The peopling of the Japanese archipelago and the formation of modern Japanese people and culture (including the Ainu people)

This post will include general information about the Jōmon period people and the peopling of the Japanese archipelago. It gives you a good overview about the formation of Japanese people, including the Ainu.

Japanese people formed from various ancient East Asian-related groups.

Noteworthy are:

  • The heterogeneous Jōmon period hunter-gatherers and fishers, which can be traced back to ancient Siberians, ancient East Asian Highlanders (Himalayans), ancient Northeast Asians, and Southeast Asians. → Jōmon period people were heterogeneous and diverse, they homogenized only during the late Jōmon period, following a population decline and food shortage. Likely also some bottleneck events. (The modern Ainu are neither a representative of the ancient Jōmon, nor their direct descendants. More about that later.)
  • The Yayoi rice-agriculturalists, from the Korean peninsula and ultimately likely from the Yangtze culture area. They were rather homogeneous and had advanced technology compared to the Jōmon locals. They did not replace the Jōmon, but merged with them, together forming the Yayoi culture.

Noteworthy is that there were strong differences between the different Jōmon period populations. Especially Hokkaido Jōmon differed greatly from other Jōmon samples, having also links to Paleolithic Siberians (samplified by the Yana sample, Upper Paleolithic people of Northern Eurasia, which had European-related ancestry and phenotype).

Here we see the various migration routes into the Japanese archipelago:

Modern Japanese can be modeled as:

Most similar to Koreans and other East Asians (Han), followed by an Central Asian/Tibetan component, Southeast Asian component and South Asian component. This may be because of the heterogeneous Jōmon period people and their genetic impact onto modern Japanese.

It is in accordance with other recent studies, modeling Japanese as 92% Liao river farmers (a combination of Northern East Asian components and Southern East Asian components, commonly found in the Liao river region and the Korean peninsula), and 8% Jōmon period hunter-gatherers (samplified by the various ancient samples). It should be noted that Jōmon ancestry among Japanese is modeled, so we not know how much the Jōmon period people contribute towards modern Japanese. It is rather hard to distinguish East Asian inter-ethnic genetic components because of the heterogeneity among the early Jōmon. Jōmon-derived ancestry is suggested to range from 8% up to 45%, depending on the test methods.

For Liao River farmers and the formation of Koreans see:

The Ainu and Jōmon are not the same and the Jōmon of Hokkaido differed from the Jōmon of Honshu or Kyushu. The historical Ainu formed from Hokkaido Jōmon, Okhotsk, and Satsumon tribes, thus are not a representative for the Jōmon period people, especially not for all of Japan!

Hokkaido Jōmon formed from Upper-Paleolithic groups of Hokkaido and Siberia and from groups migrating into Hokkaido from Honshu.

See also:

In 2021, it was confirmed that the Hokkaido Jōmon population formed from “Terminal Upper-Paleolithic people” (TUP) indigenous to Hokkaido and Northern Eurasia and from migrants of Jōmon period Honshu. The Ainu themselves formed from these heterogeneous Hokkaido Jōmon and from a more recent Northeast Asian/Okhotsk population.

Also associating this looks solely with possible Jōmon ancestry (which itself is contradictory, as they formed from heterogeneous groups during the Paleolithic and late Neolithic) is misleading. I do not understand why westerners are so fascinated by this? Northeast Europeans also received high amounts of Northeast Asian geneflow and look slightly different from contemporary Europeans (even speak Uralic languages).

My point is that Jōmon were not all European looking. Only Hokkaido Jōmon had geneflow from Paleolithic Siberians, which brought in this gene allele associated with facial features commonly found in Europeans. There than existed a North to South cline from Hokkaido to Honshu.

Jinam et al. found that there is a gene allele associated with facial features commonly found in Europeans among some Hokkaido Jōmon and Ainu. This allele is suggested to have arrived from Paleolithic Siberia with the spread of the microblade culture. A new study in 2021 found also affinity between Hokkaido Jōmon and the Yana sample (Ancient North Eurasian sample in Russia). Another previous study found 14% European-related ancestry in Hokkaido Jōmon.

A study published in the scientific journal “Nature” by Jinam et al. 2015, using genome-wide SNP data comparison, found that the many Ainu have gene alleles associated with facial features which are commonly found among Europeans but absent from Japanese people and other East Asians, but these alleles are not found in all tested Ainu samples. These alleles are the reason for their pseudo-Caucasian appearance and likely arrived from Paleolithic Siberia.

It is noteworthy that Hokkaido Jōmon differed from Honshu Jōmon quite strongly. Different groups existed in Jōmon period Japan which later homogenized during the late Jōmon period, following a population decline and food shortage.

Additionally, the Ainu did not all look European-like/Eurasian, but many looked typically Northeast Asian. The Ainu language itself is even suggested to have been originated from the Okhotsk component.

See also:

Jōmon people mostly loolek East Asian, some had the specific allele and looked mixed/Eurasian-like or Native American like.

Thus I want to make people aware that it is more complicated than simply Jōmon look, as most Jōmon also looked East Asian.

Forensic reconstructions of Jōmon period samples:

I.e. Jōmon can be somewhat compared to Native American look, which also carry both East Asian-related alleles (75%) and European-related alleles (25%).

Peruvian Native:

Kennwick man reconstruction:

These results suggest a level of inter-regional heterogeneity not expected among Jomon groups. This observation is further substantiated by the studies of Kanzawa-Kiriyama et al. (2013) and Adachi et al. (2013). Kanzawa-Kiriyama et al. (2013) analysed craniometrics and extracted aDNA from museum samples that came from the Sanganji shell mound site in Fukushima Prefecture dated to the Final Jomon Period. They tested for regional differences and found the Tokoku Jomon (northern Honshu) were more similar to Hokkaido Jomon than to geographically adjacent Kanto Jomon (central Honshu).

Adachi et al. (2013) described the craniometrics and aDNA sequence from a Jomon individual from Nagano (Yugora cave site) dated to the middle of the initial Jomon Period (7920–7795 cal BP). This individual carried ancestry, which is widely distributed among modern East Asians (Nohira et al. 2010; Umetsu et al. 2005) and resembled modern East Asian comparison samples rather than geographical close Urawa Jomon sample.

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.


Genetic data of Jōmon period people:

It is now established that the Jōmon people initially formed from heterogeneous groups, which merged during the Jōmon period in Japan. There existed a North to South cline.

The Jōmon are overall close to East Asians, and appear basal to Northeast Asians and Native Americans (per Gakuhari et al. 2020).

Gakuhari et al. 2020 could successfully analyze Jōmon samples and modern populations from Eurasia. East Asians and East Asian-related populations form a tight cluster:

Interestingly, Oceanias are as distant to East Asians as they are from Europeans. The Andamanese/Onge however are shifted towards East Asians, as they received geneflow from East Asian Highlanders and southern East Asians. Andamanese/Onge were found to have between 6% up to 45% East Asian-related ancestry, with 31% being found in analyzed Onge as average.

Lineages which are suggested to have arrived during the Jōmon period include C1a, D1, C2, F and K. The first haplogroups were F and K, followed by C and D. However K and F are less than 2% today and thus may be an echo and got early replaced by the later C1a, C2 and D. This correspond with the findings that another Paleolithic population was replaced by the early Jōmon tribes.

I.e. the shared haplogroup D can be related to an deep/divergent East Asian lineage, which contributed to the Jōmon period people and to Andamanese people, as well as Ancient Tibetans (Highlanders). Andamanese formed from this East Asian-related component and from an older Oceanic component shared with Australasians (Papuans). Another common haplogroup among the Jōmon was C1a and C2, traced back to Northeast Asians. D additionally arrived into the Andamanese about 7,000 years ago through a male migration and founder effect. Great Andamanese tribe however persevered the original haplogroups which are M and S (similar to the ones in Papuans).

A 2019 study found that haplogroup D had a positive bottleneck event shortly before the Yayoi migration and became dominant in several Jōmon tribes. D expanded from Kyushu up north and down south respectively, replacing previous lineages such as K, F and C1a. → D is not directly related to Ainu people, but became dominant throughout genetic drift. The actual haplogroup which distinguish Ainu from Japanese is C2.

Here is the distribution of haplogroup D today. Note Japan, Tibet and the Altai.

Ancient and modern Tibetans share genetic drift with the Jōmon populations (at least partially).

Per Yang et al. 2020, see:

Melinda Yang, population geneticist and historian, also concluded that Northeast Asians and Southeast Asians are closely related, genetically speaking, ultimately descending from basal East Asian source in southern China and Mainland Southeast Asia, which gave also rise to the East Asian Highlanders, Hoabhinians (at least partially) and Paleo-Siberians (ancestors of Native Americans, not to be confused with Paleolithic Siberians).

Jōmon haplotype sharing by Watanabe et al. 2021, shows that Jōmon were most similar to contemporary East Asians, but the authors note diversity among Jōmon samples, and that the Hokkaido Jōmon had gene alleles associated with facial features commonly found in Europeans. I.e. there was a North to South cline. Northern Jōmon in Hokkaido carried alleles associated with facial features commonly found in Europeans (possibly the reason why some Ainu look somewhat European or Central Asian). Additionally, the northern Jōmon shared affinity with the Yana sample of northern Siberia in Russia.

Jōmon SNPs haplotype sharing (Watanabe et al. 2021):

Tujia people and Miao people share noteworthy high amounts of SNPs haplotypes.

Jōmon PCA position:

The Tianyuan sample is ancestral to East Asians, including Jōmon and Southeast Asians, and positioned as basal. More than 45,000BC.

What languages did the Jōmon speak?

A very good question. We know that they had multiple languages. Among these were possibly Ainu, Amuric, Austronesian, Tungusic and Japonic.

Chaubey and George van Driem 2020 found evidence that Japonic was already present in southwestern Japan during the Jōmon period before the Yayoi migration.

The Japonic-speaking Jōmon people must have been drawn in to avail themselves of the pickings of Yayoi agricultural yields, and the Yayoi may have 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 people and later expanded during and after the arrival of Yayoi agriculturalists with the new merged population.

“Evergreen broadleaf forest culture, associated with the southwestern Jōmon and possibly proto-Japonic languages”

It is suggested that the southwestern Jōmon belonged to a wider “evergreen broadleaf forest culture” which stretched from southern Tibet through China to Japan. It is associated with the Azuki bean cultivation.

Later it seems that new techniques related to the Azuki bean agriculture and the domestication of the peach spreaded from southwestern Japan to China.

It is still the culture of several Tibeto-Burmese tribes in China and Northeast India.

It was characterized by the Azuki bean agriculture practiced by southwestern Jōmon and some southern Chinese groups.

Azuki and Peach agriculture during the Jōmon period:


  • Japanese are close to all East Asian and East Asian-related populations worldwide, but especially close to Korean people. Koreans and Japanese form an indistinguishable cluster, followed by Han.
  • Ainu people have heterogeneous ancestry, mostly Hokkaido Jōmon and Okhotsk, with some Yayoi and Siberian components. Thus Ainu are shifted towards northeastern Siberians (Itelmens and Chukchi) compared to Japanese people.
  • Ryukyuans are close to contemporary Japanese, but have relatively more affinity with Han and Southeast Asians, compared to contemporary Japanese.

Some Japanese individuals carry the mentioned gene allele associated with facial features commonly found in Europeans, causing the somewhat exotic look.

But as I said, such look is very seldom and often hyped by Westerners.

An association with Ainu ancestry is also misleading and a erroneous simplification.

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

As said in the beginning, East Asian-like look among Europeans is much more common than Eurasian or European-like look among Japanese. So I do honestly not understand the hype about Japanese people and the many misconceptions regarding the Jōmon period people.

I hope this post helps to clarify many questions about the Jōmon period people and the Japanese.



Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store