Eukaryogenesis: Did an Oxidative Crucible Result in Misleading Bioinformatic Analyses?

Recently, Nature published a large-scale analysis ("Dated gene duplications elucidate the evolutionary assembly of eukaryotes" by Christopher Kay and co-workers) that seems to put an end to symbiogenic models for eukaryogenesis. They state that the pre-mitochondrion arrives late, after practically all of the signature eukaryotic characteristics have evolved independently. However, this conclusion is based on reconstructed timescales for the gene duplications allowing these crucial eukaryotic cell functions. The reconstruction might be fundamentally flawed, because enhanced internal ROS formation upon endosymbiont entry would lead to both high mutation rates and strong selection for antioxidant as well as repair functions. As the endosymbiont had co-evolved with molecular oxygen, while the archaeal host had not, a phylogenetic analysis might misconstrue the higher rate of change in the host as indicative of much longer timescales for host gene duplications.