Analysis of HLA genes and haplotypes in Ainu (from Hokkaido, northern Japan) supports the premise that they descent from Upper Paleolithic populations of East Asia

The Ainu people are assumed to Ix the descendants of pre-agricultural nativ e populations of northern Japan, while the majority of population of presen t-day Japan (Hondo.Japanese) is considered to have descended mainly from po st-neolithic migrants. Sequence-level polymorphisms of the HLA-class I (HLA -A and HLA-B) genes were investigated in DNA samples of 50 Ainu living in H idaka district, Hokkaido. HLA-A*2402, A*0201, A*0206. A*2601, A*3101. B*150 1, B*5101, B*3901, and B*3501 were observed at frequencies of more than 10% and most of these have previously been found in populations of not only As ians but also North and South American Indians. A*68012 which has not so fa r been detected in Hondo-Japanese, was found in the Ainu (3%). On the other hand, several alleles common in Hondo-Japanese. including HLA-A*3303, A*11 01, B*4403, B*5201, B*5401, B*4601, and B*0702 were infrequent in Ainu (0-1 %). Correspondence and neighbor-joining analyses of various populations bas ed on HLA-A, -B and -DRB1 gene frequencies enabled distinction between Asia n, Native South American, European, and African populations. The Ainu, as w ell as Tlingit (Na-Dene), were placed midway between other East Asians. inc luding Hondo Japanese. and Native South Americans (Americans) in the corres pondence analysis. Furthermore, several HLA-A-B and HLA-B DR-DQ haplotypes common in the Ainu, are shared with some Native American populations. These observations strongly suggest a unique place for the Ainu as descendants o f some Upper Paleolithic populations of East Asia, from whom some Native Am ericans may have descended.