An updated phylogeny of the reveals that the parasitic and have independent origins.

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