Genetic variation during the Three Kingdoms period in Korea

While the genetic history of Japan has been studied rather extensively in recent years, ancient remains from the neighboring Korean peninsula have remained almost completely unsampled until 2022. Luckily, Gelabert et al. (2022) and D-N Lee et al. (2022) brought an end to the complete drought of ancient Korean samples and featured newly sequenced ancient genomes from southern Gyeongsang and Gunsan-si in South Korea. The results are highly interesting, and are sure to be especially fascinating for anyone with an interest in ancient East Asian hunter-gatherers and their genetic legacy.

During the Three Kingdoms period of Korean history, the kingdoms of Baekje, Silla and Goguryeo competed for dominance. In addition, the Gaya confederacy which consisted of multiple small kingdoms united under a common leadership, was caught up in the middle of it all. The result? A very interesting period in Korean history. Gaya was eventually absorbed by the Silla kingdom, as were the kingdoms of Baekje and Goguryeo, all through conquest. For the time being, ancient DNA has only been retrieved from the territories of what was the Baekje kingdom in the southwest of what is now South Korea, and the Gaya confederacy in what is now south-central South Korea. As such, this article will focus mainly on the genetic profile of the inhabitants of those two states.

Map of Korea during the Three Kingdoms period

Gaya confederacy samples from Gimhae

Face reconstruction of the Korean TK period individuals AKG_10218, AKG_10203, AKG_3420, AKG_10207, from Gelabert et al. (2022)

The present-day Korean population has a very substantial genetic continuity going back to the Neolithic, but the new ancient samples from Gimhae tell a curious tale about an early Medieval population that was not entirely derived just from Bronze Age Liao River-related sources, but instead one that surprisingly enough still carried significant amounts of Jōmon-related ancestry. The presence of Jōmon-related ancestry in ancient Korea is nothing new, and was mentioned in this article. Robbeets et al. (2021) discovered the existence of Jōmon-related ancestry at three different sites in Korea.

At one site, Changhang Yŏndaedo, the Jōmon-related component only made up a small percentage of the genomide-wide ancestry of the sampled individuals. In stark contrast to said individuals, samples from Yokchi-do were found to have a whopping 95% Jōmon-related ancestry. While that is a spectacular find, the ancient Korean samples from Yokchi-do on Korea’s southern coast are 6000 years old. The newly sequenced samples from Gimhae, on the other hand, are less than 2000 years old, which makes the discovery of the persistence of a Jōmon-related genetic component in the Three Kingdoms period all the more amazing.

Gelabert and colleagues collected samples from a period of time during which burials with wooden chambers and generously deposited grave goods were commonplace. Additionally, the practice of human sacrifices accompanying burials had been introduced in the region during the third century AD. While some burials from the Gaya confederacy had Buddhist motifs, many of them also show strong signs of shamanistic beliefs and an emphasis on providing the deceased with everything they would require in the afterlife. Along with rich grave goods, the aforementioned human sacrifices accompanying the burials may have been a way to do just that.The funerary practices mentioned above leave archaeologists and geneticists a lot to work with, and also allows for investigating genome-wide ancestry in relation to social status and origin.

When looking at archaeological evidence, there is quite a strong case for interaction between the Gaya confederacy and Japan, in particular the Kyushu region. For example, the design of armor in Japan during this period was heavily influenced by the smiths of the Gaya confederacy and the Baekje kingdom. Given the Gaya confederacy’s location in a region with very rich iron deposits, it is not surprising that the Gaya confederacy became well-known for its excellent iron-working. In particular, we can observe some very early and impressive horse armor in finds from Gaya. The fact that the Gaya confederacy interacted with its neighbors in both Japan and China not just through trade – but perhaps also through more direct cultural influence and ties, may be reflected in aDNA data in the future. It should be noted that it was not only through their skill in iron-working that the people of the Gaya confederacy influenced their neighbors. Gaya’s prosperity can largely be explained by having access to the aforementioned rich iron deposits and farmlands of excellent quality, but they were also seasoned traders and took to the sea to engage in trade with distant kingdoms. It is because of their commitment to maritime trade that Gaya pottery is found in Japan during the same time period.

For now, it is not certain whether one should look at Japan for an explanation of the Jōmon-related ancestry in Gimhae, or simply to look back at the Yokchi-do samples and reach the conclusion that the Jōmon-related component in the Gaya confederacy was a very old and local phenomenon. Given that Japan was the most important trade partner of the Gaya confederacy, it does not seem like a huge stretch by any means to consider the possibility of the individuals with Jōmon-related ancestry to have had more recent Japanese origins rather than being the descendants of a very old local Jōmon-like substrate. However, the current data is too sparse to allow us to know with certainty, and more samples are needed.

As established before, archaeological ties between the Gaya confederacy and Japan are strong. Even so, we can look to archaeology in order to see that the hypothesis of a local origin of the Jōmon-related ancestry in some Gaya confederacy individuals may not be that crazy, after all. There is quite a solid case for the persistence of hunter-gatherers in Korea even after the arrival of early millet and rice farmers to the region. Chris Scarre, in his book “The Human Past: World Prehistory and the Development of Human Societies” writes that the expansion of farmers into Korea likely did not involve a complete and instant replacement, but rather a close interaction between the local hunter-gatherers and the incoming agriculturalists. Scarre does, however, associate the introduction of farming in Korea with the rise of a new social elite, enabled by the food surplus provided by agriculture.

The first farmers to enter Korea were millet farmers, and they assimilated the local Korean hunter-gatherers in the later periods of the Chulmun (comb ware) culture of Korean archaeology. Early settlements attributed to the Chulmun culture are often associated with coastal and river-dwelling foragers. In Middle Chulmun, on the other hand, a very clear shift from a maritime-based hunter-gathering economy to a subsistence strategy focused more on broomcorn and foxtail millets can be observed. This likely marked the arrival of Upper Yellow River Neolithic-related ancestry and Amur River Neolithic-related ancestry into Korea. Interestingly, sites like Tongsamdong have revealed that the people of the middle period of the Chulmun culture not only consumed millet, but that their diet was still dominated by maritime foods and hunted mammals (Scarre 2018:255).

This may indicate that by the time of the Middle Chulmun culture, the hunter-gatherer substrate was still alive and well, and influenced the incoming farmers culturally (and probably genetically) as well. Later, when rice farming was introduced to Korea, we can still observe some local hunter-gatherer influence on the farmers. Namely, archaeological discoveries in the form of a conjunction of rice with distinctively local ceramics. According to Scarre, this suggests that all waves of farmers that entered Korea encountered and mixed with local hunter-gatherers, who may have been of Jōmon-related stock. Archaeology indicates that the incoming rice farmers made a stronger impact than the millet farmers had before them, which could explain why modern Koreans derive more of their genome-wide ancestry from the former than they do from the latter.

With Scarre’s reflections in mind, it is not overly far-fetched to speculate about the Gaya confederacy Jōmon-related ancestry and the possibility of it being native to Korea. Again, more samples are needed before any conclusion can be reached, of course.

Since Gimhae was the political center of the Gaya confederacy and a highly important hub for trade, it is not impossible that its population may have been more cosmopolitan than the rest of Gaya. That is one thing that may speak in favour of a Japanese origin of the Jōmon-like ancestry observed there. If samples from more remote sites during the time of the Gaya confederacy are sequenced in the future, a comparison can be made, and we will likely be able to tell if the individuals with Jōmon-like ancestry from Gimhae were simply outliers.

Among present-day Koreans, one of the most common mtDNA haplogroups is D4. The same mtDNA has been found in multiple samples from Japanese Yayoi farmers. This maternal connection, while very broad and not neccessarily indicative of the migration route of the Yayoi into Japan, is noteworthy and most definitely worth investigating further when one considers the potential path the Yayoi people took to Japan.

AKG_10203 is one of the sampled individuals from one of two sites in Gimhae featured in Gelabert et al. (2022). The burial goods indicate that this man belonged to the Gaya confederacy warrior class, and may even have been been a part of the lower class nobility. Unlike many other samples from the study, AKG_10203 had not been sacrificed. Instead, he was laid to rest in a wooden coffin together with a rich hoard of gold and bronze artefacts.

Interestingly, AKG_10203 was one of the samples with substantial Jōmon-related ancestry. Enough to make him plot in the present-day Japanese cluster, even. His Y-DNA haplogroup goes along nicely with that, as he carried haplogroup D-M64, a branch of haplogroup D that has also been found among Jōmon individuals from the Japanese sites of Funadomari, Sanganji, Toyama and Rokutsu.

Fascinatingly, it is also the lineage of the Imperial House of Japan, who belong to D-Z1504 with a TMRCA of 1800 ybp. More specifically than just D-M64, the Gimhae sample AKG_10203 most likely belonged to the downstream Z1622 subclade. It should be pointed out that the Y-DNA haplogroup lineage of D-M64 has such an old TMRCA (nearly 20,000 ybp) that AKG_10203’s paternal haplogroup is not necessarily a sure sign of him having recent Japanese ancestry. That becomes even more clear when considering the fact that the direct upstream subclade of Z1622 has been found in an ancient sample associated with the earlier mentioned Chulmun culture in South Korea. We may in fact be dealing with a scenario in which AKG_10203’s Jōmon-rich ancestry is the result of both persisting local archaic ancestry and an influx of Japanese ancestry through the cosmopolitan networks linked to the Gaya confederacy’s naval ties with Japan.

Here, as before, the question of whether the Jōmon-related ancestry in Korea during the time of the Three Kingdoms was local or foreign comes up again. Adding to that, if one takes into account the existence of ancient Korean foragers with Jōmon-related ancestry on the autosomes and (likely) D-M64 patrilineages at the time during which the incoming rice farmers encountered and mixed with the locals of the Korean peninsula, it is not at all difficult to imagine that some of them were assimilated and brought into the fold of the population that would emerge from this mix and later settle in Japan as the Yayoi people. With that in mind, the men of the Imperial family of Japan might in fact get their paternal haplogroup from Korean hunter-gatherers who adopted rice farming, mingled with the incoming farmers from what is now China and later entered Japan as a conquering force. That is just one of several possibilities, because the possibility of the imperial Y-line to be a native Jōmon patrilineage of course also still exists. That would certainly be an impressive tale of endurance and continuity.

A male human sacrifice

Moving on, another male sample from the Daesong-dong tumuli in Gimhae is AKG_10204. He was of lower status than AKG_10203 judging by his burial, having been sacrificed instead of buried in a wooden coffin. His paternal haplogroup was O1b, and unlike AKG_10203, he did not have excess Jōmon-related autosomal ancestry.

It is quite apparent that among the Daesong-dong tumuli burials from Gimhae, there was no stratification based on ancestry. Jōmon-rich genome-wide ancestry was not directly associated with neither low nor high status. For example, sample AKG_10207 was a woman who died as a human sacrifice, likely to honor a noble, and AKG_10207 was what the authors of the study calls a “non-privileged” individual. Much like AKG_10203, she had a very substantial amount of Jōmon-related genome-wide ancestry.

High-status, low coverage

Sample AKG_10218 was determined to have been a man of high social status. This sample is of low coverage and was therefore unable to receive a Y-haplogroup assignment deeper than just O. However, it is possible that he carried O1b, like one other man at the same site.

Dangbuk-ri jar coffin burial samples

The aforementioned Gaya confederacy’s Western neighbor, the Baekje kingdom, was a powerful and expansionist state during the Three Kingdoms period. Much like the Gaya confederacy, Baekje was a maritime power. D-N Lee et al. (2022) sequenced the DNA of six individuals from what would have been the territory of 6th century Baekje, all from the context of a coffin burial, which was a rather typical type of burial for commoners. Thus, the Baekje samples from this study should be fairly representative of the general genetic profile of the kingdom’s inhabitants at the time. One of the Dangbuk-ri individuals belonged to haplogroup O-CTS7620, while the other three males belonged to haplogroup Q1a (one of them to the typically Northeast-Asian M120 subclade). Finding Y-haplogroup Q would have been less of a surprise if the samples had been from Goguryeo, in which the northern regions had received more Jurchen influence.Y-DNA haplogroup Q is present at a very modest frequency among modern Korean men (slightly less than 2%), while Y-DNA O1, O2 and O3 together make up more than 70% of present-day Korean Y-DNA.

Location of the Dangbuk-ri archaeological site in Gunsan city, from D-N Lee et al. (2022)

Patrilineages aside, the Dangbuk-ri individuals look quite uniform autosomally. They all overlap with present-day Koreans, with the only slight heterogeneity among them being very small differences in Upper Yellow River Neolithic-related ancestry. The close relatedness of these samples may not tell us that much, because as the authors of the study point out, some of them were family. The researchers present QpAdm models using a two-way admixture modelling with a proxy from the Upper Xiajiadian culture and another from Late Neolithic Xitoucun in Southern China.

QpAdm model of Dangbuk-ri jar coffin individuals, from D-N Lee et al. (2022)

The Upper Xiajiadian culture proxy is what they used as a Northern source of ancestry, and with it, no Jōmon-related ancestry is detectable in the Dangbuk-ri samples, nor in present-day Koreans. However, depending on which proxy the authors of the study used as a Northern source of ancestry, the Dangbuk-ri individuals showed about 3-4% Jōmon-related ancestry. Using the Middle Neolithic proxy from Inner Mongolia is likely not a better, or more realistic choice than the Upper Xiajiadian culture reference. Therefore, it is unlikely that the Dangbuk-ri samples have any significant amounts of Jōmon-related ancestry. In that sense, they certainly differ from the Gaya confederacy samples.

PCA of 2077 present-day Eurasian samples with the Dangbuk-ri jar coffin individuals projected on top, from D-N Lee et al. (2022)

Present-day Korean Y-DNA haplogroups

  • O-M175 (>70%)
  • C-M130 (≈15%)
  • Miscellaneous (D-CTS3946, N-M23, Q-M242)

Roughly 74% of modern Korean men carry haplogroup O. While O itself is incredibly widespread, old and diverse in terms of subclade variation, Korean men are mainly split between O1b and O2a. Koreans also have a significant frequency of haplogroup C, with most clades being under C2-CTS2657. All subclades included, Y-DNA haplogroup C is present at a frequency of 14-18% among Koreans. There is a North-South gradient in terms of C2 among Koreans, with North Koreans having more of it than people in South Korea do (Kim et al. 2011, Jeong et al. 2019). In addition to the more dominant clades of O and C, Koreans also carry haplogroups D, N and Q at lower frequencies.


The absolute majority of present-day Koreans display clear signs of genetic continuity since the early Medieval period. More specifically, Koreans descend from a population identical to, or very similar to the individuals sampled from the Dangbuk-ri jar coffin burial in D-N Lee et al. (2022). While Korea clearly had some genetic variation with some more archaic profiles persisting well into the Three Kingdoms period, populations rich in Jōmon-related ancestry did not make any significant contributions to later Koreans. The Jōmon-related ancestry observed among samples from Gimhae may have been the result of persistence of older forager ancestry, but it could just as well have been the result of cosmopolitanism as a part of the Gaya confederacy’s strong maritime ties to Japan. The Gaya confederacy met its end at the hands of the Silla Kingdom and by the looks of it, so did the Jōmon-related ancestry of that period.

While present-day Koreans are genetically very similar to the samples from the Baekje kingdom published in D-N Lee et al. (2022), it is noteworthy that the study found a small amount (3-4%) of Jōmon-related ancestry in modern Koreans from Ulsan in one of the two models they provide. This could be purely a product of the modelling and the use of a subpar proxy, but it could also be real and have to do with the simple fact that Ulsan is located close to Japan.

While we now have aDNA from one of the Three Kingdoms as well as the confederacy squeezed in between them, let us hope that ancient DNA from the Silla kingdom and Goguryeo will follow soon. To be able to gain a better understanding of the persistence of archaic forager ancestry in Korea, more samples from the Jeulmun pottery period are required.


Don-Nyeong Lee et al. (2022): Genomic detection of a secondary family burial in a single jar coffin in early Medieval Korea

Shin et al. (2001): Y-Chromosome multiplexes and their potential for the DNA profiling of Koreans

Ai Hua Zhang et al. (2012): Y Haplogroup Distribution in Korean and Other Populations

SH Kim et al. (2011): High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea

Gelabert et al. (2022): Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

Jeong et al. (2019): The genetic history of admixture across inner Eurasia

Vovin, A (2013): From Koguryǒ to T’amna: Slowly riding to the South with speakers of Proto-Korean

Scarre, Chris. (2018): The human past: world prehistory & the development of human societies. London: Thames & Hudson. Part 1: The Evolution of Humanity.

Robbeets et al. (2021): Triangulation supports agricultural spread of the Transeurasian languages

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