The evolution of mitochondrial genomes in subterranean caviomorph rodents: Adaptation against a background of purifying selection

► Evolution of mitochondrial genes dominated by purifying selection (ω ratio <1). ► Two approaches suggest a link between weak/episodic selection and niche shift. ► Significantly higher ω ratio in mitochondrial genes of subterranean groups. ► Significant physicochemical changes concentrated in subterranean lineages. ► Some changes shared with others groups adapted to hypoxia.