Two Orangutan Species Have Evolved Different KIR Alleles and Haplotypes

The immune and reproductive functions of human NK cells are regulated by interactions of the C1 and C2 epitopes of HLA-C with C1-specific and C2-specific lineage III killer cell Ig-like receptors (KIR). This rapidly evolving and diverse system of ligands and receptors is restricted to humans and great apes. In this context, the orangutan has particular relevance because it represents an evolutionary intermediate, one having the C1 epitope and corresponding KIR but lacking the C2 epitope. Through a combination of direct sequencing, genotyping, and data mining from the Great Ape Genome Project, we characterized the alleles and haplotypes for panels of 10 Bornean orangutans and 19 Sumatran orangutans. The orangutan haplotypes have between 5 and 10 genes. The seven orangutan lineage III genes all locate to the centromeric region of the locus, whereas their human counterparts also populate the telomeric region. One lineage III gene is Bornean specific, one is Sumatran specific, and five are shared. Of 12 gene-content haplotypes, 5 are Bornean specific, 5 are Sumatran specific, and 2 are shared. The haplotypes have different combinations of genes encoding activating and inhibitory C1 receptors that can be of higher or lower affinity. All haplotypes encode an inhibitory C1 receptor, but only some haplotypes encode an activating C1 receptor. Of 130 alleles, 55 are Bornean specific, 65 are Sumatran specific, and 10 are shared.