An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins

Abstract

The <i>Alphaproteobacteria</i> 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 <i>Rickettsiales</i> and <i>Holosporales</i> (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the <i>Holosporales</i> has a derived position within the <i>Rhodospirillales</i>. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the <i>Alphaproteobacteria</i>. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the <i>Alphaproteobacteria</i>.