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MBE Advance Access published online on May 15, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm095
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Supertrees Disentangle the Chimeric Origin of Eukaryotic Genomes

Davide Pisani, James A. Cotton and James O. McInerney

Department of Biology, The National University of Ireland, Maynooth. Maynooth, Co. Kildare, Ireland

Corresponding Author: James O. McInerney, Department of Biology, The National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland. Email: james.o.mcinerney{at}nuim.ie, P: +353 1 708 3860, F: +353 1 708 3845

Received for publication March 13, 2007. Revision received May 9, 2007. Accepted for publication May 9, 2007.

Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5741 single gene families distributed across 185 genomes. Using our signal-stripping method we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria and the Thermoplasmatales, an Archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria because up to 83% of eukaryotic genes with a prokaryotic homologue have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulphur- or hydrogen- dependent syntrophy for the origin of mitochondria.

Key Words: supertrees • phylogenomics • tree of life • network of life • eukaryote origins


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Mol. Biol. Evol., August 1, 2008; 25(8): 1619 - 1630.
[Abstract] [Full Text] [PDF]


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