Abstract Mitochondrial DNA (mtDNA) encodes essential bioenergetic and metabolic machinery across eukaryotes, but it is susceptible to mutational damage. The high copy number, physical location and inheritance patterns of mtDNA mean that specialist approaches to mitigate such damage are needed. A common theme across many species is segregation or ‘sorting out’ of different mtDNA types—generating variance in mutant frequencies within and between generations, so that multiscale selection can act to