Figure 3. Positive selection of zinc fingers encoded by rodent Prdm9 genes.

(A) A multiple alignment of the zinc finger sequences from M. musculus C57BL/6J highlights the invariant Cys₂His₂ Zn²⁺-coordinating residues as well as positions −1, 3, and 6 that dictate the DNA-binding specificity of individual zinc fingers. Deviations from the consensus amino acid at each position are shown in boldface. In this species, positions −1 and 3 meet the criteria for positive selection [27] (highlighted in yellow and with red crosses). (B) Predicted positively selected sites in Prdm9 from diverse rodent lineages. Positive selection was inferred for each species [27] from intra-species Prdm9 zinc finger sequence alignments. Positively selected sites (P<0.05 after multiple testing correction) are shown mapped to the third mouse Prdm9 zinc finger sequence (MMM3). The majority of positively selected sites fall at positions −1, 3, and 6. (C) Estimated d_N/d_S values at four zinc finger positions (namely, −2, −1, 3, and 6) in a comparison of zinc fingers from all rodents (in contrast to the analyses of species-specific zinc fingers in (B)) for which there exists strong evidence of positive selection [27]. The P-values shown have been corrected for multiple testing. Common names to species are listed in the legend to Figure 6.