An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins
- Dalhousie University, Canada
- Université de Montréal, Canada
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.
Data availability
The genome of 'Candidatus Finniella inopinata', endosymbiont of Peranema trichophorum strain CCAP 1260/1B and endosymbiont of Stachyamoeba lipophora strain ATCC 50324 were deposited in NCBI GenBank under the BioProject PRJNA501864. Raw sequencing reads were deposited on the NCBI SRA archive under the BioProject PRJNA501864. Multi-gene datasets as well as phylogenetic trees inferred in this study were deposited at Mendeley Data under the DOI: http://dx.doi.org/10.17632/75m68dxd83.1.
Article and author information
Author details
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
- Antonis Rokas, Vanderbilt University, United States
Version history
- Received: October 3, 2018
- Accepted: February 21, 2019
- Accepted Manuscript published: February 21, 2019 (version 1)
- Accepted Manuscript updated: February 22, 2019 (version 2)
- Accepted Manuscript updated: February 25, 2019 (version 3)
- 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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An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins
eLife 8:e42535.
https://doi.org/10.7554/eLife.42535
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