Mitochondria branch within Alphaproteobacteria

It is well accepted that mitochondria originated from an alphaproteobacterial-like ancestor. However, the phylogenetic relationship of the mitochondrial endosymbiont to extant alphaproteobacteria remains a subject of discussion. The focus of much debate is whether the affiliation between mitochondria and fast-evolving alphaproteobacterial lineages reflects true homology or artifacts. Approaches such as protein-recoding and site-exclusion have been claimed to mitigate compositional heterogeneity between taxa but this comes at the cost of information loss and the reliability of such methods is so far unjustified. Here we demonstrate that site-exclusion methods produce erratic phylogenetic estimates of mitochondrial origin. We applied alternative strategies to reduce phylogenetic noise by taxon replacement and selective exclusion while keeping site substitution information intact. Cross-validation based on a series of trees placed mitochondria robustly within Alphaproteobacteria.