The low coverage data also allowed us to address a longstanding debate about whether recombination has any local mutagenic effect. Direct examination of diversity around hotspots defined from LD data is potentially biased (because the detection of hotspots requires variation to be present), but we can without bias examine rates of SNP variation and recombination around the PRDM9 binding motif associated with hotspots. Fig. 6c shows the local recombination rate and pattern of SNP variation around the motif compared to the same plots around a motif that is a single base difference away. While the motif is associated with a sharp peak in recombination rate, there is no systematic effect on local rates of SNP variation. We infer that, although recombination may influence the fate of new mutations, for example through biased gene conversion, there is no evidence that it influences the rate at which new variants appear.
