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 (NUMT) may harbor 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: (1) recent introgression from another species and (2) long-term selection. To investigate whether these intriguing possibilities play a role, we scanned the genomes of more than 1000 avian and mammalian species for NUMTs. We show that a subclass of divergent NUMTs harboring mitogenes with intact reading frames is widespread across mammals and birds. We also show that some of these NUMTs appear to be similar across species. In addition, we 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.