HLA genes and haplotypes in Ryukyuans suggest recent gene flow to the Okinawa islands

Polymorphism of HLA genes was investigated in a population sample of Ryukyu ans living on the main island of Okinawa (n = 197), in the southwestern isl ands of Japan. Serological typing was applied to class I loci (HLA-A, -B, a nd -C) and to HLA-DRB1; nucleotide sequence-level typing was performed usin g PCR microtiter plate hybridization and PCR single-strand conformation pol ymorphism methods. Ryukpuans showed a higher frequency of DRB1*0405 and low er frequencies of DRB1*1502 and DRB1*1302 compared with Hondo Japanese livi ng on main islands. Principal components and phylogenetic analyses of 12 Ea st Asian populations, including Ryukyuans, were performed based on the alle le frequencies of HLA-A, -B, and -DRB1. In the principal components analysi s 3 Japanese populations (Ryukyuans, Hondo Japanese, and Ainu) formed a clu ster and showed the highest affinity to 2 Korean populations. In the phylog enetic tree Ryukyuans and Ainu were neighbors, but the genetic distance bet ween them was larger than the distances between Ryukyuans and Hondo Japanes e and between Ryukyuans and Korean populations. The geographic dine of the predominant haplotype in Ryukyuans, A*24-B*54-DRB1*0405, suggests that an a ncestral population possessing A*24-B*54-DRB1*0405 moved into the Okinawa I slands after the divergence of Ryukyuans from the Ainu. Such a recent gene flow, probably from South China to the Okinawa Islands, is considered the m ajor cause of difference in genetic characteristics between Ryukyuans and t he Ainu.