the 'Ring of Life' ring true?
The Deep Archaeal Roots of Eukaryotes
TLDR
A comprehensive set of 355 eukaryotic genes of apparent archaeal origin identified through ortholog detection and phylogenetic analysis is described and it is indicated that, for the majority of these genes, the preferred tree topology is one with the eUKaryotic branch placed outside the extant diversity of archaea.
Phylogenomic Test of the Hypotheses for the Evolutionary Origin of Eukaryotes
TLDR
The results demonstrate that there is no phylogenetic support for hypotheses involving a fusion with a bacterium other than the ancestor of mitochondria, and it is shown that the majority of bacteria-related eukaryotic genes actually do not point to a relationship with a specific bacterial taxonomic group.
Bacterial genes outnumber archaeal genes in eukaryotic genomes
TLDR
The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involvement in metabolic processes is conserved across all eukaryotic supergroups.
...
...

References

SHOWING 1-10 OF 65 REFERENCES
Whole genome-based phylogenetic analysis of free-living microorganisms.
TLDR
A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms, indicating a single robust underlying evolutionary history for these organisms.
The genomic tree as revealed from whole proteome comparisons.
TLDR
The genomic trees presented here place the Archaea in the proximity of the Bacteria when the whole gene content of each organism is considered, and when ancestral gene duplications are eliminated.
Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences
TLDR
Using evolutionary parsimony, a newly developed rate-invariant treeing algorithm, the eukaryotic ribosomal rRNA genes are shown to have evolved from the eocytes, a group of extremely thermophilic, sulphur-metabolizing, anucleate cells that probably lacked nuclei, metabolized sulphur and lived at near-boiling temperatures.
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history.
TLDR
An attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny, by performing a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny.
Genome trees constructed using five different approaches suggest new major bacterial clades
TLDR
Extension of phylogenetic analysis to the genome scale has the potential of uncovering deep evolutionary relationships between prokaryotic lineages, and put into question the sister-group relationship between the two major archaeal groups, Euryarchaeota and CrenarchAEota, and suggest instead that Eury Archaeota might be a paraphyletic group with respect to Cren archaeota.
Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.
TLDR
A composite phylogenetic tree with two clusters corresponding to different proteins, from which the evolutionary relationship of the primary kingdoms is determined uniquely is proposed, revealing that archaebacteria are more closely related to eukaryotes than to eubacteria for all the cases.
Genomic evidence for two functionally distinct gene classes.
TLDR
Comparisons of the entire set of Methanococcus jannaschii genes with their orthologs from Escherichia coli, Synechocystis 6803, and the yeast Saccharomyces cerevisiae show that prokaryotic genomes consist of two different groups of genes.
A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.
TLDR
It is indicated that at the levels of overall amino acid sequence identity and gene content, yeast shares a sister-group relationship with eubacteria, not with archaebacteria, in contrast to the current phylogenetic paradigm based on ribosomal RNA.
Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes
TLDR
Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria and suggests that this evolution occurred in response to antibiotic selection pressures, and an alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed.
Phylogenetic Classification and the Universal Tree
TLDR
Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.
...
...