Figure 3. Novel hotspots are the sites of historic hotspot erosion.

(A) SNP frequency between B6 and CAST haplotypes for PRDM9^Dom2-dependent novel hotspots with haplotype ratio <0.2 (n = 810, points - value at each nucleotide, line - 10 bp running average, highlight - PRDM9^Dom2 motif). (B) Top – CAST haplotype-derived PRDM9^Dom2 motif for hotspots in A. Middle – Amino acid sequence for PRDM9^Dom2 zinc-finger array positions predicted to contact DNA. Bottom – Number of SNPs identified at each base pair position (background subtracted). (C) SNP frequency between B6 and SPRET (blue) or CAST and SPRET (red) for PRDM9^Dom2 novel hotspots in A. (D) SNP frequency between B6 and CAST haplotypes at hotspots unique to the KI strain (n = 2,035, hotspot represented by black line in Fig. 1D). Top – PRDM9^Cst motif derived from the B6 haplotype. Middle – Amino acid sequence for PRDM9^Cst zinc-finger array. Bottom – Number of SNPs identified at each base pair position (background subtracted). (E) Similar to C except comparing SNP frequency between B6 and SPRET (blue) or CAST and SPRET (red) for hotspots used in D. (F) Similar to E for PRDM9^Cst hotspots quantitatively higher in the KI strain compared to CAST (hotspots from Fig. 1D green line, n = 2,187).