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

Abstract

Acknowledgments: We thank Prof. Masafumi Takiguchi, Kumamoto University, Dr. Marie Lau, UCLA, and Mr. Hiromitsu Takei, Japanese Red Cross Ibaraki Blood Center, for providing us with standard genomic clones and standard genomic DNAs. We also thank Dr. Tadashi Imanishi, Mr. Hidenori Tanaka, Mr. Kouichi Kashiwase, and Dr. Atsuko Ogawa, Japanese Red Cross Central Blood Center, for helpful discussions. This study was partially supported by Grant‐in‐Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture. The Ainu people are assumed to be the descendants of pre‐agricultural native populations of northern Japan, while the majority of population of present‐day Japan (Hondo‐Japanese) is considered to have descended mainly from post‐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 Hidaka district, Hokkaido. HLA‐A*2402, A*0201, A*0206, A*2601, A*3101, B*1501, 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 Asians but also North and South American Indians. A*68012, which has not so far 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*1101, 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 based on HLA‐A, ‐B and ‐DRB1 gene frequencies enabled distinction between Asian, Native South American, European, and African populations. The Ainu, as well as Tlingit (Na‐Dene), were placed midway between other East Asians, including Hondo Japanese, and Native South Americans (Amerindians) in the correspondence 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 of some Upper Paleolithic populations of East Asia, from whom some Native Americans may have descended.