Population specific positive selection acted on the HLA class II region in Papuans

The first colonization into Oceania occurred about 47 thousand years ago. Modern Papuans are the descendants of the first immigrants and considered to have adapted to Oceanian environment over the years. The Human Leukocyte Antigen ( HLA ) plays an important role in acquired immunity and has been reported to have undergone natural selection in human populations. In this study, we examined whether natural selection has acted on the HLA region in modern Papuan genomes. We estimated integrated Haplotype Score (iHS) across the chromosome 6 and detected a signal of a strong positive selection acted on HLA class II region. A high linkage disequilibrium between a SNP with the strongest signal (rs200439840) and haplotype DRB1*15:01-DQA1*01:02-DQB1*06:02 was observed. The haplotype DRB1*15:01-DQB1*06:02 was commonly observed in Melanesia populations. Our results indicate that this haplotype was adaptive to Oceanian environment and increased by positive selection.