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The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise

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Abstract

Phylogenetic trees based on gene repertoires are remarkably similar to the current consensus of life history. Yet it has been argued that shared gene content is unreliable for phylogenetic reconstruction because of convergence in gene content due to horizontal gene transfer and parallel gene loss. Here we test this argument, by filtering out as noise those orthologous groups that have an inconsistent phylogenetic distribution, using two independent methods. The resulting phylogenies do indeed contain small but significant improvements. More importantly, we find that the majority of orthologous groups contain some phylogenetic signal and that the resulting phylogeny is the only detectable signal present in the gene distribution across genomes. Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree.

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Authors and Affiliations

  1. Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, University of Nijmegen, Nijmegen, The Netherlands

    Bas E. Dutilh, Martijn A. Huynen & Berend Snel

  2. Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

    William J. Bruno

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  1. Bas E. Dutilh
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  2. Martijn A. Huynen
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  3. William J. Bruno
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  4. Berend Snel
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Correspondence to Bas E. Dutilh.

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Dutilh, B.E., Huynen, M.A., Bruno, W.J. et al. The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise . J Mol Evol 58, 527–539 (2004). https://doi.org/10.1007/s00239-003-2575-6

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