1. Evolutionary Biology
  2. Microbiology and Infectious Disease
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An updated phylogeny of the Alphaproteobacteria reveals that the Rickettsiales and Holosporales have independent origins

  1. Sergio A Muñoz-Gómez
  2. Sebastian Hess
  3. Gertraud Burger
  4. B Franz Lang
  5. Edward Susko
  6. Claudio H Slamovits  Is a corresponding author
  7. Andrew J Roger  Is a corresponding author
  1. Dalhousie University, Canada
  2. Université de Montréal, Canada
Research Article
  • Cited 14
  • Views 3,705
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Cite this article as: eLife 2019;8:e42535 doi: 10.7554/eLife.42535

Abstract

The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.

Article and author information

Author details

  1. Sergio A Muñoz-Gómez

    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. Sebastian Hess

    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Gertraud Burger

    Department of Biochemistry, Université de Montréal, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. B Franz Lang

    Department of Biochemistry, Université de Montréal, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Edward Susko

    Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Claudio H Slamovits

    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
    For correspondence
    claudio.slamovits@dal.ca
    Competing interests
    The authors declare that no competing interests exist.
  7. Andrew J Roger

    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
    For correspondence
    Andrew.Roger@Dal.Ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1370-9820

Funding

Natural Sciences and Engineering Research Council of Canada

  • Gertraud Burger
  • B Franz Lang
  • Claudio H Slamovits
  • Andrew J Roger

Killam Trusts

  • Sergio A Muñoz-Gómez

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Antonis Rokas, Vanderbilt University, United States

Publication history

  1. Received: October 3, 2018
  2. Accepted: February 21, 2019
  3. Accepted Manuscript published: February 21, 2019 (version 1)
  4. Accepted Manuscript updated: February 22, 2019 (version 2)
  5. Accepted Manuscript updated: February 25, 2019 (version 3)
  6. Version of Record published: April 3, 2019 (version 4)

Copyright

© 2019, Muñoz-Gómez et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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