Fan et al. challenge the finding that mitochondria represent a sister group to Alphaproteobacteria1, arguing that support for thisposition can be explained by unreliable site removal methods andoutgroup attraction. The authors chose to reduce compositionalheterogeneity by replacing AT-rich Rickettsiales and mitochondriawith GC-rich alternatives and attempted to attenuate long branchattraction (LBA) effects by removing all fast-evolving lineages butone. The study suggests that mitochondria form a sister clade toRickettsiales, within the ‘Alpha-II’ clade. Here we show that the association with Alpha-II is an artefact caused by a problematic taxonand that residual support for Rickettsiales-sister can be explained byconvergent evolution of the selected mitochondria and Rickettsialestowards high %GC. We further argue that site removal methods arein fact reliable and that outgroup attraction is unlikely to explain theAlphaproteobacteria-sister tree
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