Making sense of DNA data and the origins of the Japanese

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

21.9% Chinese

1.6% Ainu

17.4% Okinawan

18.5% Unidentified

Japanese DNA sequence is made up of:

4.8% Uniquely Japanese

24.2% Korean

25.8% Chinese

8.1% Ainu

16.1% Okinawan

21% Unidentified

Chinese DNA sequence is made up of:

60.6% Uniquely Chinese

1.5% Japanese

10.6% Korean

1.5% Ainu

10.6% Okinawan

15.2% Unidentified

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.

MtDNA YAP haplogroups (Ainu, Honshu and Okinawan Japanese relationships seen)

Tajima: Frequency distributions for for 8 Y-chromosome haplotypes for 14 global populations(Ainu, Honshu and Okinawan Japanese relationships seen)

MtDNA groups of the world

Y Haplogroups of the world

Y Haplogroups of the world

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.

Interestingly, the Y chromosome study also suggested that there could be one other Japanese Paleolithic founding that found its way to the Japanese archipelago, these early ancestors carried the Y-STR haplogroup, C-M8, a Y-chromosome haplotype that is related to Indian and central Asian C chromosomes. This set of C-M8 Y chromosomes were thought to be carried into Japan sometime around just before 12,000 years ago.
The same study also concluded that Jomon genes have survived till today showing up at high frequencies in Japanese populations today (34.7%)  The scientists having charted the Haplogroup D chromosome-carrying populations who were found to exist at frequencies distributed in an inverted U-shaped pattern across the archipelago, with the highest frequencies occurring in the southern Ryukyuans (Okinawa) and the northern Ainu (Hokkaido). The results suggested to scientists that not only the distinct genetic contribution of Paleolithic ancestors but that they had intermarried (admixed) with the later income Yayoi migrant populations who were of a separate and different haplotype O  lineage.


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

Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes [full document here]

Genetic structure of the Japanese people and the formation of the Ainu population by Ken-ichi Shinoda (National Museum of Science and Nature, Tokyo)

Michael F. Hammer, , Tatiana M. Karafet, Hwayong Park, Keiichi Omoto, Shinji Harihara, Mark Stoneking and Satoshi Horai
Journal of Human Genetics / © The Japan Society of Human Genetics and Springer-Verlag 2005 /10.1007/s10038-005-0322-0

Watch the documentary “Japanese Roots” at Youtube.

Tateno, Yoshio et al., Divergence of East Asians and Europeans Estimated Using Male- and Female-Specific Genetic Markers

World Haplogroup Maps Source: J.D. McDonald

Origins of the Jomon, connections with the Asian continent

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

Longli Kang et al., Y chromosome O3 haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the eastern Himalayas

Stoneking and Delfin, The human genetic history of East Asia: Weaving a complex tapestry

13 responses to “Making sense of DNA data and the origins of the Japanese

  1. Thank you for this information. Too bad the koreans, chinese and japanese are still fighting so much. We are share some common genes. NO wonder we eat food that are so alike too.

  2. i read this article that said a japanese doctor from the university of pensylvania carried out a research among japanese, koreans and tibetans to find out the origin of the said he found that the japanese peoples were heavily influenced by the yayoi peoples dna.the yayoi peoples were from the korean peninsula and they had found a genetic marker among japanese and korean males that originated from the yayoi peoples. this genetic marker was also found at high frequencies among tibetan males.the researchers then concluded that this marker was brought to the korean peninsula by the ancestors of the yayoi peoples and also to tibet by the ancestors of the tibetans.

  3. The koreans have like 20% chinese dna and about 21% japanese dna according to several researchers. KOreans have only like 40% unqiue korean dna and the remaining dna cannot be identify. DNA is muating faster than ever. Scientist said think it use to take like 20 to 30 thousands of years for genes to mutate, but science in the pats 10 years fund dna is mutating much faster than ever. Scientist better hurry it up before dna is untraceable. Human kind adapt to their climite and environment. We are came from east africia. We mutated according to the path we took. I don’t know why people keep fight who is better. It is so ridiculous!!!!!!!!! We are are human. Until outerspace aliens invade us in the future, then us the so call human race will see us as all the same.

  4. Once joined a team like Yankees, DNA doesn’t matter, only hit rate, isn’t this true boys? So, it is here in Japan.

  5. These DNA tests aren’t fully credible. I mean how we can know the basis of classification of similar or different. Are these classification really admitted internationally by all countries with no objections? This doesn’t include the relation of Hebrew, middle easterns and other Asians. Why do you just spot on these 3 countries. There are Mongol, Khazafstan, Indonesia etc in Asia. And our all ancestors were supposely born in Africa about 60,000 years ago. Biblical perspective is a shit compared to Science figure.

    • There are several problems. One of the most obvious problems is ascertaining timing of the branching of or origin of genotypes – one study puts it this way: “It is difficult to accurately date the ancient human migrations (or mutations), because of the errors inherently involved in estimating both the effective population size of the males and the mutation rate. However, our knowledge of morphology and archaeology can help us to narrow the estimated age range”. DNA science is still a relatively new field so that the information is only as good as the number of studies that have been done. This is not the same as saying that the data is not credible. Interpretation of that data is however, obviously only as good as the amount of data or studies that have been done on a specific topic. Central Asia and Mongolia were some of the regions that lacked DNA studies the most … until recently. The study of Y or mtDNA haplogroups or types are highly informative however, they provide very specific signals of the existence of a specific people within a population. You can track lineages of people within populations to reasonable accuracy, on account of the genetic mutations and know which ones came before which ones. As more and more genetic data and studies are published, we are beginning to get a clarifying picture of the migratory trails various lineages have left all over the world. The race has been on to establish the earliest human settlement into E. Asia, and the sequence of settler arrivals – earlier theories posited arrivals from the Eurasian heartland as the earliest , recent ones say SEA-Austronesian ones by way of S. Asia were earliest, others suggest out of Island SEA. The jury is still out on the issue. Obviously, since the regions yet to be studied in depth are East Asia and Central Asia… the picture still requires much clarifying something which has to be done by comparing data from different types of studies, Y or mtDNA/autosomal/HLA antigens/ virus types/ other disease genetic data and with archaeological and anthropological data. The picture of migratory trails and lineages that is emerging is extremely complex, but it is none the less emerging and clarifying. “Why do you just spot on 3 countries?” Good question. Partly for the lack of page space. But really because it’s an ongoing analysis. I’m currently working on the possible trails from the Altai-Baikal-Mongolia region, as well as the R1b1b trails as well as the J hg trails to and from the Near East/ME as well as the Indo-Aryan Indian subcontinent. But a great many new and exciting studies have come onstream from these areas – as well as on E. Asia … only very recently, particularly in 2010 and this year. It takes time to digest these, and draw inferences for a macro-viewpoint.

  6. Let’s face it. People always move around, so it isn’t surprising to me that koreans have chinese and japanese DNA and vise versa. Japanese have korean and chinese dna, but What about chinese dna. I think they also have some variation of Japanese in northern or northeast china. My believe is migration out of africa came to populate CHina, Korea, Japan from east to west, so that explain why Japanese and korean male carry a tibetian gene. Also tibetians migrated up to the high plateau less than 3,000 years ago . TIbetian share gene pool with the ethnic chinese population except for a few gene that are different due to adaptation to the high altitude.
    Damn people should put aside their national pride. I strongly feel that we mongoloid people are related and traveled the same path out of africa. Some went to central asia, north asia, northeast asia, east asia, and then some migrated into southeast asia like vietnam. Southeast asians are either pure australoid people are they are a mixture of australoid and mongoloid race. I would like to find out more in my life about the the mongoloid asians and how they are related to each other. I like them all. I don’t know why the hate. We are all people. We should judge by indivuality and not by ethnicity or the race of the person. No race or ethnicity is better than the other race or ethnicity. I encountered too much hate while watch youtube.

    • The confusion of most of the internet talk results when people forget that what’s deemed Chinese or Japanese or Korean have to do with statehood concepts and boundaries which appeared only around 2,000 years ago give or take. Beyond that, the picture is of nomadic tribal groups, chiefdoms, migratory groups whether farmers or pastoral nomads, and further back in time, hunter-gatherers. For example, a 2009 study on Korean populations showed “recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia.” and that “haplogroup O-M122 lineages, found widely throughout East Asia at high frequencies (especially in southern populations and China), have suggested a link between these Y-chromosome expansions and the spread of rice agriculture in East Asia …archaeological evidence reveals that rice cultivation had spread to most parts of the Korean Peninsula by around 1,000–2,000 BC, introduced from the Yellow River and/or Yangtze River basin in China …northern haplogroups account for ∼60% of the mtDNA gene pool of the Koreans. In addition, southeast Asian-prevalent mtDNA lineages of (sub)haplogroups B (14.6%), M7 (10.3%), and F (9.7) are also found at moderate frequencies in the Korean population. These findings suggest that more than 30% of the Korean mtDNA pool is attributable to maternal lineages with a more southern origin. We also found the haplogroup M7a1 exclusively in the Korean population. This result is consistent with previous reports that haplogroup M7a is restricted to Japan and south Korea. Thus, the distribution pattern of mtDNA haplogroups leads us to consider that the peopling of Korea is likely to have involved multiple sources.” Modern-day East Asian populations (China, Korea and Japan) are like a combination of layered and marbled cake with visible threads of differing ingredients as well as admixtures as well. Many new studies are throwing light on these threads that run from the different migratory lines: Large-scale mtDNA screening reveals a surprising matrilineal complexity in east Asia and its implications to the peopling of the region; The emerging limbs and twigs of the East Asian mtDNA tree; The human genetic history of East Asia: weaving a complex tapestry. What we are needing to build a picture of peopling origins is a higher resolution scrutiny of the finer twigs of the branching lines…

    • This 2010 study Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia notes that “The phylogeographic distribution pattern of Hg C supports a single coastal ‘Out-of-Africa’ route by way of the Indian subcontinent, which eventually led to the early settlement of modern humans in mainland Southeast Asia” and concludes there was “a general south-to-north and east-to-west cline of Y-STR diversity is observed with the highest diversity in Southeast Asia.” The study Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122 concludes O is also from the south. And last but not least, Hg D (your Japanese and Tibetan connection) is also deemed (Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations) to have come via the southern route although there are alternative theories and there may yet be surprises to come regarding this position. Furthermore, a northern origin for major Eurasian haplogroups M, N and R has been ruled out in this 2007 study. // One of the recent 2011 studies regarding the migration out of Africa routes “Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route” confirms a dominant southern migratory route but affirms a peopling of E. Asia also took place via a northern (Central-South Asian-cum-West European route:
      “Our data, in combination with the published East Asian Y-haplogroup data, show that there are four dominant haplogroups (accounting for 92.87% of the East Asian Y chromosomes), O-M175, D-M174, C-M130 (not including C5-M356), and N-M231, in both southern and northern East Asian populations, which is consistent with the proposed southern route of modern human origin in East Asia. However, there are other haplogroups (6.79% in total) (E-SRY4064, C5-M356, G-M201, H-M69, I-M170, J-P209, L-M20, Q-M242, R-M207, and T-M70) detected primarily in northern East Asian populations and were identified as Central-South Asian and/or West Eurasian origin based on the phylogeographic analysis.

  7. ANCIENT NORTH ASIAN = small eyes with single eye lid, sharp nose with nose bridge, triangle cheek and jaw bone (ugly eyes with pretty nose) === typical Korean, Mongolian, Ainu, AmerIndian….

    ANCIENT CENTRAL ASIAN = eyes with double lid and muscle bag, round nose with no nose bridge, round cheek and jaw bone (pretty eyes) === typical Tibetan, Japanese, HakkaChinese…

    ANCIENT SOUTH ASIAN = eyes with double lid, big nose === typical Vietnamese, Thai, Cantonese….

    KOREAN = ancient HanChinese built Korean Dynasty, but Han could not outnumber the Native
    JAPANESE = ancient HanChinese outnumber the Native, but Han adepted the Native language
    TIBETAN= ancient HanChinese outnumber the Native, and still use similar ancient Han language (close to Hakka Chinese language)
    CHINESE = ancient HanChinese were almost all killed by Mongolian in 13th century. Only modern Hakka Chinese is closer to Ancient HanChinese. Northern Chinese are closer to Mongol-Manchu, Southern Chinese are closer to South Asian.

  8. You can google DNA testing and send your sample through mail to them. Damn I hate all these hate. All asians came from one common ancestor and before that Asians came out of East Africa. Please stop the hate . Those that hate where taught to hate. Usually by their parents or relatives. Please judge people individual and not as a group. I learn that myself.

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