Sequential adaptive introgression of the mitochondrial genome in D rosophila yakuba and D rosophila santomea

Interspecific hybridization provides the unique opportunity for species to tap into genetic variation present in a closely related species and potentially take advantage of beneficial alleles. It has become increasingly clear that when hybridization occurs, mitochondrial DNA (mt DNA ) often crosses species boundaries, raising the possibility that it could serve as a recurrent target of natural selection and source of species' adaptations. Here we report the sequences of 46 complete mitochondrial genomes of D rosophila yakuba and D rosophila santomea , two sister species known to produce hybrids in nature (~3%). At least two independent events of mt DNA introgression are uncovered in this study, including an early invasion of the D . yakuba mitochondrial genome that fully replaced the D . santomea mt DNA native haplotypes and a more recent, ongoing event centred in the hybrid zone. Interestingly, this recent introgression event bears the signature of D arwinian natural selection, and the selective haplotype can be found at low frequency in A frica mainland populations of D . yakuba . We put forward the possibility that, because the effective population size of D . santomea is smaller than that of D . yakuba , the faster accumulation of mildly deleterious mutations associated with Muller's ratchet in the former species may have facilitated the replacement of the mutationally loaded mitochondrial genome of D .  santomea by that of D . yakuba .