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The Origins of the Japanese people
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Author: Maciamo (last update : October 2016)



The origins of the Japanese people is not entirely clear yet. It is common for Japanese people to think that Japan is not part of Asia since it is an island, cut off from the continent. This tells a lot about how they see themselves in relation to their neighbours. But in spite of what the Japanese may think of themselves, they do not have extraterrestrial origins, and are indeed related to several peoples in Asia.

We shall have to go back a long way through history and analyse in depth the genetics, culture and language of the archipelago and try to find out whether the Japanese are indeed unique, and in what way.

During the last Ice Age, which ended approximately 15,000 years ago, Japan was connected to the continent through several land bridges, notably one linking the Ryukyu Islands to Taiwan and Kyushu, one linking Kyushu to the Korean peninsula, and another one connecting Hokkaido to Sakhalin and the Siberian mainland. In fact, the Philippines and Indonesia were also connected to the Asian mainland. This allowed migrations from China and Austronesia towards Japan, about 35,000 years ago. These were the ancestors of the modern Ryukyuans (Okinawans), and the first inhabitants of all Japan.

The Ainu came from Siberia and settled in Hokkaido and Honshu some 15,000 years ago, just before the water levels started rising again. Nowadays the Ryukuyans, the Ainus and the Japanese are considered three ethnically separate groups. We will see why.

Genetic evidence

It is now believed that the modern Japanese descend mostly from the interbreeding of the Jomon Era people (15,000-500 BCE), composed of the above Ice Age settlers, and a later arrival from China and/or Korea. Around 500 BCE, the Yayoi people crossed the see from Korea to Kyushu, bringing with them a brand new culture, based on wet rice cultivation and horses.

As we will see below, DNA tests have confirmed the likelihood of this hypothesis. About 54% of paternal lineages and 66% the maternal lineages have been identified as being of Sino-Korean origin.

DNA analysis of the Japanese people

Two kinds of DNA tests allow to trace back prehistoric ancestry. The first one is mitochondrial DNA (mtDNA), DNA found outside the cells' nucleus and inherited through the mother's line. The other is the Y-chromosome (Y-DNA), inherited exclusively from father to son (women do not have it). They are both inherited in an unaltered fashion for many generations, which allow geneticists to identify very old lineages and ancient ethnicities. According to the current limited data, the genetic composition of Japan is as follow.

mtDNA haplogroups
Frequency in Japan (n=2264)
Y-DNA haplogroups
Frequency in Japan (n=689)
N + NO
(M*, M12, M13, R9a, R11)

Paternal lineages (Y-DNA)

Just over half of Japanese men belong to haplogroup O. The vast majority belong to O2b (aka O-SRY465), a lineage found especially in Manchuria, Korea and Japan, and O3 (aka O-M122), the main Han Chinese paternal lineage. A negligible percentage of the Japanese belong to the O1a (aka O-M119), a lineage especially common in southern China, Taiwan, the Philippines, Malaysia and Indonesia, and O2a1 (aka O-M95), which is found in south-west China, Indochina, around Malaysia and in central-eastern India.

Y-DNA haplogroup D2 (aka D-M55 or D-M64.1), making up 40% of the Japanese male lineages, seems to be native to Japan. Its closest relatives are scattered around very specific regions of Asia: the Andaman Islands (between India and Myanmar), Indonesia (only a small minority), Southwest China (mostly among the Qiang ethnic group), Mongolia (also a small minority) and Tibet. Haplogroup D is thought to have originated in East Africa some 50,000 to 60,000 years before present. The first carriers of the gene would have migrated along the coasts of the Indian Ocean, from the Arabian peninsula all the way to Indonesia, then following the chain of islands up through the Philippines and using the land bridge from Taiwan through the present-day Ryukyu islands to Japan. Korea and Sakhalin was have been connected to Japan during the Ice Age, allowing D tribes to continue to south-east Siberia and Mongolia and northwest China, ultimately ending up in Tibet.

However, whereas the Japanese belong to haplogroup D2, Tibetans are part of the completely separate D3a, while some Chinese ethnic groups (e.g. Qiang people of Sichuan) belong to D1, and the Andaman Islanders of D*. It means that their most recent common ancestors goes back tens of thousands of years. In other words the genetic gap between these ethnic groups is immense, despite false appearances of belonging to a common haplogroup. Haplogroup D2 was formed 45,000 years ago, but the most recent common ancestor of Japanese D2 members lived 23,000 years ago, which means that other D2 branches may have become extinct outside Japan. Haplogroup D2 is found among the Ryukyuans as well as the Ainus, and is thought to have been the dominant paternal lineage of the Jomon people.

Haplogroup C is another extremely old lineage that left Africa approximately 60,000 years ago and spread over most of Eurasia. Two subclades of C are found in Japan: C1a1 (aka C-M8, formerly C1) and C2a (aka C-M93, formerly C3). Both are likely to have been in the Japanese archipelago since the first human beings reached the region 35,000 years ago.

Haplogroup C1a seems to have split around 45,000 years ago in the middle of Eurasia, one group going west to Europe, and the other east to Japan. C1a2 was found among the first Paleolithic Europeans (Cro-Magnons) during the Aurignacian period, and was still relatively common 7,000 years ago, both among Mesolithic West Europeans and Neolithic farmers from Anatolia. C1a2 is now nearly extinct in Europe.

Haplogroup C2a, representing also 3% of the population, is typically found among the Mongols and Siberians. It might have come with the Ainu through Sakhalin island and Hokkaido, or along with the Yayoi farmers from Korea. C2a is indeed found at both extremities of the country but is rare in central Japan, suggesting two separate points of entry.

It is known from the last surviving tribes of 'pure' Ainu people, living on the island of Sakhalin in Russia, just north of Hokkaido, that almost all of them belong to haplogroup D2, with a small minority of C2a.

Approximately 3% of Japanese men belong to haplogroup N, a lineage that is thought to have originated in China some 35,000 years ago, but underwent a serious population bottleneck during the Last Glacial Maximum (c. 24,500 to 17,500 years before present), and re-expanded after that. Japanese people belong to N1, a subclade that is associated with the diffusion of the Neolithic lifestyle from northern China to Siberia. Haplogroup N1 was found at high frequency (26 out of 70 samples, or 37%) in Neolithic and Bronze Age remains (4500-700 BCE) from the West Liao River valley in Northeast China (Manchuria) by Yinqiu Cui et al. (2013). Among the Neolithic samples, haplogroup N1 represented two thirds of the samples from the Hongshan culture (4700-2900 BCE) and all the samples from the Xiaoheyan culture (3000-2200 BCE). Haplogroup N1c is found especially among Uralic and Turkic peoples nowadays, including among the Finns, Estonians and Sami in Northeast Europe, and among the Turks in Central Asia and Turkey. It is found at low frequencies in Korea and could have arrived with the Yayoi people. Alternatively, N1 could also have entered Japan via Sakhalin and Hokkaido, as it is present among eastern Siberia tribes.

Haplogroup Q is the dominant lineage of Native Americans, but originated in Siberia. Nowadays it is found at varying, but generally low frequencies throughout Siberia, Central Asia, as well as parts of the Middle East and Europe. While haplogroup N1 seems to have propagated from northern China to Siberia, haplogroup Q would have spread the other way round, apparently only reaching northern China and Korea some 3,000 years ago with invasions from Mongolia. As this was before the Yayoi invasion of Japan, it is possible that the tiny fraction of Japanese Q lineages came with Yayoi farmers. It is unlikely to have entered Japan through Hokkaido as it is not found among tribes at the eastern extremity of Siberia, nor among the Ainus.

In conclusion, approximately 43% to 48% of modern Japanese men carry a Y-chromosome of Jomon origin. The highest proportions of Y-DNA haplogroup C and D is found in northern Japan (over 60%) and the lowest in Western Japan (25%). This is concordant with the history of Japan; the Yayoi people of Sino-Korean origins having settled first and most heavily in Kyushu and Chūgoku, in Western Japan.

Maternal lineages (mtDNA)

The matrilineal (mtDNA) landscape is more varied. There some 15 main lineages (>1%) and many more subclades or minor haplogroups.

Jomon mtDNA

At present, 131 Jomon-period skeletons have been tested in several separate studies, with samples from Kanto (n=54), Tohoku (n=23) and Hokkaido (n=54). The haplogroups identified in Tohoku and Hokkaido were D4h2, M7a and N9b, with also D1a and G1 in Hokkaido.

Haplogroup N9b was clearly dominant in northern Japan during the Jomon period, making up over 60% of the matrilineal lineages. Today, N9b is also found among the Udege people of eastern Siberia, just north of the islands of Hokkaido and Sakhalin.

Haplogroup G1 is a typically Siberian lineage, completely absent from China, and found only at low frequencies in Korea (2.5%). It most common in eastern Siberia, particularly among the Negidals in the Khabarovsk Krai, among the Chuvans of Chukotka, where it exceeds 25% of the female lineages, and among the Itelmens and the Koryaks of the Kamchatka Peninsula, who have over 50% of G1 lineages. G1 has a frequency of 2.5% in Japan, but 22% among the Ainu, who have intermarried over the centuries with tribes from eastern Siberia via Sakhalin and the Kuril Islands. It is therefore not surprising to find in in ancient Hokkaido as well as among modern Ainu.

Haplogroup D4h seems to be native to Japan, while D1 is not normally found among East Asians but among Native Americans. How did D1 end up in Paleolithic Hokkaido is still unknown. D1 might first appeared in Siberia then migrated to the Americas, and that a few women carrying these lineages married into other Siberian tribes that eventually came into contact with the Ainu, after many generations of geographic drift. It should be said, however, that D1 now extremely rare in the modern Japanese population and may even have become extinct since the Jomon period.

Samples from Kanto were more varied and suggests that migrations from the continent might have happened before the Yayoi period. They included haplogroups A (7.4%), B (9.3%), D4h (18.5%), F (1.9%), G2 (1.9%), M7a (3.7%), M7b (1.9%), M8a (9.3%), M10 (33%) and N9b (5.6%).

Like N9b, haplogroups M7 and M10 are extremely ancient lineages that are associated with the some of the earliest migrations of Homo sapiens to East Asia over 50,000 years ago. M7b, M7c and M7e have been found in southern China, Indochina, and the Philippines. M7a, M7b and M7c were all found during the Jomon period and are still found in modern Japan. However, about 60% of Japanese M7 members belong to M7a, which is really specific to Japan.

Haplogroup G2 is found in 5% of the Japanese population, but only 4% of the Ainu. It has a very different geographic distribution, being absent from eastern Siberia, but relatively common in Korea (6%), northern China (6.5%), Mongolia (10%), Tibet (11%), Nepal (14%) and even Central Asia.

It is not clear at present why typically Sino-Korean haplogroups like A, B, F and M8a were already present in the Kanto during the late Jomon period. These may represent early migration of farmers from the continent, many centuries before the Yayoi invasion. The Late Jomon people are known to have cultivated a variety of plants, including rice, barnyard millet, buckwheat, barley, soybeans and taro potatoes. Many of these, including rice and millet are very unlikely to have been domesticated independently by the Jomon hunter-gatherers, and almost certainly required the migration of farmers from China or Korea. Catherine D'Andrea reported evidence for Late Jomon rice, foxtail millet, and broomcorn millet dating to the first millennium BCE in Tohoku, which means that an even earlier introduction of agriculture would have taken place in western Japan.

Yayoi mtDNA

78 mtDNA samples from the ancient Yayoi people have been tested to date. Half of them belonged to haplogroup D4, while 15% belonged to haplogroup A and another 15% to haplogroup B. The remaining samples were made up of haplogroups F, M8, N9a and Z.

The presence of haplogroup Z is particularly interesting as it is a typically Siberian lineage, also found among the Uralic populations of Northeast Europe, including the Sami of northern Fennoscandia. Uralic speakers share the patrilineal haplogroup N1c which seems to have originated with Neolithic farmers or herders from Manchuria (=> see Y-DNA section above). Modern Japanese possess about 1.5% of mtDNA Z and Y-DNA N, which could both represent ancestry from those Manchurian Neolithic farmers.

Other lineages

Haplogroup M9a is found in 2% of the Japanese population. It the most common lineage that still hasn't been found in either Yayoi or Jomon samples. M9 is also fpund in China and Tibet. The much rarer haplogroup M12 only makes up 0.1% of the Japanese population, and is found especially on the Chinese island of Hainan, but also at low frequencies in mainland China and Korea. The equally rare M13 (0.2%) is found chiefly among the Mongols, Tibetans and some Siberian ethnic groups like the Yakuts and Dolgans.

Haplogroups C (C1, C4a, C5) and Y are North Asian lineages with frequencies of respectively 0.35% and 0.40% in Japan. Haplogroup C is common of Siberia and Mongolia and is otherwise rare in East Asia. It is still unclear when it arrived in Japan. Haplogroup Y is found at the western and eastern ends of Siberia. Although very rare in Japan, it is considerably more common among the Ainu (about 20%), both inside and outside Japan. It hasn't been found so far in either Jomon or Yayoi samples. The Ainu would have acquired these haplogroups through population exchange (intermarriages, probably) with their Siberian neighbours. This could also explain how Y-DNA haplogroup C3 and N, two paternal lineages typical of Mongolia and eastern Siberia, permeated the Ainu stock.

Another interesting discovery is the 0.5% of haplogroup HV identified among the modern Japanese. HV is a very old lineage (40,000 years old) typical of the Middle East, with frequencies progressively fading as one advances through Europe, Central Asia and Siberia. Haplogroup HV may have been brought by Neolithic farmers or Bronze Age Proto-Indo-European speakers from the Pontic-Caspian Steppe to Siberia and Mongolia. Its negligible presence in Korea and Japan could be explained by the fact that these two populations intermingled a bit with from Bronze Age Mongols, from whom they acquired horses and bronze working. To this day, the Mongols have between 10 and 15% of European or Middle Eastern DNA inherited from Neolithic farmers and Bronze Age Indo-Europeans. The Koreans and Japanese only have traces of European DNA (about 0.1%), but it is present.

Autosomal DNA analysis

Genome-wide SNP genotypes of the Japanese show that people from northern Japan (Tohoku and Hokkaido) are the most distantly related to the Han Chinese, while those from Western Japan (Kyushu, Chūgoku, Kinki) are the closest. This confirms the theory of the continental Yayoi invasion from Kyushu.

Okinawan people were shown to be a clearly distinct ethnic group, falling in a separate genetic cluster from other Japanese.

The Austronesian connection

The Paleolithic Jomon people appear to have come from Austronesia during the Ice Age, before Japan was resettled by Bronze-age rice farmers from the continent. The Chinese had previously expanded southward to South-East Asia. The original inhabitants of Indonesia and the Philippines might have been related to Dravidians of Southern India. Y-haplogroup C, which has been associated with the first migration of modern humans out of Africa towards Asia, is relatively frequent in Kerala (southern tip of India) and Borneo. These early Austronesians are thought to have been the ancestors of the Ice Age settlers of Japan.

From a linguistic point of view, Bahasa Indonesia/Melayu and Japanese language share only a few similarities, but nonetheless striking ones. Apart from the very similar pronunciation in both languages, there is the same hierarchical differences in personal pronouns. For example "you" is either anda or kamu with the same meaning and usage as anata and kimi in Japanese. Likewise, the Japanese verb suki ("to like") translates suka in Bahasa. Such similarities are probably more than mere coincidences, and may reveal a common origin. Furthermore, in both languages the plural can be formed by simply doubling the word. For instance, in Japanese hito means "person", while hitobito means "people". Likewise ware means "I" or "you", whereas wareware means "we". Doubling of words in Japanese is so common that there is a special character used only to mean the word is doubled (々) in written Japanese. In Bahasa, this way of forming the plural is almost systematical (person is orang, while people is orang-orang). Expressions like ittekimasu, itteirashai, tadaima and okaeri, used to greet someone who leaves or enter a place, and which have no equivalent in Indo-European languages, have exact equivalents in Malay/Indonesian (selamat jalan, selamat tinggal...).

Another evidence of the migration of haplogroup D from the Indian Ocean to Japan is that Tamil language (from Tamil Nadu in South India) also bears some uncanny similarities with Japanese language. Naturally, these languages having evolved separately for maybe 40,000 years, only a tiny fraction of the common roots have subsisted, but enough to confirm that such a common origin might indeed have existed, in a very distant past.

Japanese matsuri (festivals) resemble so much Balinese ones that one could wonder if one was not copied from the other. During cremations in Bali, the dead body is carried on a portable shrine, very much in the way that the Japanese carry their mikoshi. Balinese funerals are joyful and people swinging the portable shrine in the streets and making loud noise to scare the evil spirits. Basically, Balinese religion is a form of Hinduism that has incorporated the aboriginal animistic religion. Japanese Shintoism is also a form of animism, and is practised side-by-side with Buddhism, a religion derived from Hinduism, sometimes blending the two religions in a syncretism known as Shinbutsu-shūgō.

There are lots of other cultural similarities between ancient cultures of Indonesia and Japan. For example, both Balinese temples and Japanese shrines, as well as traditional Japanese and Balinese houses have a wall surrounding them, originally meant tp prevent evil spririts from penetrating the property. Despite the radical changes that Indonesian culture underwent after the introduction of Islam and Christianity, and the changes that Buddhism brought to Japan, it is still possible to observe clear similarities between the supposed original prehistoric cultures of the two archipelagoes.

The Korean connection

Japanese and Korean languages are both classified by linguists as Altaic languages, along with Mongolic, Tungusic and Turkic, among others. Nevertheless, Japanese is so distant from Mongolic and Turkic than the similarities are hardly more evident than those with Indonesian or even Tamil.

Korean language, however, is much closer to Japanese. The grammar is very similar, and both have imported about half of their vocabulary from Chinese, which makes these three languages almost mutually understable in the written form, thanks to Chinese characters (rarely used in Korea nowadays, except in place names). Native Korean and Japanese words are often related when comparing Old Korean and Old Japanese, but few of them are really obvious to modern speakers.

Ancient Korea was divided in three kingdoms, Baekje, Silla and Goguryeo, each with their own distinct language. Jared Diamond, a renowned UCLA anthropologist, argues in an article for Discovery Magazine that the modern Korean language is derived from that of the ancient Kingdom of Silla, the eastern Korean kingdom that unified Korea, whereas the Old Japanese spread by Yayoi farmers would be derived from the ancestral language of the northern Kingdom of Goguryeo.

Mindset and values in Japan and South Korea are deeply intertwined, thanks to the strong influence of Confucianism, Taoism and Buddhism in both countries. This is obvious from the corporate culture (e.g. discipline, seniority system), the strict politeness system, or the Taoist/Buddhist value of simplicity and humility. These cultural aspects all ultimately stem from China. That's why Japan and Korea are considered branches of the Chinese civilisation.

The Japanese colonisation of Korea (1895-1945) has left of a lot of resentment on the Korean side and a sense of superiority mixed with repressed shame and denial on the Japanese side. This is why both Koreans and Japanese are often reluctant to admit their similitudes. However, thanks to natural affinities in sensitivities and tastes, South Korea and Japan appear to be culturally closer as ever nowadays.

Sources and reading recommendations

Ancient Japanese DNA

Modern Japanese DNA

Ancient East Asian DNA

Modern East Asian DNA

History & Antropology

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