Fig. 6

Selection for diversification in PSG N and B2 domains. a Nucleotide sequences of N domain exons of PSG paralogs from ape and NWM species with ≥3 PSG as well as a subset of OWM species were compared pair-wise in all combinations for each indicated species and the ratio of the rate of nonsynonymous (dN) and synonymous mutations (dS) was calculated and the mean ratios (± SEM) were plotted. In addition, the average of dN/dS means (± SEM) for the analyzed species within the ape, OWM and NWM subgroups were calculated (forth panel). For comparison, the same calculations were performed for CEACAM1-like paralogs (CEACAM1, 3, 5, 6) of the same primate subgroups (fifth panel). The means (± SEM) of N exon dN/dS ratios were also calculated for PSG ortholog pairs which could be reliably identified for closely related ape (Ggo, Hsa, Ppa, Ptr; Hmo, Nle) and OWM species (Cat, Mfa, Mle, Mml, Mne, Pan) but not for NWM by phylogenetic analyses and for comparison for CEACAM1 orthologs of the same species or all NWM species. The means of all pairwise orthologous PSG gene N exon comparisons for the above indicated species within ape (35 comparisons) and OWM subgroups (117 comparisons) are shown. In addition, the dN/dS ratios for the N domain exons of CEACAM1 and CEACAM19 orthologs of 22 primate species including lemurs and lories were calculated. b dN/dS calculations for selected apes, OWM and NWM using all retrievable IgC-like domain exon nucleotide sequences with open reading frames were performed as in a and compared to dN/dS values for the corresponding N exon sequences (mean ± SEM). c The cumulative frequencies of nonsynonymous (green curves) and synonymous substitutions (red curves) along the N exons of paralogous PSG from selected great apes as well as primate CEACAM1 and CEACAM19 orthologs were determined. Note the rapid accumulation of nonsynonymous mutations in the CC’C″FG β-strand regions (black broken lines) which indicates selection for diversification. This contrasts with conserved regions between CC’C″ and FG β-strands (red broken lines). The location of CC’C″ and FG β-strand regions determined by 3D modeling are indicated by gray boxes above the graphs. Note the relative steady accumulation of synonymous substitutions indicated by gray broken lines. The location of LYHY and RGD motifs are shown by red and blue lines, respectively. The number of analyzed genes is indicated in lower right corner. A1, A2, B2, IgC-like domain exons; N, N domain exon; NWM, New World monkey; OWM, Old World monkey. For assignment of acronyms to common species names refer to Supplementary Table 1. d Regions of positive selection within PSG N domains differ between species. Sites within N domain exons (x-axis) with episodic diversifying selection as detected by MEME (red arrows) were plotted against the p-value (level of significance; y-axis). The species from which the PSGs were analyzed are indicated. Note that in different species sites under positive selection differ in number and location