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A few thousand years ago the islands of Japan were settled by a group of rice farmers, ushering in the Yayoi period. Prior to this Japan was home of the Jomon culture, which is notable for being a pre-agricultural society which may have innovated to produce the world’s earliest pottery. Because everything before ~500 A.D. in Japan is prehistory (this date being generous) the relationship of the Jomon and Yayoi, and the ethnogenesis of the Japanese people as a homogeneous group, is somewhat speculative. But, it does seem one group of Jomon descended people persisted in northern Honshu, the Emishi. Finally, it is usually understood that the indigenous people of Hokkaido, the Ainu, have some relationship to the Jomon.

220px-Bjs48_02_AinuThe Ainu are of interest because they do not exhibit many of the traditional characteristics of Northeast Asian people in their phenotype. Ergo, they are termed the “hairy Ainu.” Early anthropologists noting the physical uniqueness of the Ainu speculated that they were a lost branch of the white race. But even early ABO blood group analysis suggested that this was not the case. Rather, the closest relatives of the Ainu were the peoples of Northeast Eurasia. Nevertheless, it does seem striking that the Ainu do not exhibit the distinctive features of many other East Asians. I think this makes more sense though when you consider that it is likely that the East Asian physical type is not quite as primal as we might think. The latest work from genetics indicates very rapid population expansion out of the loci of agricultural activity on the North China plain over the past 10,000 years. The relatively uniformity of physical type and genetic relatedness across East Asia today may have more to due with demographic expansion that genetic connectedness through gene flow over long periods of time.

Much of this can be gleaned by inference, implication, and intuition. A new paper in Molecular Biology and Evolution uses explicit model testing to infer whether the modern Japanese the products of population replacement, admixture, or cultural diffusion. In other words, are the Japanese total cultural and biological descendants of the Yayoi. Are the Japanese total cultural and partial biological descendants of the Yayoi. Or, are the Japanese total cultural descendants of the Yayoi, but total biological descendants of the Jomon. The paper, Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data, reports that the middle hypothesis, genetic admixture, is highly supported when compared to the other two.

There are few interesting points. First, reference population matters. I’m rather sure that the Ainu samples they used as proxies for Jomon are imperfect because the Ainu today have recent Japanese admixture, and, as they note the Jomon themselves exhibit population structure (i.e., the Ainu are one lineage of post-Jomon people). This structure goes back to the late Pleistocene, over 10,000 years ago. The divergence between the ancestors of the Jomon and the Ainu goes back ~20,000 years ago, about when East Asian peoples began to diversify in the wake of the Last Glacial Maximum. The estimates for Jomon ancestry are probably inflated by the admixture in the Ainu, but dampened by the fact that the Ainu are not prefect proxies for the Jomon. Additionally, the reference population for the Yayoi, whether Koreans or North Chinese, has an effect.

But these are minor details. The major conclusion in a qualitative sense is that the modern Japanese are predominantly descended on the whole from the Yayoi farmers, but have a substantial minority component of indigenous Jomon ancestry. This almost certainly varies as a function of geography, the modern Japanese people likely can be used to obtain a “ghost phylogeography” of the Jomon whom they absorbed, as presumably admixture occurred locally a fair amount.

• Category: History, Science • Tags: Japan, Jomon, Yayoi 
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Randy McDonald just pointed me to a 2008 paper in AJHG, Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies. It speaks to an issue I brought up earlier in my post, Sons of the farmers, the story of Japan, which describes the ethnogenesis of the Japanese modern people from the Yayoi culture. The Yayoi presumably brought rice from the Asian mainland, probably from what is today southern Korea. But the Japanese islands were not uninhabited before this period. Japan was home to the Jomon culture, which has a rather storied history in the annals of archaeology. The Jomon seem to have been a predominantly hunter-gatherer population which was also sedentary, and engaged in the production of objects such as pottery which are normally associated with more advanced farming societies. I have a difficult time crediting the ~13,000 year period of continuous development which is attributed to the Jomon, but, it does seem likely that the period between 2,000 and 2,500 years before the present did mark a sharp cultural discontinuity in the Japanese islands, as Jomon gave way to Yayoi.

A related issue to this indisputable cultural shift is the question of whether it was accompanied by a demographic transition. This particular debate is fraught with politics, but we have enough genetic information that we can hazard a tentative guess. It does look like the Jomon-Yayoi cultural shift was accompanied by a significant demographic transition. In particular, the Ainu of the north and the inhabitants of the Ryukyu islands in the south seem distinctive from the majority of Japanese who inhabit the core islands. The hypothesis that these peoples are more related to the Jomon, or directly descended from them. One must distinguish these two groups though; the Ainu remained culturally distinctive from the Japanese, in lifestyle and language before their de facto absorption into the Japanese of late. In contrast, the people of the Ryukyus today seem to be clearly related to the southern Japanese in both language and lifestyle. If the Ryukyu islanders preserve more of the Jomon ancestral heritage, it may simply be due to the dilution of the signal of the original Yayoi pioneers as they moved south.

But there is another piece of the puzzle which has always been a point of curiosity for me: what happened to the non-Japanese populations of northern Honshu? Termed Emishi, these people retained a distinctive identity in northern Honshu until ~1,000 years ago. Fragmentary references in the historical texts make it clear that these people did not speak Japanese natively, and were physically different in appearance, being a “hairy” and “bearded” people. This is how the Ainu were also described, and because of the Emishi’s geographical proximity to Hokkaido it is presumed there may have been a cultural continuity. It turns out that the 2008 paper hints at the genetic imprint of the Emishi.

First, some preliminaries. The authors drilled down to between 100 and 150 thousand SNPs. While 10,000 random markers is sufficient for inter-continental distinctions, a floor of 100,000 is probably optimal for more fine-grained examinations. They had the HapMap populations, which included Africans, Europeans, Chinese, and, some Japanese. But their big data set were nearly 7,000 Japanese from all over the islands. I assume this is large enough that one can down-weight the probability of problems with representativeness due to small sample sizes. Below is a table of Fst values. This basically measures between population genetic distance. There are two things to focus on. First, the Okinawan sample, from the Ryukyu islands, is clearly more distant from all the main island samples. This is what we’d expect. But second, notice that the highest value of genetic distance is between Tokai-Hokuriku and Tohoku.

Tokai-Hokuriku and Tohoku are both on Honshu, the former in the center of the island, between Tokyo and Osaka, and the latter to the far north. Tohoku then is coterminous with the former Emishi region. Some of the patterns here are made clear by the recent history of migration within the Japanese islands. Tokyo is in Kanto-Koshinstsu, and is naturally a magnet for individuals from all over the country. Hokkaido was settled by Japanese only within the last 200 years, and not through gradual expansion from Tohoku to the south.

Another way to look at the genetic variation is a PCA plot. The y axis represents eigenvector 1, the largest dimensions of variation in the data set, and the x axis eigenvector 2, the second largest dimension. On all the plots you see the HapMap Chinese from Beijing on the top left of the plots. You can see here the difference in sample sizes. The cluster to the bottom and center represents Okinawans. The primary central cluster represents individuals from the main islands of Japan. Each panel highlights a different geographical region. So you see, for example, that individuals from Kanto-Koshinetsu are relatively well distributed across the whole “Japanese” area of the plot. Okinawans are primarily in their own cluster, as expected. The regions closer to mainland Asia are shifted in that direction on eigenvector 2. Finally, notice that the Tohoku population represents a vertex of a triangle where the two other positions are held by the Okinawans and Chinese. The authors here argue that skewed distribution of the Tohoku sample is evidence of disproportionate assimilation of a native pre-Yayoi element. Of course it could just be isolation by distance, as Tohoku is furthest from the Asian mainland aside from Hokkaido.

I don’t think we have much more to go on right now. But as we proceed into the future and data sets become more widely available, and analytic techniques more powerful, I wonder if we can reconstruct the Emishi from the chromosomal segments of the people of Tohoku which seem to “jump out” of the Japanese genetic background. And we can always hold out hope for DNA extraction from Jomon burials!

(Republished from Discover/GNXP by permission of author or representative)
• Category: History, Science • Tags: Agriculture, Genetics, Genomics, Japan, Jomon, Yayoi 
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Ainu in 19th century Hokkaido, and rice paddies

Unlike some islands Japan has a long history of human habitation. More interestingly, under the Jomon culture the Japanese archipelago was home to one of the earliest, if not the earliest, societies which used pottery. The Jomon do not seem to have been intensive agriculturalists. Rather, with a widespread marine littoral they likely maintained extremely high population densities, and at least semi-sedentary habitation patterns, simply through a hunting & gathering mode of production. Pacific Northwest Amerindians are likely a good analogy. They also relied on a dense stock of marine life to maintain population densities of a high level and a sedentary lifestyle.

About 2,000 years ago the Yayoi people arrived in Japan. The first Yayoi settlements are in northern Kyushu. These people brought intensive agriculture, in particular rice agriculture, to the Japanese archipelago. The general assumption is that the Yayoi are the precursors of the Japanese who entered into the international system of East Asia during the Tang dynasty in the second half of the first millennium. The Ainu of Hokkaido are presumed to be the descendants of the remaining Jomon people, maintaining a hold in the northern island because of its ecological unsuitability to Japanese agriculture.

The question is: what proportion of the ancestry of modern Japanese is Jomon/Ainu, and what proportion is Yayoi? The dynamics here are nicely constrained by the fact that Japan is a relatively isolated island system. The Yayoi seem to have arrived at one discrete moment in history, and rapidly expanded in ~1,000 years to all the main islands of Japan, though the full settlement of Hokkaido commenced in the 19th century. Interestingly, parts of northern Honshu seem to have had a distinct post-Jomon culture down to ~1000 AD.

Conveniently the HapMap has both Japanese and Chinese samples, but often there hasn’t been too much focus on the differences between these two groups because they’re very close in a global context when compared to the Yoruba or Europeans. In more recent analyses of East Asian groups the coverage seems to be better with various Chinese ethnic groups, but relatively few samples from Siberian populations. The latter are critical because the supposition is that these are the groups which would have the most affinities with the Jomon, due to the culture and contacts of the Ainu which evident during the modern period.

Dienekes most recent post on K = 15 ancestral components in ADMIXTURE clarifies some issues in this regard. There are multiple Han Chinese and Japanese samples, as well as a wide range of East Asian and Siberian groups. I’ve reedited and formatted K = 15 a bit, with the aim of focusing on the relationships of the Japanese in particular.


First, it is reasonable that the Denver and Singapore Chinese sample would have a greater proportion of the orange “Southeast Asian” component, Han in the United States are mostly from southern regions of China. Notice that the Japanese don’t have this component at all. The Japanese have more of the light gray component, which is modal among the Nganassan of the Arctic coast of Central Siberia. Unlike the Chinese the Japanese also have the blue component which is modal in Eastern Siberia, and also found in many North American groups (many omitted). Finally, it is interesting that the Japanese have the light yellow component in both of the samples Dienekes ran through ADMIXTURE. Going through his spread sheet, here’s are some of the populations sorted by this component (number 13):

Population 13
Melanesian 99.99
Paniya (South Indian tribe) 6.18
Malayan 2.85
North Kannada 1.44
Malay, Singapore 1.34
Sakilli (South Indian) 1.02
Japanese 0.71
Japanese #2 0.7
Papuan 0.56
Cambodians 0.53
Ethiopians 0.51
Yizu 0.48
Ket 0.41
Uygur 0.39
Yakut 0.08
Chinese, Beijing 0.06
Chinese, Singapore 0.03
Chukchi 0.03

This is basically Melanesian. Strangely, though at low proportions, the Japanese have much more of this than mainland Chinese, or most East Asians period. They’re in the same range as Cambodians, and topped only by maritime Southeast Asians and Indians. I find this interesting because Japanese Y chromosomes are often of haplogroup D, also common among the Ainu. This lineage spans various isolated regions of eastern Eurasia, such as the Andaman Islands. The implication is that D is a relict of a large set of populations which have slowly been absorbed by expansions of other groups. Additionally, some physical anthropologists have observed similarities in the morphology of the remains of the Jomon people and Australian Aborigines. I am inclined to chalk that up to the general robustness of non-farming populations, but it is something to consider.

But my primary point about writing this post was to offer some judgment as to the provenance of the modern Japanese. I think that looking at these results, and also keeping in mind other results on East Asian genetics, I’m of the mind that Japan looks to be a classic case where farmers totally marginalized hunter-gatherers. In other words, the modern Japanese are predominantly descendants of farmers from the Korean peninsula who arrived ~2,000 years ago. The alternative is that the Jomon were more similar to mainland East Asians in Korea and China than they were to Siberian peoples, which seems unlikely if the Ainu give us any clue as to the culture of the Jomon. This seems more implausible in light of the fact that the Japanese do seem to have some affinities to Siberian people, to a greater extent than the northern Chinese of Beijing (Beijing is a large city, so likely this sample has people who are descendants of ‘reverse colonists’ from the South as well).

If this inference is correct then it is an amazing instance of demographic expansion and replacement. In much of the civilized world intensive farmers replaced extensive farmers in fertile regions in prehistoric times. Or at least during periods when textual evidence is thin on the ground. In contrast, in Japan the process persisted right up until the margins of written history. Additionally, we can peg the arrival of the Yayoi culture very well chronologically because of the discontinuity. Assuming 25 years per generation, in 40 generations the Yayoi had totally extirpated the post-Jomon cultures across all of the Japanese islands except Hokkaido. And, it is notable that the Jomon are generally judged to have been a relatively numerous for hunter-gatherers. Their longevity in Japan as a continuous culture also attests to their success. This narrow specific case may have larger implications for the demographic-genetic patterns we see in the rest of the world.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ainu, Archaeogenetics, Genetics, Genomics, Japan, Jomon 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"