Genetic structure of the Japanese and the formation of the Ainu population Ken-ichi Shinoda National Museum of Nature and Science, Tokyo Mitochondrial DNA mitochondria Structures of mtDNA nuclear genome 3 billion 16,569 base pair History of the analysis 1980’s Analysis of the DNA digestion pattern with restriction enzymes. 1990’s Analysis of sequence in a region of the mitochondrial genome that undergoes frequent mutation. 21th century Analysis of the complete DNA sequence of mitochondrial genomes. Human migration and formation of mitochondrial DNA haplogroups 60,000-20,000 BP. A X D C A B D JT A B H F U D 20,000 BP.- X I B C N U N A D R My M L2 M N M N L3 L L1 Mx M Q B C L1 N P A D L2 L3 Mz Nz L0 150,000-60,000 BP. Y Z A G C M7a N9b D4 D5 M8a M7b B5 B4 F E M7c Distribution center of each haplogroup MtDNA haplogroup frequencies of mainland Japanese N9a F N9b D4 B5 B4 M9 M8 D5 M7c M7b A M7a G Tanaka et al. 2004 Korea D4 Japan Northern China Frequency distribution of haplogroup D4 in each population Jomon vs. Yayoi 40,000 BP. 15,000 BP. B.C. 1,000 A.D. 300 Paleolithic Jomon Yayoi Historic Jomon female Immigrant Yayoi female Jomon Yoyoi The American Journal of Human Genetics 83, 445–456, October 10, 2008 Relatedness between 7003 Japanese Individuals Han Chinese 中国人 Mainland Japanese Okinawa For the Japanese individuals, there were two main clusters: the Hondo cluster (red plus signs) and the Okinawa cluster (green crosses). Dual structure model (K. Hanihara 1991) （Okhotsk 5-10 century） Palaeolithic to Jomon Yayoi Historical 40,000-12,000 BP. 3,000-1,700 BP. 1,700 BP. - Comparison of haplogroup frequencies between the Jomon, Yayoi, and modern Japanese populations. D4 M8 Z A N9a B F n= 78 M8 Z M10 M N9b Y M7 N9 F D4 D5 G M7a bc A a B n= 1312 D4 D4h2 G M7a M8 M10 N9b B F n= 119 D5 M7 A bc D4 is most common in the Japanese and Yayoi populations. BSP of female effective population size (Nef) through time for Japanese mtDNA lineages. LGM Initial population growth Rapid population growth PLoS ONE 6(6): e21509. Population estimates by Koyama (1984) 5,000-4,000BP 40,00-30,00BP 6,000-5,000BP 3,000-30,00BP 10,000-6,000BP Moving on to rice agriculture Original place of rice agriculture 5000 BP. 3000 BP. 3000 BP. Comparison of haplogroup frequencies between Okinawa, Ainu, and modern Japanese populations. M8 M10 M N9b Y M7 N9 Other D G M7a bc A a B F n=1312 D G M7a M7bcM A N9b B F Other n=372 M7 D G M7a bc A N9b B F Y n=51 Hokkaido Jomon M7a N9b D4h2 G1b N9b M7a D4 D4h2 Tohoku Jomon Kyushu Yayoi M7a N9b B4 M10 Kanto Jomon Z A D4 M8 D4 F M7bc M8 N9a F B4 G2 D5 Distributions of haplogroups G and Y of each population Ainu Haplogroup G Haplogroup Y Population History of Hokkaido 7th century 13th century Jomon to Epi-Jomon Satumon Ainu Okhotsk culture 5th century 9th century D4 9% other 2% M7a 5% D4h2 G1b G1b D 17% Y19% 24% 10% 18% Y 33% F 2% G1b Y 43% B 2% 11% M7a 6% Z 1% M7b 1% N9b 8% G N9b C 5% M9 1% M7a 7% M8a 1% 25% 65% N9b A 7% N9b A 8% 21% A 4% M7a 11% 16% M7b,c 4% B4 3% C5a 4% B4 1% Jomon Okhotsk culture Recent Ainu Modern Ainu (Edo era) Thank you .