Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and D. 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 (mtDNA) 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 Drosophila yakuba and D. santomea, two sister species known to produce hybrids in nature (~3%). At least two independent events of mtDNA introgression were uncovered in this study, including an early invasion of the D. yakuba mitochondrial genome that fully replaced the D. santomea mtDNA native haplotypes and a more recent, ongoing event centered in the hybrid zone. Interestingly, this recent introgression event bears the signature of Darwinian natural selection and the selective haplot...