The DNA sequencing picture that emerges today shows the central Honshu people of Japan to be genetically just a little closer to Sino-Tibetan and Han Chinese (from the Jiangsu region who were possibly rice-farming immigrants during the Yayoi era) evidenced by the specific genetic Y markers found in Japanese today (ie O3a5, O3a and O1), in their mix than to modern-day Koreans whose ancestors contributed significantly to the Japanese gene pool probably during Koguryo and Paekche migrations into Japan of the Kofun era to Asuka eras.
One surprising point that emerges from a look at both mtDNA and Y Haplogroups charts, is that the Koreans show an even closer genetic affinity to Okinawans (and therefore to the Jomon stock) than mainland Honshu Japanese do themselves…comprising 17.4% of their DNA sequence compared to the Japanese 16.1% of their DNA sequence.
Satoshi Yamaguchi’s studies
In recent years, more archaeological and genetic evidence have been found in both eastern China and western Japan to lend credibility to this argument. Between 1996 and 1999, a team led by Satoshi Yamaguchi, a researcher at Japan’s National Science Museum, compared Yayoi remains found in Japan’s Yamaguchi and Fukuoka prefectures with those from early Han Dynasty (202 BC-8) in China’s coastal Jiangsu province, and found many similarities between the skulls and limbs of Yayoi people and the Jiangsu remains. Two Jiangsu skulls showed spots where the front teeth had been pulled, a practice common in Japan in the Yayoi and preceding Jōmon period. The genetic samples from three of the 36 Jiangsu skeletons also matched part of the DNA base arrangements of samples from the Yayoi remains. Surprisingly, Japanese also display the highest frequency of haplogroup O3a5, which is a Han Chinese and Sino-Tibetan specific O3 branch.
Japanese Haplogroup O3a5 (O3e) 10/47= 23%
This frequency is about 5% higher than the frequency of O3a5 among Manchus, Koreans and other Northeast Asians.
For North Koreans, the frequency of O3a5 is even lower than some Tungusic populations. Overall, the Koreanic haplogroup O3 were the least influenced by Sinitic populations.
Whereas pure haplogroup C3 (M217-no subclade) was observed at a high frequency among Tungusic (20%) and Koreanic (16%) populations. The frequency of haplogroup C3 among Japanese was only 1%. This means that Japanese origins were not as prominently from Siberia as was commonly thought, since Japanese bear more of C1, whereas C3 is found only in northern populations of Japan.
Haplogroup D was observed among Japanese (25%) and Tibetans (40%); it was also observed among Han Chinese, Mongolians and Koreans.
The DNA sequence SNP study done by Japanese researchers in 2005 (the biggest contributor of DNA of each East Asian people is bolded) showed the following results:
Korean DNA sequence is made up of:
40.6% Uniquely Korean
Japanese DNA sequence is made up of:
4.8% Uniquely Japanese
Chinese DNA sequence is made up of:
60.6% Uniquely Chinese
The biggest components in Japanese are Chinese, Korean, Okinawan.
A closer look at the Chinese gene pool
The shared Chinese gene pool between Japanese and Koreans is thought to be formed of Dong-Yi stock (originating from China’s Shandong peninsula) that later formed the Puyo peoples of the Paekche kingdom and Koguyro kingdoms of the Korean peninsula.
mtDNA haplogroup A which is widespread in Asia today occurs at levels below 10%, but reaches higher concentrations in some parts of China, Korea and Japan.
“Some ethnic Chinese populations, such as the Dong and the Yi, carry haplogroup A at levels as high as 30%. One branch of the haplogroup, A4, reaches levels of more than 15% among mitochondrial DNA samples collected in the city of Wuhan in central China. In the Spittoon… Ancient China’s famous Terracotta Army was constructed by men bearing haplogroup A. Check the Spittoon to learn more about these ancient builders.” — Source: An Introduction to Haplogroups: An Interactive Activity Activity developed by Meredith T. Knight at Tufts University
Ancient mtDNA in Siberia Haplogroup A was widespread in Siberia in ancient times. One study of skeletal remains discovered near Siberia's Lake Baikal estimated the haplogroup was present in 13-26% of the region's population 7,000 years ago, and is almost exclusively among the Chukchi and the Yupik, two small indigenous groups from northeastern Siberia.
M7, a widespread haplogroup found in China, Japan, Southeast Asia and the Pacific Islands. [M8, a widespread haplogroup in central and eastern Asia that eventually sent an offshoot to the Americas. M9, which appears to have arisen in Tibet.] While Haplogroup M is widespread throughout South and East Asia, it originates from the Indian sub-continent where it is more diverse on there than anywhere else in the world.
Overall, Japanese are closest to Tibetans and Han Chinese, but only marginally more so than to the Koreans.
The Ainu who are widely considered to be of the “old” proto-Mongoloid stock closely related to the Tibetan Buryat and Yakut peoples, and descended from the Jomon people who lived in the Tohoku area until they were later pushed northwards into Hokkaido, afterwhich they resided around the Sea of Okhotsk, mainly Hokkaido, Sakhalin, Kuril Islands and the tip of Kamchatka. However, the DNA sequences show that Ainu are actually more remotely distanced from the Jomon than is commonly believed, as they were influenced by Siberians (as with Koreans). Evidence is the haplogroup C3 (no subclade) occurs at moderately high frequencies among these populations.
The above mtDNA studies relate to maternal line gene flow, the following Y chromosome study of male-mediated gene flow shows a slightly different picture but the sharing of the common haplotypes still reveal strong affiliations of both Japanese and Koreans to the Chinese and of the Japanese to the Koreans:
Population studies of genetic markers such as HLA variation and mitochondrial DNA have been used to understand human origins, demographic and migration history. Recently, diversity on the nonrecombining portion of the Y chromosome (NRY) has been applied to the study of human history. Since NRY is passed from father to son without recombination, polymorphisms in this region are valuable for investigating male-mediated gene flow and for complementing maternally based studies of mtDNA. Haplotypes constructed from Y-chromosome markers were used to trace the paternal origins of Korean. By using 38 Y chromosome single nucleotide polymorphism markers, the genetic structure of 195 Korean males was analyzed.
The Korean males were characterized by a diverse set of 4 haplogroups (Groups IV, V, VII, X) and 14 haplotypes that were also present in Chinese.
The most frequent haplogroup in Korean was Group VII (82.6%). It was also the most frequent haplogroup in Chinese (95%) as well as in Japanese (45%). The frequencies of the haplogroups V, IV, and X were 15.4%, 1%, and 1%, respectively. The second most frequent haplogroup V in Korean was not present in Chinese, but its frequency was similar in Japanese.
Source of study: Sunghee Hong, Seong-Gene Lee, Yongsook Yoon, Kyuyoung Song /University of Ulsan College of Medicine, 388-1 Poongnap-dong, Songpa-ku, Seoul, Korea
Finally, the Y haplogroup chart below shows the relations between the various groups of Asia and their varying degrees of affinity or remoteness to each other.
Another study published in 2005 on 81 sets of Y chromosomes of six populations across Japan showed:
– The Japanese have at least two very deep pre-Yayoi ancestral Y chromosome lineages (D-P37.1 and C-M8) that descend from Paleolithic founders who had diverged from the mainland and that were then isolated from those populations on the mainland for a very long time. Scientists thought these D lineages to mean the Jomon populations in Japan once upon a time the same ancestors as Tibetans from central Asia who are found with the highest frequency of continental D lineages is found in central Asia. Scientists hypothesized that the area between Tibet and the Altai Mountains in northwestern China is the most likely geographic source of Paleolithic Japanese founding Y chromosomes. ( Historical records suggest that Tibetan populations were derived from ancient tribes of northwestern China that subsequently moved to the south and mixed with the southern natives in the last 3,000 years.) A separate recent mtDNA study on the Haplogroup M12 – the mitochondrial component of Japanese genes, the counterpart of Y chromosome D lineage – also confirmed the direct connections of Japanese haplotypes with Tibet. This rare haplogroup is possessed only by mainland Japanese, Koreans, and Tibetans, with the highest frequency and diversity in Tibet. These Paleolithic ancestors were thought to have migrated into Japan sometime around 20,000 years ago.
In a nutshell, what we can evince and conclude from all the DNA data that has been presented is that the Japanese people are a people with mixed diverse origins, formed from many waves of migrations from various locations in the remote past as well as in the more recent past.
Tajima, Atsushi, Studies on the geographic distribution of the human Y DNA variation
Genetic structure of the Japanese people and the formation of the Ainu population by Ken-ichi Shinoda (National Museum of Science and Nature, Tokyo)
Watch the documentary “Japanese Roots” at Youtube.
World Haplogroup Maps Source: J.D. McDonald
Y Chromosomal DNA and the Peopling of Japan by Michael F. Hammer and Satoshi Horai
An Introduction to Haplogroups: An Interactive Activity Activity developed by Meredith T. Knight at Tufts University
B. Mohan Reddy et al., “Austro-Asiatic Tribes of Northeast India Provide Hitherto Missing Genetic Link between South and Southeast Asia” on the origin of O-M95 in northeast India
Stoneking and Delfin, The human genetic history of East Asia: Weaving a complex tapestry