Sexually antagonistic evolution of mitochondrial and nuclear linkage

Across eukaryotes, genes encoding bioenergetic machinery are located in both mitochondrial and nuclear DNA, and incompatibilities between the two genomes can be devastating. Mitochondria are often inherited maternally, and theory predicts sex‐specific fitness effects of mitochondrial mutational diversity. Yet how evolution acts on linkage patterns between mitochondrial and nuclear genomes is poorly understood. Using novel mito‐nuclear population‐genetic models, we show that the interplay between nuclear and mitochondrial genes maintains mitochondrial haplotype diversity within populations, and selects both for sex‐independent segregation of mitochondrion‐interacting genes and for paternal leakage. These effects of genetic linkage evolution can eliminate male‐harming fitness effects of mtDNA mutational diversity. With maternal mitochondrial inheritance, females maintain a tight mitochondrial–nuclear match, but males accumulate mismatch mutations because of the weak statistical associations between the two genomic components. Sex‐independent segregation of mitochondria‐interacting loci improves the mito‐nuclear match. In a sexually antagonistic evolutionary process, male nuclear alleles evolve to increase the rate of recombination, whereas females evolve to suppress it. Paternal leakage of mitochondria can evolve as an alternative mechanism to improve the mito‐nuclear linkage. Our modelling framework provides an evolutionary explanation for the observed paucity of mitochondrion‐interacting genes on mammalian sex chromosomes and for paternal leakage in protists, plants, fungi and some animals.