Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree

  title={Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree},
  author={Manolo Gouy and Wen-Hsiung Li},
HOW many primary lineages of life exist and what are their evolutionary relationships? These are fundamental but highly controversial issues1. Woese and co-workers2–4 propose that archaebacteria, eubacteria and eukaryotes are the three primary lines of descent and their relationships can be represented by Fig. 1a (the 'archaebacterial tree') if one neglects the root of the tree. In contrast, Lake5,6 claims that archaebacteria are paraphyletic, and he groups eocytes (extremely thermophilic… 
Radical views of the tree of life.
  • H. Ochman
  • Biology
    Environmental microbiology
  • 2009
The tripartite division of cellular organisms into three domains – the Bacteria, the Archaea and the Eukarya – has become so ingrained that most of us have all but forgotten (or did not even know)
Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes
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.
Evolution of Archaebacteria: Phylogenetic Relationships Among Archaebacteria, Eubacteria, and Eukaryotes
Using pairs of duplicated genes, elongation factors Tu and G and the catalytic and noncatalytic subunits of ATPase, a composite phylogenetic tree is inferred from which the evolutionary relationship among the urkingdoms is determined uniquely.
Protein-based phylogenies support a chimeric origin for the eukaryotic genome.
The hypothesis of a chimeric origin for the eukaryotic cell nucleus formed from the fusion of an archaebacteria and a gram-negative bacteria is supported.
Archaea and the origin of eukaryotes
A brief history of the changing shape of the tree of life is outlined and how the recent discovery of a myriad of diverse archaeal lineages has changed the authors' understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes is examined.
Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.
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.
Genome beginnings: rooting the tree of life
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.
Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the archaeal domain
Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), which support the archaeal tree and disprove the “eocyte tree”.
Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes.
It is shown that universal phylogenies of ribosomal RNAs and RNA polymerases built by ignoring variation are biased toward the archaebacterial tree because of attraction between long branches, while taking among-site rate variability into account gives support for the eocyte tree.


The Origin of Eukaryote and Archaebacterial Cells
It is argued that the most primitive eukaryote was a phagotrophic archezoan, with no chloroplasts, no mitochondria, no microbodies, and no stacked smooth cisternae forming a Golgi dictyosome, but possessing a single cilium with a sheaf of rootlet microtubules surrounding the single nucleus that divided by a closed mitosis.
Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences
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.
Reintedness of archaebacterial RNA polymerase core subunits to their eubacterial and eultaryotic equivalents
The sequence of the genes encoding the four largest subunits of the RNA polymerase of the archaebacterium Methanobacterium thermoautotrophicum was determined and putative translation signals were
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
  • C. Woese, G. Fox
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1977
A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: the eubacteria, comprising all typical bacteria, the archaebacteria, and the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony.
  • J. Lake
  • Biology
    Molecular biology and evolution
  • 1987
The method of evolutionary parsimony accurately predicts the tree, even when substitution rates differ greatly in neighboring peripheral branches (conditions under which parsimony will consistently fail), as the number of substitutions in peripheral branches becomes fewer, the parsimony and the evolutionary-parsimony solutions converge.
  • J. Felsenstein
  • Economics
    Evolution; international journal of organic evolution
  • 1985
The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
On the Problem of Discovering the Most Parsimonious Tree
  • W. Fitch
  • Biology
    The American Naturalist
  • 1977
An alternative approach, using a Prim-Kruskal network on the avoidable discordancy distances, is given together with a procedure for interpreting such networks in terms of a phylogeny that appears more natural than the dendrograms usually employed in the interpretation of singlelinkage diagrams.