The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies.

人们对种群中线粒体 DNA 变异的性质和程度以及它如何影响性状知之甚少。在这里，我们对 169只果蝇的线粒体基因组进行了重新测序遗传参考面板线，确定了 231 个变体，这些变体沿 12 个线粒体单倍型分层。我们确定了 1,845 例线粒体核等位基因失衡，从而暗示线粒体单倍型反映在核基因组中。然而，没有重大的适应度影响与线粒体核失衡有关，这表明这种失衡反映了线粒体水平的种群结构，而不是基因组不相容性。尽管线粒体单倍型对线粒体呼吸没有直接影响，但一些单倍型与压力和代谢相关的表型相关，包括男性的食物摄入。最后，通过线粒体基因组的相互交换，我们证明了与高食物摄入相关的线粒体单倍型可以挽救低食物摄入表型。一起，