Nonsynonymous versus synonymous substitution rates for pairwise comparisons between N domains. The number of nonsynonymous substitutions per nonsynonymous site (dn) and the number of synonymous substitutions per synonymous site (ds) was calculated using the method of Yang and Neilson  for pairwise nucleotide comparisons. The N1, N2 and N3 domains of mouse PSGs (mN1, mN2 and mN3, respectively), the N1 domain of rat PSGs (rN1) and the N domain of human PSGs (hN) comprised individual data sets that were analysed in the following comparisons: mN1 vs mN2; mN1 vs mN3; mN2 vs mN3; mN1 vs rN1; mN1 vs hN. (A) Plot of dn against ds where each data point represents a pairwise comparison of a nucleotide sequence taken from each set under comparison. The 45° line of equivalence is drawn where dn = ds. (B) Box and whisker plot of dn/ds calculated from the pairwise comparisons of all sequences in one dataset against all sequences in the other dataset. Significant differences of p < 0.0001 (calculated by the Mann-Whitney method) were observed between all comparisons except intra-mouse comparisons.
McLellan et al. BMC Evolutionary Biology 2005 5:39 doi:10.1186/1471-2148-5-39