Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes

Sporadically genetic material that originates from an organelle genome integrates into the nuclear genome. However it is unclear what processes maintain such integrations over evolutionary time. Recently it was shown that nuclear DNA of mitochondrial origin (NUMTs) may harbour genes with intact mitochondrial reading frames despite the fact that they are highly divergent from the host's mitochondrial genome. Two major hypotheses have been put forward to explain the existence of such mitocoding nuclear genes: (i) recent introgression from another species and (ii) long-term selection. To investigate whether these intriguing possibilities play a role we scanned the genomes of more than 1,000 avian and mammalian species for NUMTs. We show that the subclass of divergent NUMTs harbouring mitogenes with intact reading frames are widespread across mammals and birds. We show that some of these NUMTs appear to have similarity across species. We also demonstrate that many mitochondrial-coding NUMTs exhibit signs of long-term selection. In a subset of these NUMT genes, we detected evolutionary signals consistent with adaptive evolution, including one human NUMT shared among seven ape species. These findings suggest that NUMT insertions may occasionally be functional.