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The Japanese as a creation of the Christian Era

The traditional model, which I’ve alluded to before on this weblog before, is that Japan is a synthesis of Jomon and Yayoi, with the latter dominant, and bringing rice-agriculture to the islands. A new paper in Science indicates it may be more complicated than that.

Ancient genomics reveals tripartite origins of Japanese populations:

Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.

The Kofun period begins around 300 AD. The implication here is that there was a mass migration from the Asian continent less than 2,000 years ago, likely from Korea. The first agriculturalists, the Yayoi, seem to be a mix of native Jomon and individuals with strong affinities to populations in Manchuria.

Here’s a stylized representation that captures the turnover:

The Jomon are interesting because these results indicate low effective population, and, deep connections with ANE (Ancient North Eurasians). They also seem a clade deep within Northeast Asians, dating to the Pleistocene.

In any case, the authors admit that their sampling of the Yayoi is weak, so there needs to be follow-up here. If it does turn out that the Japanese are mostly Kofun-period, then I think that recalibrates our sense of its history a great deal. The Japan of the 7th century which enters into history was a very young nation.

19 thoughts on “The Japanese as a creation of the Christian Era

  1. Interesting the connection between the ANE and Jomon.
    In 23andMe’s latest update my father (Irish), gets 0.2% Japanese – possibly an ANE trace?

  2. Said enough about this paper in the open thread already, but yeah, can’t reiterate hard enough with them having relatively few Yayoi (2), sampled at low coverage, who seem relatively diverse in Jomon proportion bearing in mind this paper and Robbeets preprint (

    In the Robbeets preprint, we find that the Yayoi from two other sites have proportions of Jomon related ancestry that are similar to or only 2x present day Japanese, and we have a Bronze Age (1st Millennium BCE) site on the Korean peninsula, up fairly near the South-North border, has about 20% Jomon ancestry (with earlier sites in Korea from middle and late neolithic having up to 95% Jomon ancestry).

    All the samples tend to have relatively low coverage and SNPs; this might be a consequence of Japanese scientists liking to do the early work themselves first and then having less capability on this than the European / US centres, at the moment? Hence this collaboration between Dublin and Japanese scientists got more data out. Hopefully in future there will be bigger and more diverse panels of Yayoi samples from collaborations between the Western labs and Japanese scientists, like how the Wang paper last year ( gave Jomon samples that average about 40x as much coverage/SNPs as the previous samples sequenced by Japanese labs and publications. Hopefully there is no actual limitation in the availability of Yayoi skeletal remains.

    I suspect these Yayoi from the Shimomotoyama Rock Shelter will be outliers and the actual difference between Yayoi->Kofun period will prove to be likely less (half to a third the size of the turnover here?) as a sample set builds up.

    Also any parallel change in Korea – the Robbeets preprint shows this person at 650 BCE who they model with around 20% Jomon ancestry… When did that change to the current proportion, which is detectable but much less than even present day Japanese (about 10-15%)? Important for Japan because surely Korea is the point from which later influences streamed into Japan. Was Korea’s “Three Kingdoms Era” (57 BCE to 668 AD) perhaps deeply connected with ongoing migration out of Northeast China?

  3. Are the Ainu pure Jomon?

    What is the linguistic evidence?

    Wikipedia says: “its ultimate derivation and relation to other languages is unclear. Japonic languages have been grouped with other language families such as Ainu, Austroasiatic, Korean, and the now-discredited Altaic, but none of these proposals has gained widespread acceptance.”

  4. @Walter, it is somewhat unclear because the papers with good quality ancient Jomon genomes from last year don’t tend to be the same as those that have Ainu data (which is restricted by Japanese). It’s probably not total, but substantial (80% or something?).

  5. Didn’t see that coming. But, it seems like a 1300 year gap between Yayoi and Kofun with different regional affiliations can be thought of properly as distinct waves of migration and not just one mixed wave that extended over time. From the introduction to the paper:

    “Before the arrival of farming cultures, the archipelago was occupied by diverse hunter-gatherer-fisher groups belonging to the Jomon culture, characterized by their use of pottery. The Jomon period began during the Oldest Dryas that followed the Last Glacial Maximum (LGM), with the earliest pottery shards dating to ~16,500 years ago (ka ago), making these populations some of the oldest users of ceramics in the world. Jomon subsistence strategies varied and population densities fluctuated through space and time, with trends toward sedentism. This culture continued until the beginning of the Yayoi period (~3 ka ago), when the arrival of paddy field rice cultivation led to an agricultural revolution in the archipelago. This was followed by the Kofun period, starting ~1.7 ka ago, which saw the emergence of political centralization and the imperial reign that came to define the region.”

    FWIW, describing it as “the Christian era” is particularly confusing in this context as none of the three waves were Christian or had any Christian influence in that time period.

    The three part origin story does help explain why so little Jomon culture survives despite a meaningful genetic contribution.

  6. Interesting, influx of East Asian into Japan started at fall of Han dynasty (three kingdoms) during the most kaotic time with northern barbarians uprisings/invasions and forming north/south dynasties. Also northern Han, Manchu, and Japanese share almost complete genetic overlaps, which have more distance from southern Han together. But northern Han are the tallest people in East Asia. It is believed that island environment shrink all species sizes including human.

  7. @Matt:
    Do you have the papers for the earlier Jomon-like ancestry in Korea? That’s super interesting. I didn’t realize that the indigenous population of the Korean peninsula may’ve been originally related to that of Japan. Sad to think of all these people overrun and diluted. Could the posited relationship of Japanese to other languages on the mainland have been obscured by heavy, early influence by Jomon languages? If, as has been speculated, the Yayoi came from the Korean peninsula, they would have then had a much longer period of contact with Jomon-like peoples.

  8. @Otanes, the only adna paper with any Korean coverage so far is this one – It’s a preprint so may be revised, but check out Fig. 3a on page 14, and check out the associated supplements. There are Jomon like samples in the very southern tip Korea at the Late Neolithic and that sample with admixture sample up in Central Korea at the Bronze Age. Possibly native to the peninsula (expanded there after LGM), but also possibly reletively arrival of ancestry from Japan – we just don’t know. There are also 100% Jomon like samples from the Ryukyus.

    In a way it is sad to see the replacement of peoples, but on the other hand, these were small groups to begin with, so in a way contributing approximately 10% to one of the world’s largest ethnic groups (the Japanese) is not such a bad outcome considering how reduced they were by the Last Glacial Maximum, and is better than what happened to a lot of groups (like the groups from Guangxi who left absolutely no trace at all). Not as good as the core East Asian group that seems to have come out of it without these harsh bottlenecks that we see in Jomon and WHG, but still not the worst outcome. And depending on the scenario, and what the Japanese language is, some of their language and culture may survive (perhaps even if only in a creole form).

    (On another note, prompted by IC’s comment I gathered some Fst scores for Japanese vs other East Asian populations, using the relative high quality data from the Human Origins 1240k panel – . The degree of divergence between Japanese and CHB (Beijing Han) is quite considerable and much greater than between CHB and the general Han Chinese pool. It seems like a small amount of this Jomon ancestry, and their other contributions, is quite strong in pushing Japanese apart from CHB, while it interestingly has no role in pushing them further away from West Eurasians or Africans, who are the same distance from JPN and CHB.)

  9. @Matt:
    Without an absurd natural law dictating that the smartest always triumph, I’m curious if we lost more capable and brighter people who simply weren’t present in great enough numbers to defend themselves against an onslaught of agitated, malnourished agriculturalists. I can’t remember where I came across it, but I distinctly recall a paper by a Japanese anthropologist of the early 20th century recording Ainu brain weights as being about as much greater than the Japanese subjects’ average as modern Northeast Asians’ are compared to Western Europeans. I know that bigger does not always equal better, looking at, say, neanderthals and all the extra space allocated to the occipital lobes. There’s no way of knowing without analysis I’m not qualified to perform, on a bunch of Ainu and Jomon skulls.

    Considering their early achievements and surprising complexity before Yayoi intrusions, one has to wonder. Then again, you are right in pointing out how their inheritance is present, perhaps even in alleles associated with intellectual ability. Maybe I have some sort of stupid, autistic obsession with “preservation”.

  10. “It is believed that island environment shrink all species sizes including human.”

    Are you serious? Japan is much larger than, for example, the U.K.

  11. @otanes, possible; though I’m not sure the Ainu or Ryukyuans (enriched in Jomon ancestry too, though far less than Ainu) tend to rock IQ test outcomes over the main Japanese. (Some Japanese researchers tend to claim Ryukyuans do a little worse, though I’m unsure what this is due to).

    Generally in Asia / Eurasia, where cranial capacity peaks in the very NE Siberia – (after Beals) – people don’t seem to do better on tests / education outcomes than people from more southern parts of East Asia (or people from West Eurasia?). I think when the Russians break out data on the national minorities who do well in schooling or tests, it’s not so much like peoples with heavy amounts of NE Asian ancestry (who seem like they should have higher cranial capacity on Beals) do noticeably well. Or likewise in Russian regional PISA for areas richer in the high cranial capacity groups.

  12. Japan, Taiwan, Singapore, all now share similar development historis.

    Japan had inflow of Han people during chaotic time around fall of Han dynasty, which transformed Japanese society. Very likely slow process with piecemeal assimilation into Native culture.

    Taiwan had Han colonization much faster during late Ming Dynasty with Dutch East India company which practice replacement policy to native people.

    Singapore was the most recent one done by British more or less similar to Dutch approach. But it is able to form new culture like Japan.

  13. First of all, thanks to Mr. Khan and some of the commenters here (“Matt” in particular) for the many fascinating details.

    These days my memory of things I read and studied earlier seems to be fading, but I think it was Gina Barnes who once wrote about the practice of referring to peoples of Goguryeo, Baekje, Silla, Gaya Confederacy (or Mimana) and Yamato as “Koreans” or “Japanese” quite anachronistic and indeed detrimental to understanding who they were at the time.

    From the historical perspective (rather than genetic), it seems that the Korean Peninsula at around the time of the Three Kingdoms period was inhabited by two groups of people (who, no doubt, had varying degrees of intermixtures), those of the southerly “Samhan” origin and later arrivals from the “Buyeo” peoples from today’s Manchuria. I think they roughly correspond to the Silla and Gaya peoples for the former and Goguryeo and Baekje peoples (or at least their elites) for the latter.

    I am curious as to how these two groups tie with the inhabitants of Japan at the time and what kind of genetic evidences, if any, exists to determine their respective ethnogeneses.

  14. “3rd month, 15th day. Fifty-six immigrants from Koryö were settled in the province of Hitachi. They were given lands, received an allowance of grain, and made to pursue their avocations in peace.”

    Interesting that the parts of the Nihon Shoki mentioning immigration from Koryö may have a historical basis (at least the timing appears to match up).

  15. Japanese history does record a fair amount of migration from China and Korea during this exact time period. However, nowhere near what this new genetic data implies.

    Very interesting that at least ~1/3 of Japanese Y lineages still descend from the Jomon (assuming they account for all of Y haplogroup D in the islands), despite two overwhelming waves of foreign migration. Perhaps a parallel to what happened with haplogroup I in Europe?

  16. Or haplogroup D in Tibet as the other analogy.

    I2 in Middle Neolithic Northern Europe does seems potentially particular analogous as you note – both might be scenarios where the haplogroup gets established as the local patrilocal lineage between some early interaction of frontier Neolithic people and frontier HG, and then remains at high frequency despite continued geneflow from Neolithic migrants due to local patrilineal “dominance”.

    Although the later story of I2 and I1 in North and Central Europe might be kind of different – for I2 anyway it looks plausible to me it was reintroduced at a good frequency back into the north after Corded Ware culture by Bronze Age cultures with links to SE Europe (like Unetice) and probably around 7-10% across North Europe from West to East today (up to possibly double that in Belarus, Ukraine and Russia). I2, which in the Middle Neolithic was from HGs, in the Bronze Age was potentially from the BA Southeast (barring geographically restricted subclades which were rare true survivors from MN North/Central Europe). I1, which accounts for another 10% ish in the belt from Poland to UK (lower than that in Belarus, Ukraine and Russia and up to 30% in Central Europe and North Germanic groups), is also mysterious, appearing pretty suddenly with Germanic cultures or slightly preceding proximate groups after really nothing prior (or only some distantly related samples in Mesolithic people) prior to that.

  17. This makes a lot of sense. We have known that Chinese and Korean missions with Wa were essential in creating the roots of Japanese culture as we would recognise them. That said, it always seemed that if the Yayoi were part of this transformation, then surely a literate and sinophile Japan would have arisen earlier.

    I think this ties in well to what we do know: The Yayoi introduce changes to Japan, but these are not part of the East Asian package (save for rice) and this ties into the relative “foreignness” of Wa in Chinese literature. If these were East Asian migrations, then the Chinese and Koreans would have indicated closer customs, but these same to be very different.

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