The island nation of Japan has a long and rich history that includes periods of relative isolation from the rest of the world. With the start of the Heian period in 794 AD, a distinct and unique Japanese culture had risen. A clan-based society with a strong literary culture and a centralized government, Japan’s early history is impressive and even includes the nationalization and equal distribution of land, among other reforms. Buddhism entered Japan from Korea, but Japanese buddhism has a lot of Chinese influences. During Japan’s feudal era, a ruling elite class of warriors known as the Samurai emerged. Following the emergence of this warrior class, various clans came into power as shoguns, a sort of military dictator. Several Mongol invasions of Japan were repelled, and long periods of brutal civil war caused by the disputes between feudal warlords characterizes much of Japan’s subsequent history. Shoguns and emperors would come and go, and at one point the country adopted an isolationist policy that lasted for 214 years and severely limited contacts with the rest of the world.

But who were the ancestors of these people? Despite the homogenous character of the Yamato genetic profile (mainland ethnic Japanese), the ultimate genetic origins of the Yamato was long believed to have been dual in nature. The latest research, however, suggests that the Japanese ethnogenesis can not be explained simply by admixture between the Jomon and Yayoi peoples. Rather, recently published studies have provided a great deal of new data and samples which indicate that the people of Japan, which of course includes the Ainu people and the Ryukyuans, mainly descend from three major ancestral groups. These 3 groups can be divided into three ancestry components, which are the Jōmon, Yayoi and Kofun components.

The hunter-gatherers of the Jōmon period

The Jōmon period can be divided into many phases, but the period as a whole is generally said to have lasted from 14,000 BC until 1000 BC. The people of the Jōmon period were mainly hunter-gatherers who subsisted on fish, meat and to some extent, various seeds and beans that they cultivated. Jōmon pottery is some of the world’s oldest, and the Jōmon people used relatively advanced tools made from shells and bone. While the people of the Jōmon culture are often described as foragers, they tended to be more sedentary than hunter-gatherers in other corners of the world. De Boer et al (2020) describes the Jōmon as “hunter–gatherer–fisher–horticulturalists” which is a fitting description. Their more sedentary nature is believed to have been because there was not as much competition for game and territory in Japan as in some other places, as it was sparsely populated at the time. However, the final stage of the late Jōmon period may have been accompanied by an increasing shortage of food as a result of the climate becoming colder. A study by Watanabe et al (2019) suggested that the population size of the Jōmon took a serious hit during this period, and shrunk signficantly. They were able to come to this conclusion using Bayesian skyline plots, which is a method that is used to calculate historical effective population sizes.

The ancestors of the Jōmon people were Paleolithic hunter-gatherers who were likely the first humans to settle in Japan. Some of them may have come from Southeast Asia, while others settled Japan from Siberia (as Hokkaido, Sakhalin, and the Siberian mainland were all connected by a land bridge during the last Ice Age). There was geneflow into Japan from Northeast Asia during the Jōmon Period, as well as from the Tibetan Plateau and possibly southern China.

Some skeletons from the Jōmon period reveal a very robust build, described by some early physical anthropologists as “Cro-Magnoid”. This led some anthropologists to believe that the Jōmon were a “Caucasoid” or Western Eurasian people, but modern DNA research has revealed that this was not the case. The highly robust, square and typically Paleolithic features of some Jōmon remains are similar in appearance to some European Cro-Magnon skeletons only as a result of convergent evolution, likely a result of cold climate adaptations. The Jōmon people were East Eurasians, and not directly related to ancient or modern Europeans. It’s easy to assume that the Jōmon people were homogenous, but recent studies have shown that it wasn’t quite so, either. In fact, the Jōmon seem to have been the result of a mix formed from at least two different population movements into Japan, which could explain their not entirely uniform Y-DNA lineages.

The DNA analysis of two remains from ancient Funadomari Jōmons, one male and one female, showed Y-DNA haplogroup D1b2 and mtDNA haplogroups N9b1. In addition, Y-DNA from Jōmon samples from Cooke et al. (2021) also yielded several samples of haplogroup D. Haplogroup D is not particularly widespread in present day Asia. It is mainly found at high frequencies in 2 populations: the Japanese and the Tibetans. D is also found among indigenous Andamanese islanders. The dispersion of this lineage is very ancient, and the D-carriers have since then diverged enormously from each other autosomally. The Japanese/Jōmon branch of haplogroup D (D-M55/D1a2) is in fact believed to have been isolated from other branches of D for about 50,000 years. It is not known with certainty where haplogroup D originated, but a likely place of diversification is somewhere in Central Asia, from where early D-carriers migrated into East Asia. It is also possible that some of the very first East Eurasians carried haplogroup D, and that it rose in frequency in some places due to multiple very ancient expansions. As an example of its scattered ancient distribution, haplogroup D was found in a Hoabinhian forager in what is now Malaysia. The hunter-gatherer in question has the sample ID Ma911 and his genome was published in McColl et al. (2018).

As such, the Japanese D1 haplogroup represents a very ancient, Paleolithic migration into Japan. As for mitochondrial haplogroup N9b1, it seems to have been the most common maternal haplogroup among most northern Jōmon groups. N9b1 is not very common in the Japanese population today, as it barely reaches a frequency of 2%. Below is a map showing the distribution of paternal haplogroups in the Japanese population as well as other populations in East Asia.

Clade 1, which represents haplogroup D-M55 (colour pink on this map) is present at a whopping 81.3% among males of the Ainu people in Hokkaido, a telltale sign of their paternal Jōmon ancestry. Among mainland Japanese males, the Jōmon-derived haplogroup D-M55 is carried by approximately 35.8% of the men. Haplogroup D-M55 is also found at a high frequency among Yamato males in northern Japan, and among Rykyuans. D-M55 reaches its lowest frequency in places like Chūgoku and Kyushu in Western Japan, where Yayoi paternal input was the strongest and where Jōmon-related paternal lines did not persist as much. Considering that the mainland Japanese population derive the bulk of their autosomal DNA from the Yayoi (about 88%), we can clearly observe a male-biased geneflow where Jōmon males contributed a lot paternally, or were reproductively successful, despite their autosomal DNA quickly being diluted by the DNA component of the far more numerous Yayoi immigrants. To clarify; the Jōmon paternal haplogroup can be found at a 35% frequency among Japanese males, but the total Jōmon autosomal DNA only makes up between 12-18% of the modern Japanese genome. Ryukyuans have significantly higher Jōmon admixture, roughly 27%. In the Ainu population, Jōmon admixture may be as high as 79%.

As such, it would appear that Jōmon males were very succesfully assimilated into the agricultural Yayoi population that entered Japan. This is a pattern in archaeogenetics that is definitely not unique or exclusive to Japan. We can observe the same pattern in Europe as well as in Oceania, where incoming farming populations moved to new places and incorporated hunter-gatherers (especially hunter-gatherer males) into their cultures. The case is often that the autosomal contribution by the hunter-gatherers was low, while their Y-DNA haplogroups remained at relatively high frequencies, suggesting a male-biased geneflow.

The Jōmon genomes that have been sequenced as a part of academic papers thus far show a type of ancestry that is deeply diverged from the type of ancestry commonly found in mainland East Asia. The Paleolithic ancestors of the Jōmon must have diverged fairly early from mainland East Asians. However, it is unlikely that the Jōmon were completely isolated from geneflow from mainland East Asia until the Yayoi arrived. More ancient DNA samples are required in order to confirm this, but the mtDNA of Jōmon samples hints at connections not only to Siberian populations, but also to ancient populations in northern and coastal southern East Asia.

Another Y-DNA haplogroup that is present among males of the Ainu people is C2a. It may represent another migration from Siberia through Sakhalin into Japan, or it could have arrived to Japan along with the D-M55-carriers. In any case, this suggests that while the majority of the Jōmon males carried D-M55, a minority of them also carried C2a. Roughly 15% of Ainu males belong to C2a. This haplogroup is the most common Y-DNA lineage among Mongolians as well as among certain indigenous populations of Siberia. It is also possible that haplogroup C1a1 was present among Jōmon males, likely also a lineage that arrived from Siberia. A study published by the Cambridge University Press in 2020 proposed that males carrying haplogroup C1a1 were in fact the first migrants from Siberia into Japan, and that they were followed by males carrying haplogroup C2. The latter were, according to the study, the first people to speak Japonic languages. However, the evidence in this case is not conclusive, and the linguistic propositions of the study should thus be taken with a grain of salt.

Something interesting about C2 is that according to a very recent study by Xiaowei Mao and colleagues (May 2021), C2 appears to have been a very common Y-DNA lineage among Paleolithic northeast-Asian populations in mainland Asia. This suggests that macrohaplogroup NO was still contained mostly to southern China during the Last Glacial Maximum.

Considering that modern Ainu people have some typical Siberian mitochondrial haplogroups like G1, this indicates that there have been strong contacts between Siberian populations and the ancestors of the Ainu. These indications of contact between the Jōmon and Siberian and coastal East Asian populations should not come as a huge shock, because it was quite unlikely from the start that the Jōmon would turn out to be a completely isolated Paleolithic group with a 100% frequency of D-M55 and no outside admixture. They were certainly a Paleolithic remnant, but they do appear to have had some admixture from their neighbouring populations even long before the Yayoi migration/invasion.

Now, we have discussed the Paleolithic Y-DNA lineages of the Jōmon as well as their genome-wide profiles. The Yayoi males, on the other hand, likely mainly carried haplogroups O1 and O2, which we will get into more in a second. Haplogroups O1 and O2 are represented as clade 2 and clade 3 in the map featured earlier in the article (colours dark green and purple). So, let’s get into who the Yayoi were…

Migrants from the Korean peninsula: the Yayoi people

The Yayoi people were a continental East Asian group that most likely arrived in Japan by crossing the Tsushima Strait. The arrival of the Yayoi people in Japan marks the end of the Jōmon period. Their arrival used to be estimated at around 300 BC, but more recent archaeological evidence suggests they may have arrived as early as 1000 BC. The Yayoi people were more sedentary than the Jōmon, and practiced metalworking and weaving. They brought with them the art of wet rice farming, which enabled them to sustain a significantly larger population than the previous inhabitants of Japan had been able to, since rice is a comparatively stable food source. In fact, the arrival of the Yayoi people may not exclusively have been a bad thing for the Jōmon people. As mentioned earlier in this article, there was famine by the end of the Jōmon period as a result of the climate becoming much colder. The Yayoi migrants seem to have helped the population of Japan bounce back in terms of size, much due to the advanced farming they brought with them. As they mixed with the Jōmon, the previously dwindling population size recovered quickly.

The “signature” Y-DNA haplogroup of the Yayoi people would have been O-SRY465, also known as O2b. In modern times, O-SRY465 reaches its peak in Western Japan, which is congruent with Yayoi autosomal ancestry peaking there as well. Unsurprisingly, O-SRY465 is at its lowest frequency in Hokkaido and in Okinawa, places where Yayoi paternal lines did not take root as much as in Western Japan. While SRY-465 is the most common branch of haplogroup O in Japan, there are many other branches present among Japanese men. The Yayoi brought not only O-SRY465, but also O-M122 and even a small minority of haplogroup N lineages, the latter being present at about 3% among Japanese men today.

In Cooke et al. (2021) new DNA samples from Yayoi individuals were published. The question here, however, is how representative these Yayoi genomes are of the Yayoi population as a whole. Due to the small number of samples, it’s still a little too early to draw conclusions. As stated by the authors of the study, the sampled Yayoi individuals are from a region where Yayoi skulls are morphologically similar to Jōmon skulls, hinting at a higher percentage of Jomon-related ancestry in these individuals. This is not the case for Yayoi skulls in most other regions. Addtionally, they’re from a time period during which the admixture between the Jōmon and Yayoi was at its peak. So, caution is to be exercised here. Based on this new data we can, however, make some guesses. Before going there, it’s important to keep in mind that even the authors of the study admit that their sampled Yayoi data is limited, so take the information about the Yayoi samples with a medium sized spoon of Japanese sea salt. With that said, let us have a look at the Yayoi individuals from Cooke et al.!

These Yayoi samples display significant Jōmon-related ancestry, strongly indicating that as soon as they entered Japan, they started mingling with the Jōmon. Another option is that they were already admixed with a Jōmon-like component prior to entering Japan. Genomes from Korea published in Robbeets et al. (2021) suggests that Jōmon-like ancestry was already present in Korea in 4000 BC. In fact, samples from the southern coast of Korea from this time were found to carry a whopping 95% of Jōmon-related ancestry. Others, like the Korean samples from Changhang, did not carry nearly as much Jōmon-related ancestry as the those from the southern coast, but still had a significant amount. In any case, it is very clear that the two Yayoi samples published in Cooke et al are very different from other Yayoi samples.

All things considered, Cooke et al. (2021) may be overestimating the percentual amount of mainland East Asian-related ancestry that was brought in by Kofun migrants, because other Yayoi samples have more of the mainland East Asian ancestry than the ones in this study. If we compare the Kuma-Nishioda Yayoi and Shimomotoyama Yayoi samples published in Robbeets et al. (2021) to the Yayoi samples from Cooke et al. (2021), it becomes very clear that it was not common for Yayoi people to derive 60% of their ancestry from a Jōmon-related source. Rather, between 10% and 35% Jōmon-related admixture seems to have been the average for the Yayoi, with the rest being a mix of Neolithic Yellow River-related mainland East Asian ancestry and Northeast Asian Amur-related ancestry. This mixed East Asian component is referred to as the “Upper Xiajiadian” component in Robbeets et al. and is modelled as approximately 60% Northeast Asian and 40% Yellow River-related admixture.

As mentioned above, the Yayoi people also had a Northeastern Asian ancestry component, and this component differs from both Han-related ancestry and from the deeply diverged Jōmon-related component. This component most likely dispersed from around Manchuria to Korea before reaching Japan. Cooke et al models the Yayoi in the study as deriving roughly 40% of their total ancestry from this Northeast-Asian population and the remaining 60% being Jōmon-related. Again, however, most Yayoi people would have been much less Jōmon-like and far more like the Yayoi published in Robbeets et al. (2021).

Therefore, it appears that while the genetic impact of later Kofun migrants was significant, it wasn’t quite as massive as Cooke et al. (2021) implies. The two Yayoi samples published in this study are in all likelihood outliers, having significantly more Jōmon-related admixture than the majority of the Yayoi population would have had, which distorts their (the authors of the study) view of the genetic turnover in later eras somewhat.

A large percentage of the autosomal DNA among Japanese people today comes from the Yayoi people, which partially explains the genetic similarity between the Han Chinese, Koreans, and the Japanese.

Robbeets et al. (2021) concludes that the most significant migration to Japan was that of the Yayoi people. This may very well turn out to be correct, although in light of the data from Cooke et al. there can be no doubt that the Kofun period brought with it a strong genetic shift and was accompanied by a reduction in Jōmon ancestry as well as Northeast Asian ancestry, and an increase in mainland East Asian Yellow River-related ancestry. Just how much of the mainland East Asian ancestry present in modern Japanese people arrived with the Yayoi or with the Kofun, however, remains to be seen. More samples are needed before we can come to any conclusions in this regard.

The Yayoi are often believed to have brought the Japonic languages to Japan, although there is an ongoing debate about that. Connecting DNA and languages is almost always difficult, although some exceptions like the Indo-European languages, the Austronesian languages, and the Uralic languages are fairly easy to associate with certain Y-DNA and autosomal admixture. These are exceptions, however. A possible and underestimated factor in regards to the emergence of Japonic may be the linguistic influence of the Jōmon of Kyushu, who were the first Jōmon people encountered by the Yayoi people. As this intermingling was of vital importance to the formation of later populations of Japan, did a pre-Yayoi substrate enter what was to become the Japonic languages? Or was it that the pre-Kofun language became the substrate and the Kofun people later brought the main component of the Japonic languages? That is all up for speculation, and will surely be a topic of debate for many years to come.

In terms of physicality, there is a very strong contrast between the remains of Yayoi individuals and Jōmon individuals, which has piqued the interest of many Japanese physical anthropologists and resulted in many studies. As expected from an agricultural population, the Yayoi were rather gracile and slender, especially when compared to the Jōmon. Differences like that are very commonly observed between ancient hunter-gathering and agricultural populations, all across the globe.

Kofun period immigrants, how significant was their genetic contribution?

The Kofun period began at around 300 AD and is characterized by the distinct tomb mounds that were built for the ruling class at the time, and is also the period during which the Yamato clan rose to power and, eventually, established Japan’s imperial dynasty.

Recently published studies have given us plenty of new data and samples to work with, and they suggest that the Japanese ethnogenesis can not be explained just through a dual admixture model between Jōmon and Yayoi. Rather, Japanese people descend from three major ancestral groups. Cooke et al. (2021) identified a third component, which the study attributes to mainland East Asian migrants of the Kofun period. According to the authors of the study, the third (and largest) portion of Japanese DNA is this Kofun period mainland East Asian DNA. Let us go through the data and evaluate just how accurate that conclusion is. First, let us look at an ancestry model from Cooke et al. that should by all means be viewed with caution:

In this model, the use of what is very likely two outlier Yayoi individuals as a proxy for Yayoi ancestry among ancient and modern Japanese reveals its flaws.

As mentioned earlier in this article, given the overestimation by Cooke et al. in regards to the percentual amount of mainland East Asian ancestry brought in during the Kofun period as a result of using Yayoi samples that are by all means genetic outliers as a proxy for Yayoi ancestry, we should definitely be vary of reaching hasty conclusions about the exact size of Kofun genetic contribution. Had this same model been attempted using the more typical and representative Yayoi samples from Robbeets et al, it could have provided an excellent model for the genomic transitions that took place in Japan throughout the ages.

So, the Kofun period brought a very significant amount of mainland East Asian-related ancestry into Japan, but likely not as much, percentually speaking, as Cooke et al. suggests. Additionally, it’s important to note that genetic sampling of royal individuals from Kofun tombs is currently not allowed in Japan, which means that current as well as upcoming Kofun samples in the near future will most likely be from individuals who may have had a lower status in society. As the study notes, the three Kofun individuals in it are indeed lower-ranking individuals. It’s anyone’s guess as to if there were any significant autosomal differences between low-status and high-status Kofun individuals (there probably weren’t), but it’s usually the Y-DNA of the elites that ends up increasing in frequency, and the matter of Kofun Y-DNA is complicated by the fact that we will likely never see the Y-DNA haplogroups of Kofun elites.

In terms of Y-DNA, only 1 Kofun sample has been obtained thus far. Interestingly, he belonged to haplogroup O3a2c. Of course, this is not a lot go by, and is far from telling us the whole story about the Y-DNA frequency of the Kofun immigrants, but it may be a hint of things to come.

Genetic differences between modern Ainu, Japanese mainlanders and Ryukyuans

Japan has a regional genetic variation that is fairly significant, but a Ryukyuan or an Ainu individual is still more related to a Japanese mainlander than they are to anyone outside of modern Japan.

There is significant genetic affinity between Ryukyuans and the Ainu, despite their geographical distance (with the modern Ainu mainly inhabiting northern parts of Japan, while Ryukyuans inhabit the southernmost pole of Japan). Ainu people in Hokkaido are in fact genetically closer to Ryukyuans than they are to mainland Japanese people, although they are of course related to the latter as well. This is simply because the Jōmon DNA component has remained higher in the Ainu and Ryukyuan populations.

An ancient DNA sample from the remains of a Jōmon individual from Ikawazu (sample IK002) featured in the 2019 study “Jomon genome sheds light on East Asian population history” shows that the autosomal profile of the Jōmon people was a type of very archaic, early diverged, coastal East Eurasian. An analysis of Sanganji Jōmon from Kanzawa-Kiriyami et al (2016) suggested that a population like the Sanganji Jōmon mixed with a southern Siberian population of the Okhotsk culture in order to form the modern Ainu population. The study suggests that the indigenous Nivkh people may be a good proxy for what the Okhotsk people were like, genetically.

Modern Hokkaidu Ainu people derive 79.3% of their autosomal DNA from a population identical to, or similar to, Jōmon individual sample IK002. Mainland Japanese people have signficantly less DNA from IK002-like people, but they do have some serious genetic affinity to Jōmons like IK002 nonetheless.

There is also inter-regional heterogenity, or at least significant genetic variation, among ancient Jōmon samples and likely among early Ainu people as well. The southern Jōmon probably had significantly less Siberian genetic influence than the northern Jōmon, but the difference is unlikely to have been huge. Future samples will be able to determine just how much regional variation there was among the Jōmon.

Exactly how much Jōmon DNA do the modern Japanese have?

The answer is that it depends how we measure it. Some studies have used the DNA of modern Ainu individuals as a proxy for Jōmon ancestry. This approach makes for a less than ideal accuracy when estimating the percentage of Jōmon DNA, as the modern Ainu derive approximately 79% of their DNA from Hokkaido Jōmon, and the rest from other sources that are the result of more recent admixture events. Jinam et al (2015) takes this slightly misleading approach and uses Ainu people as a proxy for Jōmon ancestry and continental Asians (Han Chinese and Koreans) as a proxy for Yayoi ancestry. What this does is give us a somewhat distorted view of the exact ancestry proportions, but studies like that are still useful for gaining a basic understanding of the percentages of ancestry components in Japan.

Below is an admixture model made using G25 that shows the percentages of various ancestral components in modern day Japanese people.

Unfortunately, there is still a lack of proper ancient DNA samples from some areas in East Asia which means that there is also a lack of ancient populations to use as references, making the model less than ideal. I used an ancient Mongolian population, a Chinese Neolithic population from Boshan, a Japanese Jōmon population, a Chinese Late Neolithic population from the Western Liao river, as well as an ancient Siberian population. Despite the suboptimal proxy populations, it becomes clear that the autosomal Jōmon DNA component is probably not higher than 16% in the present-day Japanese population, which is also supported by most studies on the topic. The lack of high coverage Yayoi genomes from mainland Japan may make the Jōmon component look slightly inflated.

Moving on, now that we have samples from the Kofun period it becomes easier to create an admixture model for the modern Japanese. To make a comparison to the aforementioned G25 model, the Japanese can be modelled as solely Kofun and still get a better, more accurate fit than the previous model. The Kofun average, of course, includes roughly 15% Jomon admixture, which much like suggested by Cooke and Robbeets, indicates that Jomon ancestry among the Japanese has not shrank since the Kofun period.

Consistent with other studies, Robbeets et al. (2021) models the present-day Japanese mainlanders as having about 15% Jōmon admixture. Robbeets and colleagues used a Jomon sample from Rokutsu as a proxy for Jōmon ancestry, which is of course a far more viable reference for Jōmon ancestry than the modern Ainu samples (who have Yayoi admixture) used by Jinam et al. (2015). Below is a table with admixture proportions in modern and ancient Japanese and mainland East Asian populations, from Robbeets et al:

Furthermore, in alignment with models from other studies, Cooke et al. (2021) also estimates that modern-day Japanese people have, on average, roughly 15% Jomon ancestry.

If we make a simple PCA using G25 we can see that the Japanese average (represented simply by “Japanese” on the PCA) clusters with the Kofun samples who in turn occupy an intermediate position between mainland East Asians like the Han and the Jōmon. Below is an example of what that looks like:

Summary

So, a Paleolithic hunter-gatherer-fisher population populated Japan about 30,000 years ago. This population eventually gave rise to the Jōmon period that started in 14,000 BC. Around 300 BC, or possibly even slightly earlier (as early as 1000 BC), an agricultural and metalworking population known as the Yayoi migrated to Japan. Once there, they encountered, mingled with, and assimilated the previous Jōmon inhabitants. This intermingling seems to have been relatively harmonious and peaceful, as the Y-DNA lineages of the Jōmon did not disappear, as sometimes happens in prehistory when one larger and more technologically advanced population invades the territory of a smaller less advanced population.

Due to their limited population size, the Jōmon did not contribute massively in terms of autosomal, total DNA to modern mainland Japanese people. However, Jōmon paternal lines are disproportionately common among Japanese people despite the limited autosomal contribution, suggesting perhaps that some Jōmon clans were quickly and succesfully assimilated into the Yayoi system and rose to a high status. In light of recent data indicating a strong genetic impact by Kofun period immigrants, the prevalence of the Jōmon-derived Y-DNA haplogroup D-M55 among modern Japanese people is even more remarkable, as this paternal lineage has been present in Japan since its very first inhabitants arrived without being extinguished.

The Ainu people have been used as a proxy for Jōmon ancestry in some studies. They are however, not a perfect proxy, since they are estimated to derive “only” 79% of their DNA from a Jōmon source. The Ainu population was most likely formed through mixing of Hokkaido Jōmon with a Siberian population, probably of the Okhotsk culture. Then, there was subsequent mixing with mainland Japanese people, from which the Ainu acquired Yayoi DNA.

In summary, all Japanese people have DNA from both the Jōmon and the Yayoi, as well as from the Kofun period immigrants. Jōmon autosomal DNA persisted at higher levels in Hokkaido and the Ryukyu Islands, while Yayoi autosomal DNA is the strongest in Chūgoku. The Jōmon paternal lineage D-M55 is found at a lower frequency in Chūgoku (28~%) and is present at much higher percentages in Hokkaido Ainu (81%) and Ryukyuans (about 46%). The Yayoi-derived haplogroup O lineages are present at a higher frequency in Chūgoku. Despite this, both Yayoi and Jōmon Y-DNA haplogroups are found in every single sub-population of Japan.

There is nothing that suggests that the Jōmon population was exterminated or otherwise involved in serious warfare with the Yayoi. DNA indicates that the Jōmon were assimilated by the Yayoi in a rather peaceful process and that these two groups are ancestral to all Japanese people. However, the arrival of the Yayoi people resulted in a quick end to the Jōmon way of life.

In addition to Jōmon and Yayoi ancestry, the Japanese have signficant ancestry from the Kofun period people. How much of the Neolithic Yellow River-related ancestry among the modern Japanese comes from the Kofun immigrants and how much comes from the Yayoi remains to be seen, however, as more samples are still required in order to reach a conclusion. This is especially true since the two most extensive studies on the topic somewhat contradict each other in terms of what the source of the bulk of this ancestry is.

References

Gakuhari et al (2020): Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations https://www.nature.com/articles/s42003-020-01162-2

Hammer et al (2006): Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes https://www.nature.com/articles/jhg20068

Wang et al (2018): Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889524/

Yang, Melinda (2020): Ancient DNA indicates human population shifts and admixture in northern and southern China https://science.sciencemag.org/content/369/6501/282

Jinam et al (2015): Unique characteristics of the Ainu population in Northern Japan https://www.nature.com/articles/jhg201579

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Shi et al (2008): Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605740/

Cambridge University Press (2020) Munda languages are father tongues, but Japanese and Korean are not https://www.cambridge.org/core/journals/evolutionary-human-sciences/article/munda-languages-are-father-tongues-but-japanese-and-korean-are-not/9F302F4A80E691B05F424312CA03BCDE

Shinoda, Ken-ichi (2019): Ancient DNA Analysis of Skeletal Samples Recovered from the Kuma-Nishioda Yayoi Site https://www.kahaku.go.jp/research/publication/anthropology/download/30/BNSM_D300401.pdf

Mao et al (2021): The deep population history of northern East Asia from the Late Pleistocene to the Holocene https://www.sciencedirect.com/science/article/abs/pii/S0092867421005754

Kanzawa-Kiriyama et al (2016): A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan https://www.nature.com/articles/jhg2016110

Kim, Soon-Hee et al (2011): High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087676/

Cooke et al. (2021): Ancient genomics reveals tripartite origins of Japanese populations https://www.science.org/doi/10.1126/sciadv.abh2419

Robbeets et al. (2021): Triangulation supports agricultural spread of the Transeurasian languages https://europepmc.org/article/ppr/ppr370464

© Genomic Atlas 2021