Fig. 3.

Application of the RhesusBase PopGateway in illustrating primate regulations and their functional implications. (A) The ratios of nucleotide diversity (π) for nonsynonymous sites to synonymous sites were summarized in boxplots, for human-specific pseudogenes and their functional orthologs in rhesus macaque, respectively. (B–D) For a candidate genomic region under balancing selection, the haplotype structures in 31 macaque animals (62 haplotypes) were shown in hierarchical clustering chart (B). The evolutionary relationship of these haplotypes were further summarized in (C), with the size of each node proportional to the haplotype frequency, and the numbers on branches representing nucleotide substitution sites. Pairwise mismatch distribution of these haplotypes were further calculated and shown, by counting the number of differences between all pairs of the 62 haplotypes (D). The multimodal distribution recapitulates the existence of two major types of haplotype.