archaebacterial origin of eukaryotes

The origin of the eukaryotic genetic apparatus is thought to be central to understanding the evolution of the eukaryotic cell. Disagreement about the source of the relevant genes has spawned competing hypotheses for the origins of the eukaryote nuclear lineage. The iconic rooted 3-domains tree of li...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2008-12, Vol.105 (51), p.20356-20361
Main Authors: Cox, Cymon J, Foster, Peter G, Hirt, Robert P, Harris, Simon R, Embley, T. Martin
Format: Article
Language:English
Subjects:
Amino acids
Archaea
Archaebacteria
Bacteria
Base composition
Biological Evolution
Biological Sciences
Cells
Chemical composition
Crenarchaeota - genetics
Eukaryotes
Eukaryotic Cells
Genes
Genes, Archaeal - genetics
Genes, Bacterial - genetics
Genetics
Genomes
Genomics
Modeling
Models, Genetic
Nucleic Acids - genetics
Phylogenetics
Phylogeny
Protein Biosynthesis - genetics
Simulations
Transcription, Genetic - genetics
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Summary:The origin of the eukaryotic genetic apparatus is thought to be central to understanding the evolution of the eukaryotic cell. Disagreement about the source of the relevant genes has spawned competing hypotheses for the origins of the eukaryote nuclear lineage. The iconic rooted 3-domains tree of life shows eukaryotes and archaebacteria as separate groups that share a common ancestor to the exclusion of eubacteria. By contrast, the eocyte hypothesis has eukaryotes originating within the archaebacteria and sharing a common ancestor with a particular group called the Crenarchaeota or eocytes. Here, we have investigated the relative support for each hypothesis from analysis of 53 genes spanning the 3 domains, including essential components of the eukaryotic nucleic acid replication, transcription, and translation apparatus. As an important component of our analysis, we investigated the fit between model and data with respect to composition. Compositional heterogeneity is a pervasive problem for reconstruction of ancient relationships, which, if ignored, can produce an incorrect tree with strong support. To mitigate its effects, we used phylogenetic models that allow for changing nucleotide or amino acid compositions over the tree and data. Our analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0810647105