The Jomon contributed little to the Japanese

A few months ago there was a preprint with an ancient Japanese genome, Jomon genome sheds light on East Asian population history. I read it but didn’t say anything at the time. I read it again, partly because I’m reading a history of Korea where the Wa, the early Japanese, show up to intervene in mainland affairs. This cameo made me think more deeply about what happened in Japan several thousand years ago.

The above genome comes from Honshu, and dates to 2,500 years before the present. And yet it’s quite different from modern Japanese! Here is the abstract:

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

Let me be frank: the term basal probably is somewhat misleading. Ancient DNA in East Asia is in its infancy. We don’t really know what’s going on, and what went down. But I can offer a guess.

I think in the next few years we will realize that there was a massive demographic expansion out of a few agricultural hearths in the eastern regions of what we now call China during the early Holocene. The Sino-Tibetan peoples, Austro-Asiatic, and Austronesian are derived from this series of expansions. But with hindsight, I think we will see that the peoples to the north and east of China proper, are also downstream of this agricultural revolution.

Within China proper a secondary expansion occurred, dating to the rise of the Chinese civilization. This ‘erased’ a lot of the variation in southern China, and a quasi-panmixia was enforced through the Chinese dynastic cycles, as northerners moved south and vice versa.

In the first figure, the Treemix panel shows that only ~3% of the modern Japanese ancestry needs to be accounted for by an edge from this Jomon genome. This implies that there was massive population replacement of the Jomon by the Yayoi people, from southern proto-Korea. I say “proto-Korea,” because the origins of the ancestors of the modern Korean culture seem to be located much further north, in what is the border region of Manchuria and North Korea today. The Yayoi is quite possibly derived from one of the indigenous peoples of the southern Korean peninsula, who were assimilated by the expanding Koreans as they moved southward around 0 A.D.

Within the preprint, the authors seem to converge on two facts. First, the Ancestral North Eurasian (ANE) admixture into much of East and Southeast Asia was minimal but much more substantial in Siberia. This is entirely plausible, though I think there needs to be more ancient East Asians besides Tianyun to conclude there isn’t some basal fraction The authors suggest that shared drift between Hoabinhian hunter-gatherers in ancient Southeast Asia and the Jomon individual confirm the likely southward origin of modern-day East Asians. I suspect the inference is correct, though I don’t know the shared drift tells us that much without more samples.

In the preprint, the authors observe that this is a much stronger affinity among coastal East Asians to the Jomon sample than from interior peoples. I don’t know what to say about this, except that it seems likely to me that coastal pre-agricultural populations would have greater numbers than interior peoples.

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5 thoughts on “The Jomon contributed little to the Japanese

  1. I’m surprised it seems so low here as previous work seemed to suggest a higher contribution.

    It seems that this makes it tricky to explain the prominence of Ainu modal D y-dna haplogroups at frequencies in the model Japanese at 30-50% that seem essentially non-existent in Koreans?

    Jomon ancestry also suggested to be responsible for dip in derived EDAR frequency in Japanese relative to Koreans, but I guess that doesn’t work if Jomon ancestry is at 3%.

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  2. If you check out YFull.com, it looks like D currently is in the midst of a bit of a sampling bonanza, there’s a bunch of new kits under analysis under one of the primary branches, D-CTS11577. None of the new samples have countries associated yet, but it looks most of them will probably end up being Chinese. And interestingly, of the current Chinese Ds reported on YFull (admittedly only a small sampling), none of them appear to be Tibetans, though there are some Yunnan and Sichuans, which are right next door. It’s interesting that Japanese D seems to be mostly under D-Z3660, making it phylogenetically closer to Anadamanese (and possibly Hoabhinian) D clades, giving some credence to the paper’s contention of a more southernly origin for the Jomon.

    D in general is an interesting haplogroup, given how spatially diverged it is from its sibling E. Hopefully one day we can get a clear picture of where DE first coalesced and diverged.

    Regarding the new underestimate of Jomon ancestry in contemporary Japanese populations, I haven’t had a chance to read the paper yet but did they try corroborating the TreeMix ratio with any f4 tests? That’s supposed to be the gold standard for determining actual admixture percentages within populations right? Razib, I know you’ve used TreeMix in the past so I assume you trust it, but I remember Davidski on Eurogenes saying he wasn’t crazy about it, he said he found the outputs to be unreliable for one reason or the other.

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  3. Another datapoint, using the data for the ILK002 Jomon sample and various East Eurasians from the Global25 PCA test by Eurogenes and then processing these through PCA: https://imgur.com/a/ggfH54k

    Tends to suggest higher input to Japanese related to ILK002 – looks around 10%-20%…

    10% would be close to compatible with the admix graph results from the paper (“We carried out admixture graph modelling to further characterize the contributions of IK002-related ancestry … The range of admixture fractions with good model fit is generally quite wide, with best fit models show IK002-related contributions of 8%, 4% and 41% into Japanese, Devil’s Gate Cave and Ami, respectively (Fig. S8). We note that while the substantial contribution into Ami seems at odds with the lower f4 statistics compared to Japanese, the lineage admixing with Ami shares only a very short branch with IK002 , suggesting a contribution from a distinct group with an early divergence from the IK002 lineage.”). And the ADMIXTURE results (“Subsequently, we carried out model-based unsupervised clustering using ADMIXTURE[42] (Fig.S5). Assuming K = 10 ancestral clusters (Fig.1B), an ancestral component unique to IK002 appears, which is the most prevalent in the Hokkaido Ainu (average 79.3%). This component is also shared with present-day mainland Japanese as well as Ulchi (9.8% and 6.0%, respectively)”). It seems more like the treemix may be outlyingly low?

    (Fit of Jomon->Ainu 79.3% embeds into Jeong 2016 estimate of Ainu->Japanese 17.8% – https://www.genetics.org/content/202/1/261 – as 14%).

    But maybe the G25’s test is compressed the Jomon sample towards East Asians. And maybe some of the affinity to Jomon in this test reflects East-to-West patterns in early East Eurasian populations that were erased by later admixture there and preserved in Japan?

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  4. On a side note, Japan’s desire to conquer Korea must be a subconscious need to reclaim the land taken from their ancestors by invaders from the north of the peninsula. This would make the rivalry between the Japanese and the Korean very deep-seated indeed.

    On another side note, by virtue of geography, the North Koreans could claim to be true heirs to the ancestral Koreans, while the South Koreans are a bunch of assimilated ‘barbarians’ who happen to assume a Korean entity and Korean language.

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  5. “In the first figure, the Treemix panel shows that only ~3% of the modern Japanese ancestry needs to be accounted for by an edge from this Jomon genome. This implies that there was massive population replacement of the Jomon by the Yayoi people, from southern proto-Korea.”

    Like @Matt, and for essentially the same reasons, I am inclined to think that 3% just has to be way too low. The Y-DNA D in Japan (in a clade with a quite remote TMCA relative to the clades found in Tibet, India, the Silk Road, the Andamans) is very hard to explain with any non-Jomon source. (The distribution of Y-DNA D and the phylogeny of Y-DNA D also tends to point to a northern route rather than a southern one, although perhaps the Han just obliterated the intermediate populations.)

    There was indeed a steady flow of Northern Chinese women into Japan from the Yayoi arrival until really into the early 20th century, while male migration to Japan seemed to pretty much drop to a trickle after the initial wave of migration, so it wouldn’t be surprising if there was more indigenous Y-DNA than mtDNA in Japan contrary to the usual pattern, causing Y-DNA D to overstate the indigenous ancestry proportions. But, the numbers just aren’t big enough to bridge the gap between the Y-DNA implication and the autosomal data if the autosomal data is just 3%. Likewise as Matt notes, the Jomon-Ainu similarity is too great for the replacement to be that big with such a big Ainu component in the Japanese from other studies.

    As another reality check, even if it isn’t the most reliable source, to just rely on the admittedly imperfect measure of physical appearance, the Japanese are really not that difficult to distinguish on sight from Koreans, while there is a lot more overlap in range of appearance between Northern Han Chinese people and Koreans. Yes, there’s a distinction, but it isn’t as marked and most Koreans are within the range of Northern Han Chinese variation which isn’t true of Koreans v. the Japanese, or the Northern Han Chinese v. the Japanese. A population that has only a 3% autosomal introgression from a source population just isn’t going to be that visibly different from the source population. But, a population that has 10%-30% introgression is going to be visually distinctive and to something much closer to the degree that we observe between the Japanese and mainland East Asians.

    Another reason that this is a hard sell is, that as I learned from this blog, there were huge swaths of Japan’s main islands that weren’t under the control of Yayoi-derived cultures and states until ca. 1000 CE, cutting by 60% the number of generation ago in which this massive replacement could have occurred, and also disfavoring the idea of massive replacement because if the Yayoi had such a decisive advantage that they managed 97% population replacement, they would have swept the entire Japanese archipelago in 200-300 years or less (around the time frame for the massive replacement seen in Britain and left not even a tiny relict community of non-Indo-European language speakers that survived even into the earliest attested Roman or pre-Roman era), when in fact we know that it took the Yayoi more like 1500+ years to take all of Japan, and even then left a minority language speaking and genetically distinct Ainu population that wasn’t completely wiped out into the present.

    The weirdness of 23andMe ancestry of Korean-Japanese with lots of Koreans seeming to be a large percentage Japanese, when historically the reverse hypothesis, that lots of Japanese people have substantial, but not overwhelming Korean ancestry, seems more likely.

    Further, the track record of fishing based food producers vis farmer/herders seems everywhere to be better than that of terrestrial hunter-gatherers. But the Jomon were definitely of the former type and were sufficiently non-nomadic enough to be one of the very earliest adopters of fragile pottery.

    Could it be that IK002 is atypical and has a lot of recent Northeast Asian ancestry perhaps, as people with that ancestry do seem to have seeped into Japan from the North? Or, is there just something off about the analysis method used? The latter seems more plausible than the former.

    This paper is far enough from the priors established by multiple prior papers some examining ancient DNA that serious skepticism is in order. If I were in the team that got that result, I’d be very concerned that we might have a mistake somewhere in either the data collection or the analysis.

    “I say “proto-Korea,” because the origins of the ancestors of the modern Korean culture seem to be located much further north, in what is the border region of Manchuria and North Korea today. The Yayoi is quite possibly derived from one of the indigenous peoples of the southern Korean peninsula, who were assimilated by the expanding Koreans as they moved southward around 0 A.D.”

    Possibly. The Yayoi certainly aren’t a straightforward branch linguistically off the branch of Korean languages that produced modern Korean. Whoever the pre-Yayoi were in Korea, their descendants were on the losing side of some major struggles on the Korean Pennisula.

    But, the Japanese language, which almost certainly has its roots in the Yayoi language which doesn’t even have all that much time depth (comparable to Biblical Greek v. modern Greek), since there is virtually no Ainu influence lexically in modern Japanese, is a lot closer to Korean than it is to Chinese linguistically, and probably even closer to poorly attested lost dialects of Korean, even if one doesn’t accept the full Altaic language family hypothesis. This suggests a relatively northern origin for the proto-Koreans as well.

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