Jōmon people, Jōmon culture and the roots of the Japanese people.

19 min readFeb 26, 2021

The Jōmon people (縄文人) are any of the many ancient people living in Japan. They arrived in Japan more than 45,000 years ago. It is now confirmed that they were not a homogeneous population but consisted of several groups which migrated into Japan during the Jōmon period.

The diverse Jōmon are ancestral to Japanese. In prehistory, many different ethnic groups migrated into Japan and slowly formed the Jōmon period population known today. We can not speak from a single Jōmon race. Today scientific and genetic evidence have shown that the Jōmon period people consisted of many distinct ethnic groups from various regions of Eurasia, which partially mixed with each other to form new groups within Japan. Later, during the Yayoi period, several Jōmon tribes were assimilated while others went extinct or were replaced.

Japanese people are genetically close to all East Asian people and are nearly indistinguishable from Koreans or (northern/northeastern) Han Chinese.

Haplogroups do not play an important role in determining ancestry or genetic relationship. Haplogroups make up less than 2% of the currently analyzeable DNA. Additionally haplogroups have or are made up from STRs, which may differ greatly even if classified as same haplogroup name. Japanese have on average about 55% haplogroup O, 25% haplogroup D, 16% C and 4% N, per Sato et al. 2014. These are commonly found in East Asians.

The reference population for the Japanese (Yamato) used in Geno 2.0 Next Generation is 89% East Asia, 2% Finland and Northern Siberia, 2% Central Asia, and 7% Southeast Asia & Oceania, making Japanese approximately ~100% East-Eurasian. Genealogical research has indicated extremely similar genetic profiles between these groups, making them nearly indistinguishable from each other and ancient samples.

Japanese people were found to share high genetic affinity with the ancient (~8,000 BC) “Devils_Gate_N” sample in the Amur region of Northeast Asia.

While it is generally agreed that modern Japanese formed from both Yayoi and Jōmon populations, the exact origin of the Jōmon people was, until 2021, rather controversial. It was known that the Jōmon were a heterogeneous people consisting of different ethno-linguistic groups which migrated into Japan during different times periods.

The major migration routes into Japan during the Jōmon period and the Yayoi period:

About the Jōmon period population:

According to study “Jōmon culture and the peopling of the Japanese archipelago” by Schmidt and Seguchi (2014), the prehistoric Jōmon people descended from diverse paleolithic populations with multiple migrations into Jōmon-period Japan. They concluded: “In this respect, the biological identity of the Jomon is heterogeneous, and it may be indicative of diverse peoples who possibly belonged to a common culture, known as the Jomon”.

See:

http://www.jjarchaeology.jp/contents/pdf/vol002/2-1_034-059.pdf

The genetic roots of the Jōmon period population can be traced back to the Tibetan Plateau, Taiwan/Southeast Asia, Northeast Asia, and ancient Siberia.

Watanabe et al. 2021 analyzed for the first time 7 Jōmon period individuals and found strong genetic heterogeneity. Like a previous anthropologic study from Kondo et al. 2017, the genetic results from Watanabe et al. 2021,found that there was a North to South cline and genetic diversity within the Jōmon period population of Japan.

While southern Jōmon people were mostly East Asian genetically, northern Jōmon had more complex ancestry, including geneflow from ancient Siberians. Hokkaido Jōmon and the historical Ainu samples were found to have DNA alleles associated with facial features commonly found in Europeans, but absent from contemporary Japanese and East Asians. These alleles likely arrived through geneflow from an ancient/extinct Siberian population (not modern Siberias, which are related to East Asians), and are the reason for the “exotic look” of certain Ainu. The study however found that the Hokkaido Jōmon were not homogeneous.

Hokkaido Jōmon samples were found to have 47,6% alleles of ABCC11 gene and 68,9% alleles of EDAR gene, common in continental East Asians and southern Jōmon. This means that the Hokkaido Jōmon already were shifted towards contemporary East Asians and that the ancestors of the Ainu already had East Asian looking people among them. This further means that the East Asian looking Ainu are as Ainu as the pseudo-Caucasian looking ones. The East Asian look does not come from recent admixture with Japanese, but was already present in the ancestral proto-Ainu of Hokkaido. Additionally, Ainu seem to lack any haplogroup O, associated with the Yayoi contribution.

See:

https://doi.org/10.1101%2F2020.12.07.414037

Some quotes from the study of Watanabe et al. 2021:

The genetic relationship between Jōmon samples and other Asian populations revealed further heterogeneity among the Jōmon samples.
In contrast to a previous study (Mc Coll 2018 and Chuan-Chao Wang et al. 2020/2021, which suggested partially shared ancestry between Ikawazu Jōmon sample (IK002) and Andamanese Onge, the new results did not find strong evidence for a partially shared ancestry, but in contrary geneflow from an East Asian-related population, basal to East and Northeast Asians, into both the Jōmon period people and less into the Andamanese Onge respectively. Additionally, the results do not find evidence for a noteworthy relation between coastal East Asians and Jōmon, or a hypothetical coastal migration route. Contrary, the majority of Jōmon samples appear closer to Inland and East Asian Highlanders, such Tibetans, Tujia and Miao people. The genetic evidence suggests that an East Asian source population near the Himalayan mountain range, basal to East and Northeast Asians, contributed high amounts of ancestry to the Jōmon period people, and less to ancient Southeast Asians.
The authors concluded that this points to an inland migration through southern or central China towards Japan, rather than a coastal route. Another ancestry component seem to have arrived from Siberia towards Japan and was more common in the northern Jōmon of Hokkaido and Tohoku. The seven Jōmon samples were generally closer to modern East and Northeast Asians as well as Central Asians (Xibo) and rather distant from ancient and modern Southeast Asians (Fig.5).
As previous morphological studies, such as Kondo et al. 2017, the genetic data confirmed that the Jōmon period people were heterogeneous and differed from each other depending on the region. A North-to-South cline was detected, with the southern Jōmon of Kyushu, Shikoku and southwestern Honshu being closer to contemporary East Asian people, while the northern Jōmon of Hokkaido and Tohoku being more distant from East Asians. SNP data revealed that southern Jōmon samples had largely SNP haplotypes associated with continental East Asians and East Asian phenotypes, while northern Jōmon had partially distinct SNP haplotypes, including alleles for facial features absent in East Asians and southern Jōmon. Hokkaido Jōmon samples were found to have 47,6% alleles of ABCC11 gene and 68,9% alleles of EDAR gene, common in continental East Asians and southern Jōmon. The study results confirmed the “dual-structure theory” regarding the origin of modern Japanese, but found that noteworthy amount of East Asian associated alleles were already present within the Jōmon period people prior to the migration of continental East Asians during the Yayoi period. The authors stated that this is the first comprehensive genetic evidence for heterogeneity among the Jōmon period population of Japan.
The comparison of Jōmon samples and other populations revealed that Ryukyuans are closest to southern Jōmon while Ainu are closest to northern Jōmon of Hokkaido. Ryukyuans and Ainu differed from each other quite noteworthy. Mainland Japanese (Yamato) were more distant from Jōmon samples, but like Ryukyuans closer to southern Jōmon samples. Japanese from different regions had different amounts of Jōmon-derived SNP alleles, ranging from 17,3% to 24% samplified by southern Jōmon, and 3,8% to 14,9% samplified by northern Jōmon. Jōmon-derived SNP alleles associated with phenotype and which are absent from other East Asians were found to be rare at only 2,4%.
Kinki- and Shikoku-Japanese were found to have the highest amount of Yayoi-derived ancestry rather than Kyushu-Japanese, which may be explained by a lower population number of Jōmon period Shikoku compared to Jōmon period Kyushu.

→ The majority of Jōmon people looked either East Asian or largely East Asian. Genetically, the Jōmon people were most closely related to certain Inland East Asians and some coastal East Asians. A strong Northeast Asian component was also detected.

Here the SNPs sharing between Jōmon period samples and modern populations shows that they were most similar to contemporary East Asians and also anthropologically part of the “Mongoloid cluster”.

These results are in accordance with other recent studies such as Boer et al. 2020 and Yang et al. 2020, as well as with Gakuhari et al. 2020.

Forensic reconstruction of Jōmon period individuals show that they were mostly East Asian looking:

Modern Japanese people:

Takeuchi et al. 2017 analyzed and compared the whole genome of Japanese people and found that modern Japanese nearly overlap with modern Koreans.

See:

https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0185487

The study revealed that the Japanese as a whole, have some genetic components from all of the Central, East, Southeast and Siberian populations, with the major components of ancestry profile identical to Korean and Han Chinese clusters. The major components of the Japanese Hondo cluster is similar to the Korean (87–94%), followed by Han Chinese 1 (3–8%) clusters. The genetic components from the Southeast Asian (Thais, Vietnamese and Malays) cluster were larger for the Ryukyuans — Southeast Asian (4–6%) — in comparison to the results found in the Hondo cluster — Southeast Asian (1–2%).

You can see here the ancestry overlap between Koreans and various regions of Japan is around 90 percent:

(Colored bars represent ancestry overlap). You can see the Shimane area has the highest overlap with Koreans of the groups they tested, which makes sense given the proximity to Korea geographically.

The earliest written records about people in Japan are from Chinese sources. These sources spoke about the Wa people, the direct ancestors of the Yamato and other Japonic agriculturalists. The Wa of Na received a golden seal from the Emperor Guangwu of the Later Han dynasty. This event was recorded in the Book of the Later Han compiled by Fan Ye in the 5th century. The seal itself was discovered in northern Kyūshū in the 18th century.

Early Chinese historians described Wa as a land of hundreds of scattered tribal communities. Third-century Chinese sources reported that the Wa/early Yamato lived on raw fish, vegetables, and rice served on bamboo and wooden trays, clapped their hands in worship (something still done in Shinto shrines today), and built earthen-grave mounds. They also maintained vassal-master relations, collected taxes, had provincial granaries and markets, and observed mourning. The Wei Zhi (Chinese: 魏志), which is part of the Records of the three Kingdoms, first mentions Yamataikoku and Queen Himiko in the 3rd century. According to the record, Himiko assumed the throne of Wa, as a spiritual leader, after a major civil war. Her younger brother was in charge of the affairs of state, including diplomatic relations with the Chinese court of the Kingdom of Wei. When asked about their origins by the Wei embassy, the people of Wa claimed to be descendants of the people of Wu, a historic figure of the Wu Kingdom around the Yangtze Delta of China, however this is disputed.

Japonic speakers were also present on the southern and central “Korean Peninsula”. These “Peninsular Japonic agriculturalists” were later replaced/assimilated by Koreanic-speakers (from southern Manchuria) likely causing the Yayoi migration and expansion within the Japanese archipelago. Whitman (2012) suggests that the Yayoi agriculturalists are not related to the proto-Koreans but that they were present on the Korean peninsula during the Mumun pottery period. According to him, Japonic arrived in the Korean peninsula around 1500 BC and was brought to the Japanese archipelago by the Yayoi agriculturalists at around 950 BC, during the late Jōmon period. The language family associated with both Mumun and Yayoi culture is Japonic. Koreanic arrived later from Manchuria to the Korean peninsula at around 300 BC and coexist with the descendants of the Japonic Mumun cultivators (or assimilated them). Both had influence on each other and a later founder effect diminished the internal variety of both language families.

However a study, published in the Cambridge University Press in 2020, concluded that there was a large migration of ancient Northeast Asians from the Amur region (between 6,000BC and 16,000BC), which introduced the Incipient Jōmon culture typified by early ceramic cultures such as the ones found at Ōdai Yamamoto I Site or Aoyagamiji site in the Tottori prefecture. These ancient Northeast Asian Jōmon population may be linked to the arrival of the Japonic languages, rather than the later Yayoi rice-agriculturalists, meaning that the Japonic languages are one of the Jōmon languages. Genetically they were close to modern Northeast Asians and Mongolians and are associated with the haplogroups C1a1 and C2 in Japan.

The rest of the theory is similar, with Peninsular Japonic being replaced by Koreanic agriculturalists. I.e. Japonic arrived much earlier in Japan during the early Jōmon period through a migration of Northeast Asians into Japan, which than created the indigenous Jōmon culture. The Yayoi agriculturalists are of different linguistic origin and got assimilated into the Japonic Jōmon.

The Japonic-speaking Early Jōmon people must have been drawn in to avail themselves of the pickings of Yayoi agricultural yields, and the Yayoi may have prospered and succeeded in multiplying their paternal lineages precisely because they managed to accommodate the Jōmon linguistically and in material ways.

Similarly a study by Yosuke Igarashi 2017 already proposed a homeland for Japonic within Jōmon period Japan. According to him and his results, Japonic was the language of the southern Jōmon period Japan and later expanded during and after the arrival of Yayoi agriculturalists.

Proposed phylogenetic tree of the Japanese language family.

I.e. Proto-Japonic expand from Japan and not with the Yayoi migration. Japonic can be linked to a Northeast Asian linguistic phylum.

Japonic and its link to Koreanic the Northeast Asian linguistic phylum.

We know that Japonic languages diversified about 2,000 years ago. Japonic started to diversify and expaned during and after the Yayoi period/migration. However the Yayoi likely did not spread Japonic nor Koreanic. Koreanic and Japonic were spoken by a population with genetic relationship to Northeast Asians and the ancient Devils_Gate_N sample (8,000 BC).

This is also suggested by Roobbets, which concluded that the Yayoi spoke an “para-Austroasiatic” language. Roobbets links the spread of Koreanic and Japonic to Northeast Asian agriculturalists and pastoralists, rather than rice-agriculturalists.

The estimation of a splitt between Japonic and Koreanic only 3,000 or 4,000 years ago is invalid and no reliable evidence exists either. No linguistic analysis supports that. The fact that there is no reliable amount of shared vocabulary nor cognates suggests that if Japonic and Koreanic are related, this must have been far more back in time. Most linguists agree that genetics should not be used as solely link for languages, but also archeologic and historical information.

Chaubey and Georg Van Driem (2020) concluded, based on these evidence, that Japonic splitted from a common ancestor with Japonic quite early and arrived in Japan already during the early Jōmon period.

They link the genetic and archeologic evidence of an Northeast Asian migration from the Amur region and the Liao region into Japan to the spread of pre-proto-Japonic, which than got isolated there for some time. Later, the Yayoi rice-agriculturalist caused the diversification and expansion of proto-Japonic about 2,000 years ago.

I.e. the Yayoi can neither be linguistically nor genetically be linked to the Northeast Asian component (i.e. the Devils_Gate_N sample in the Amur region) and thus did not spread the Japonic or Koreanic languages.

Here is what they finally concluded:

The Japonic-speaking Early Jōmon people must have been drawn in to avail themselves of the pickings of Yayoi agricultural yields, and the Yayoi may have prospered and succeeded in multiplying their paternal lineages precisely because they managed to accommodate the Jōmon linguistically and in material ways.
The dual nature of Japanese population structure was already advanced by Miller, who proposed that the resident Jōmon population spoke an Altaic language ancestral to modern Japanese, and this Altaic tongue underwent Austronesian influence when the islanders absorbed the bearers of the incursive Yayoi culture.
The original ‘para-Austroasiatic’ tongue of the Yayoi was lost except perhaps for loan words denoting agricultural terms. Notwithstanding a possible Austronesian presence in the Sakishima islands from Formosa at the end of the third millennium BC, any alleged ‘Austronesian’ influence on Japonic would have had to antedate the arrival of the Yayoi in Japan, deriving from the Lóngshān interaction sphere connecting the Dàwènkǒu culture of Shāndōng with Formosa and other coastal cultures, e.g. Qīngliángǎng in northern Jiāngsū, Mǎjiābāng in the Yangtze delta.

I.e. the linguistic origin of Japonic is from one of the Jōmon period populations, which can be traced back to ancient Northeast Asians, related to the Devils_Gate_N sample. This is the link between Koreanic and Japonic and their distant link to Mongolic/Tungusic/Turkic.

The Jōmon harbored this Northeast Asian component, while the Yayoi were rice-agriculturalists from the Yangtze area or the Shandong peninsula.

Summary: pre-proto-Japonic existed in southwestern Jōmon period Japan and possibly in the southern Korean Peninsula. The people speaking pre-proto-Japonic (and pre-proto-Koreanic) were close to the Devils_Gate_N sample. Later, rice-agriculturalists (Yayoi) arrived from the Shandong peninsula (or the Yangtze) to Manchuria and northern Korea, contributing rice-agriculture to the early Koreans (and mixing with them). Than these agriculturalists further migrated into Japan, again contributing and mixing with the local Japonic-speakers.

These events leaded to the expansion and diversification of proto-Japonic and proto-Koreanic respectively.

This is the only reliable way to link Japonic with Koreanic and the putative Altaic/Transeurasian phylum. This also explains the lack of shared vocabulary.

As example: Indo-European languages diversified about 4,000 years ago and share a large amount of vocabulary. The same counts for Sino-Tibetan or Austroasiatic.

Afroasiatic even diversified already 10,000 years ago and still has substantial shared vocabulary.

This further suggests that the link between Japonic and Koreanic must be far back in time.

Evidence for several migrations during the early Yayoi period exists. There is evidence that Austronesians also arrived in Kyushu (Azumi and Hayato/Kumaso tribes). Ainuic hunters and fishers expanded from the Okhotsk Sea down through Hokkaido into Tohoku. Ainu dialects diversified and expanded about 1,500 years ago from northern Hokkaido.

See:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062243

The historical Emishi were a heterogeneous group of various tribes which rejected the Yamato Imperial Court. While it is agreed that some Emishi tribes likely spoke an language related to Ainu, most spoke a divergent Japonic dialect, close to the historical Izumo dialect/language.

Additionally, the evidence of rice cultivation by the Emishi and the use of horses, strengthen the link between ancient Izumo Japanese and the Emishi. According to the theory, the Emishi are the Izumo Japanese which got pushed away from the Yamato Japanese, which did not accept any concurrence to the imperial rule. Per Boer et al. 2020.

The Yamato Japanese expanded and replaced/assimilated all other Japonic and non-Japonic groups.

This is the origin of the Yamato Japanese people (and other Japanese ethnicities).

Yamato Japanese are the dominant ethnic group in Japan and make up about 98,5% of the total population of Japan.

While the closest relatives of Japanese are Koreans, followed by Han-Chinese and other Northeast Asians, all East-Eurasian populations are rather closely related to each other.

Rowold et al. 2020 found that East-Eurasians (represented in the study by East and Southeast Asians) “were most distant to both West-Eurasians and Sub-Saharan Africans and formed a completely separate genetic cluster.”

Some information about the Jōmon culture:

Reconstruction of the Sannai-Maruyama Site in the Aomori Prefecture. The site shares cultural similarities with settlements of Northeast Asia and the Korean Peninsula and also with later Japanese culture, pointing to continuity between ancient and modern Japanese culture.

Jōmon clay mask, bearing similarities to clay masks found in the Amur region.

The Jōmon culture is one of the oldest cultures of the world. It is noted for the oldest kind of pottery and the unique designs. Jōmon culture has similarities with Siberian Paleolithic (Lake Baikal region) and also with archeological cultures in China. It is a matter of dispute if the oldest pottery of the world is from Japan or China.

Jōmon pottery is also known to have similarities with Native American pottery styles from Ecuador and the Northwest Coastal cultures of North America.

The dogū are famous Jōmon statues and there are tourist versions which you can buy in history shops or museums.

Jōmon also used obsidian, jade and different kinds of wood. The Jōmon created many jewelry and ornamental items. The Magatama was likely invented by one of the Jōmon tribes and is commonly found in Japan. It can be traced back to Northeast Asian traditions and later also found in other East Asian cultures. Koreans and various Steppe nomads also used similar items, but later in time.

The Jōmon did not use steel (at least, there is no evidence for that) and used hardened wood for spears and sword-like objects as well as bows.

The Jōmon culture was largely based on food collection and hunting, but it is also suggested that the Jōmon people practiced early agriculture. They gathered tree nuts and shellfish, laid the foundations for living such as hunting and fishing, and also made some cultivation. They used stoneware and pottery, and lived in a pit dwelling. Jōmon people cultivated the Azuki bean and used several plants too.

Recently in 2021, evidence for rice and millet agriculture was found in Honshu. It is also suggested that the peach was cultivated by some Jōmon tribes.

Jōmon period clay figure from the Yamanashi Prefecture.

Jōmon culture was quite advanced and not a simple hunter-gatherers culture. It is no coincidence that the Jōmon had the earliest pottery and high artistic abilities.

The various Jōmon tribes are to a varying degree ancestral to Japanese people. Some linguists note the possibility that Japonic is actually one of the many Jōmon languages which survived. Similarly Chaubey et al. 2020 concluded that Japonic may have already be spoken in the Jōmon period on Kyushu, Shikoku and Honshu.

The Japonic-speaking Early Jōmon people must have been drawn in to avail themselves of the pickings of Yayoi agricultural yields, and the Yayoi may have prospered and succeeded in multiplying their paternal lineages precisely because they managed to accommodate the Jōmon linguistically and in material ways.
The dual nature of Japanese population structure was already advanced by Miller, who proposed that the resident Jōmon population spoke an Altaic language ancestral to modern Japanese, and this Altaic tongue underwent Austronesian influence when the islanders absorbed the bearers of the incursive Yayoi culture.
The original ‘para-Austroasiatic’ tongue of the Yayoi was lost except perhaps for loan words denoting agricultural terms. Notwithstanding a possible Austronesian presence in the Sakishima islands from Formosa at the end of the third millennium BC, any alleged ‘Austronesian’ influence on Japonic would have had to antedate the arrival of the Yayoi in Japan, deriving from the Lóngshān interaction sphere connecting the Dàwènkǒu culture of Shāndōng with Formosa and other coastal cultures, e.g. Qīngliángǎng in northern Jiāngsū, Mǎjiābāng in the Yangtze delta.

The Jōmon harbored this Northeast Asian component, while the Yayoi were rice-agriculturalists from the Yangtze area or the Shandong peninsula.

Jōmon culture is noted to share similarities to Native American cultures and Siberian (Altaian and Buryat) as well as Northeast Asian cultures.

Reconstruction of Jōmon period clothing found in Honshu:

In contrast the clothing style brought by the Yayoi agriculturalists:

Aspects of the Jōmon culture were used in the famous video game “The Legend of Zelda: Breath of the Wild”. You may know this game.

Nintendo’s art director Takizawa Satoru said that the Jōmon culture was the inspiration for the “Sheikah slates, shrines and other ancient objects” in the game.

A recreated Jōmon village in the form of an experience park (Sarashina no Sato), which offers different activities, can be visited in Chikuma, Nagano.