Why does the target-recognition site in PRDM9 have unusually high mutation rates?

The gene PRDM9, responsible for the location of recombination hotspots in mammals, exhibits one of the highest mutation rates in the human genome. This has a direct impact on the life expectancy of recombination hotspots and the variability of the recombination landscape. Why would PRDM9 evolve such a high mutation rate? Here we explore this question by formulating and analysing population genetics models for modifiers of mutation rates at PRDM9 and modifiers of mutation rates at PRDM9's target sites. By letting mutation rates evolve, we find that natural selection indeed favours the evolution of high mutation rates at PRDM9 and low mutation rates at PRDM9's target sites. However, considerations about linkage disequilibrium and genetic drift suggest that only high mutation rates at PRDM9 are likely to evolve. Our modifiers of mutation rates at PRDM9 are most likely to evolve in close linkage with the PRDM9 locus. This is consistent with the binding domain in PRDM9 adopting a zinc-finger structure-molecular structure with high intrinsic mutation rates. Interestingly, our results are an exception to the reduction principle in modifier theory. We draw parallels between our results and another exception to the reduction principle: when genes are evolving in fluctuating environments. We suggest that the red-queen dynamics that characterize the coevolution between PRDM9 and its target can generate a fluctuating genomic environment that drives the evolution of our modifier of mutation rates at PRDM9.