Phylogenetic ancestry of Metamonada proteins points to a common origin of mitochondria in all eukaryotes.

Hypotheses concerning eukaryogenesis, the evolution of eukaryotic cells, differ in the relative timing of mitochondrial acquisition. Recently, a serial endosymbiotic hypothesis proposed that hydrogenosomes and mitosomes (MROs) in Metamonada originated from an independent endosymbiosis, later replaced by Alphaproteobacteria-related mitochondria, contradicting the paradigm of mitochondrial presence in the last eukaryotic common ancestor. This serial endosymbiotic hypothesis implicitly predicts the scarcity of alphaproteobacterial genes from Metamonada genomes, because they never contained this endosymbiont. We tested this prediction using a set of 1,399 and 97 proteins inferred for the Metamonada ancestor and confined to their MROs, respectively. We detected five and 14 orthologous groups (OGs) with alphaproteobacterial affiliation in the respective datasets. None of these OGs was present in oxymonads, a Metamonada subgroup lacking MROs, thus serving as blank references. Our data are therefore consistent with the ruling paradigm that mitochondria and MROs originated from an Alphaproteobacterium during a single common endosymbiosis.