Changes in selection intensity on the mitogenome of subterranean and fossorial rodents respective to aboveground species

Several rodent lineages independently acquired the ability to dig complex networks of tunnels where fossorial and subterranean species spend part or their whole life, respectively. Their underground lifestyles imposed harsh physiological demands, presumably triggering strong selective pressures on genes involved in energy metabolism like those coding for mitochondrial proteins. Moreover, underground lifestyles must have increased inbreeding and susceptibility to population bottlenecks as well as restricted migration, leading to small effective population size (Nₑ) that, in turn, must have reduced the effectiveness of selection. These stringent environmental conditions and small Nₑ might be still operating as antagonist factors of selection efficacy in these rodents. In this report, we tested, in a phylogenetic framework, how the intensity of selection on protein-coding mitochondrial genes (mt-genes) fluctuated along the evolution of fossorial and subterranean rodents respective to aboveground lineages. Our findings showed significant selection relaxation in most mt-genes of subterranean hystricomorphs (African mole-rats, tuco-tucos, and coruro), while only in three mt-genes of fossorial hystricomorphs (degus, red vizcacha rat, and fossorial spiny rats) selection efficacy was strongly reduced, probably due to demographic constraints. Conversely, selection intensification was found to have occurred in three mt-genes in fossorial sciuromorphs (ground squirrels, chipmunks, marmot, and allies). Our findings indicated that evolution of mitogenomes in fossorial and, mainly, in subterranean rodents was a complex output of a balance between intense ecological and physiological pressures, together with demographic constraints leading to genetic drift that, in turn, might have resulted in relaxed selection in hystricomorphs.