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The Origins of the Japanese people

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.






Japan on Globe

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
Y-DNA haplogroups
Frequency in Japan (n=689)
A
7.5%
C1
3.5%
B4
8%
C3
3%
B5
4%
D1
0.1%
C
0.5%
D2
40%
D4
30%
N + NO
2%
D5
5%
O1
1%
F
5.5%
O2a
1%
G
6%
O2b
31%
HV
0.1%
O3
18%
M7
18.5%
Q
0.5%
M8a
1.5%
   
M9
1.5%
M10
1.5%
M11
0.5%
N9
3.5%
Y
0.1%
Z
1.5%
   
Others
5%

Paternal lineages (Y-DNA)

54% of Japanese men belong to haplogroup O, and more precisely to the subgroups O3 and O2b. Both of them could be of Han Chinese or Korean origin. A negligible percentage of the Japanese are O1 or O2a, two lineages that trace their roots among southern Chinese or south-east Asian people.

Y-DNA haplogroup D2, making up 36% of the Japanese male lineages, is interesting because it is only found in 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 years before present. The first carriers of the gene would have migrated along the coasts of the Indian Ocean, through Indonesia, and gone up to Japan, South-East Siberia, then moved inland to Mongolia, with the last part of the group continuing as far as Tibet. However, whereas the Japanese belong to haplogroup D2, Tibetans are part of the completely separate D3a, the Qiang of 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.

Along with D2, C1 is the other haplogroup unique to Japan. Both are likely to have been in the Japanese archipelago since the first human beings reached the region 35,000 years ago. They would have come from Austronesia, probably using the land bridge from Taiwan through the present-day Ryukyu islands. The presence of haplogroup D in a minority of Indonesian people confirms the link between the two countries.

The 3% of haplogroups N may be of Siberian or Chinese origin. Haplogroup C3, representing also 3% of the population, is typical of the Mongols and Siberians. It might have come with the Ainu through Sakhalin island and Hokkaido, or along with the Yayoi farmers from Korea. C3 is indeed found at both extremities of the country but is rare in central Japan, suggesting two separate entries.

As for the Ainu, it is known from the last surviving tribes of "pure" Ainu (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 C3. It would mean that the aboriginal people of Japan, the Ryukyuans and the Ainus, commonly known as the Jomon people, are ultimately related as members of haplogroup D2.

In conclusion, approximately 43% 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 15 main lineages and many more subclades or minor haplogroups. Those that can be associated with a Sino-Korean origin include haplogroups A (mostly A4 and A5), B (mostly B4 and B5), C, D (mostly D4 and D5), F, M8a, M9, M10, M11 and Z. Together they are present in 67% of the Japanese maternal lineages.

At present, 70 Jomon-period skeletons have been tested in two separate studies (although both in Hokkaido only). The haplogroups identified were D1, D4h2, G1b, M7a, N9b. The dominant lineage was by far N9b. Haplogroup N9b is unique to Japan and is the maternal equivalent of C1 and D2 on the paternal side. N9a is found in Southeast Asia, parts of China, and throughout Japan, but is absent from Korea or Eastern China, and is consequently also surely of Jomon origin. M7, although present in most of East Asia, is almost always represented by the M7a subclade in Japan, and has been associated with the Jomon and Ainu people.

Haplogroups G and Y are normally found in Western and Eastern ends of Siberia. These lineages are more common among the Ainu, both inside and outside Japan. 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 permeated the Jomon stock.

Haplogroup D1 is normally not found among East Asians but among Native Americans. How did this lineage end up in Paleolithic Hokkaido is still unknown. It should be said, however, that D1 is now extremely rare in the modern Japanese population, if it still exist at all. The most likely explanation is that D1 first appeared in Siberia then migrated to the Americas, and that a few women carrying this lineage married into other Siberian tribes that eventually came into contact with the Ainu then Jomon people, after many generations of geographic drift. 0.1% of haplogroup HV have also been identified among the modern Japanese. HV is a very old lineage (40,000 years old) typical of Europe, with frequencies fading through the Middle East, Central Asia and Siberia. Its negligible presence in East Asia is surely the result of a very long series of women being married to neighbouring communities. The main point of entry to East Asia would have been Xinjiang, where about half of the DNA is of European origin.

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/Malaysia 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 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 aborigenal animist religion. Japanese Shintoism is also a variety of animism, and is practised side-by-side with Buddhism, a religion derived from Hinduism (Buddha himslef was born a Hindu). 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.

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

  • Japanese Population Structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: Effects on population-based association studies, Yamaguchi-Kabata et al.(2008)
  • Ancient mtDNA from Jomon skeletons
  • Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia, Adachi et al. (2011)
  • Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes, Hammer et al.
  • Origin of the Japanese people and language
  • A History of Japan: From Stone Age to Superpower, by Kenneth G. Henshall
  • Guns, Germs, and Steel, by Jared Diamond
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