Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
Sebastian Hess
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada; Institute of Zoology, University of Cologne, Cologne, Germany
Gertraud Burger
Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
B Franz Lang
Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
Edward Susko
Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada; Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
Claudio H Slamovits
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
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.
