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Nuclear compensatory evolution driven by mito-nuclear incompatibilities

Mitochondrial function relies on the coordinated expression of mitochondrial and nuclear genes, exhibiting remarkable resilience regardless the susceptibility of mitochondrial DNA (mtDNA) to accumulate harmful mutations. A suggested mechanism for preserving this mito-nuclear compatibility is the nuclear compensation, where deleterious mitochondrial alleles drive compensatory changes in nuclear genes. However, prevalence and conditioning factors for this phenomenon remain debated, with empirical evidence supporting and refuting its existence. Here, we investigate how mito-nuclear incompatibilities impact nuclear and mitochondrial substitutions in a model for species radiation under selection for mito-nuclear compatibility, similar to the process of mtDNA introgression. Mating eligibility relies on genetic (nuclear DNA) and spatial proximity, with populations evolving from partially compatible mito-nuclear states. Mutations do not confer advantages nor disadvantages, with no optimal nuclear or mitochondrial types, but individual fitness decreases with increasing incompatibilities, driving the demand for mito-nuclear genetic coordination. We find that selection consistently promotes compensation on incompatible nuclear genes, resulting in more substitutions than compatible or non-interacting genes. Surprisingly, low mitochondrial mutation rates favor compensation, as do increased selective pressure or a higher number of mismatches. High mitochondrial mutation rates boost substitutions in initially compatible nuclear genes, relaxing the selection against mito-nuclear incompatibilities and mirroring the compensatory evolution. Moreover, the presence of incompatibilities accelerates species radiation, but richness at equilibrium is not directly correlated with substitutions' response, revealing the complex dynamics triggered by mitochondrial introgression and mito-nuclear co-evolution.

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