Genetic structure of the Japanese and the formation of the Ainu population

Ken-ichi Shinoda National Museum of Nature and Science, Tokyo

Structures of mtDNA 16,569 base pair

Mitochondrial DNA

mitochondria

nuclear genome 3 billion

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.

L

Human migration and formation of mitochondrial DNA haplogroups

L1

L1

L0

L2

L3 L2

L3

M N

150,000-60,000 BP.

I U

H JT

R U N

N

N

M

M

M N P

Q

A B

D

F

My

Mx

Mz Nz

60,000-20,000 BP. A

B X

C

D

A D

B C

A D

A

B

X C

D

20,000 BP.-

D4 C

A Z

Y

G

D5 M8a

B5 B4

E

M7b

M7a N9b

F M7c

Distribution center of each haplogroup

MtDNA haplogroup frequencies of mainland Japanese

D4

A G M7a

M8

M9

B5

N9a F

D5 M7b M7c

B4

N9b

Tanaka et al. 2004

Frequency distribution of haplogroup D4 in each population

D4

Japan

Korea

Northern China

Jomon vs. Yayoi

Yayoi Historic

40,000 BP.

Jomon Paleolithic

A.D. 300 B.C. 1,000 15,000 BP.

Immigrant Yayoi female Jomon female

Jomon Yoyoi

中国人

For the Japanese individuals, there were two main clusters: the Hondo cluster (red plus signs) and the Okinawa cluster (green crosses).

Relatedness between 7003 Japanese Individuals

Han Chinese

Mainland Japanese

Okinawa

The American Journal of Human Genetics 83, 445–456, October 10, 2008

Historical 1,700 BP. -

Palaeolithic to Jomon 40,000-12,000 BP.

Dual structure model (K. Hanihara 1991)

（Okhotsk 5-10 century）

Yayoi 3,000-1,700 BP.

M7a D4

D4

M7 bc

M8

M8

M10

M10

M7 bc

M

Z

A

A

N9 a

N9b

B

B

N9b F

Y

n= 1312

n= 78

n= 119

G

M8 N9a

Z

F

D4 is most common in the Japanese and Yayoi populations.

D4 D4h2

D5

D5

G M7a

A

F

B

Comparison of haplogroup frequencies between the Jomon, Yayoi, and modern Japanese populations.

BSP of female effective population size (Nef) through time for Japanese mtDNA lineages.

PLoS ONE 6(6): e21509.

Initial population growth LGM

Rapid population growth

Population estimates by Koyama (1984)

5,000-4,000BP

10,000-6,000BP

6,000-5,000BP 40,00-30,00BP

3,000-30,00BP

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.

D

M7a

M7a

M7a

D

D

M7 bc

M7bc

M8 M10

M7 bc

M

M

A

A

A

N9 a

N9b

N9b

N9b

B

B

B

F

F Y

Y

Other

F Other

n=1312

n=372

n=51

G

G

G

N9b G1b D4h2 M7a

Hokkaido Jomon

N9b M7a Tohoku Jomon

M7a N9b Kanto Jomon

D4h2

B4

F M7bc

M10

M8 D4

D4

M8 D4 A Z

N9a B4 F

Kyushu Yayoi

G2 D5

Distributions of haplogroups G and Y of each population

Ainu

Haplogroup G

Haplogroup Y

Jomon to Epi-Jomon Satumon Ainu Okhotsk culture

7th century 13th century

B 2% G

25% M7a 16%

D 18%

N9b 8%

M7b,c 4%

other 2%

F 2%

A 4%

Y19%

Modern Ainu

Population History of Hokkaido

D4h2 17%

G1b 11%

M7a 7% N9b 65%

Jomon Okhotsk culture

B4 3%

M7a 6%

G1b 24%

A 8% N9b 11%

Y 43%

C 5%

Recent Ainu (Edo era)

M7b 1%

B4 1%

D4 9%

M7a 5%

Z 1%

Y 33%

N9b 21%

G1b 10%

A 7%

C5a 4%

M8a 1% M9 1%

5th century 9th century

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