Model for the evolution of Prdm9 alleles and hotspot erosion.

(A) Predicted timeline for the origin of Prdm9 alleles based on SNP frequency found at hotspots comparing B6 and CAST to SPRET. PRDM9^Cst hotspots show an increase in SNPs in the B6 background, suggesting this allele was active in a shared lineage between M.m. castaneus and M.m. domesticus. PRDM9^Dom2 hotspots do not have increased SNPs in the CAST background suggesting this allele was never active in M.m. castaneus. (B) The PRDM9/hotspot lifecycle. Evolutionary erosion driven by biased PRDM9 initiation of recombination decreases hotspot activity over time at many hotspots in parallel. Mutation of Prdm9 creates a new binding domain subsequently shifting the genome-wide position of hotspots.