The Yayoi of the Doigahama Site Were Mostly Immigrants｜A Genome That Overturned the Northeast Asian Origin Theory

Who are the Japanese? Even now, in the late 2020s, almost nothing has been settled in answer to this question. As I see it, there are two main reasons. One is that the particular circumstances of an island nation make the question all the more complicated to unravel. The other is that the situation in East Asia stands in the way of joint research.

Amid all this, a site discovered nearly a hundred years ago has lately been drawing quiet attention once again. It is the Doigahama site in Yamaguchi Prefecture. Doigahama is a small settlement facing the Hibiki Sea on the Sea of Japan side, and it hardly ever draws notice.

For anyone interested in anthropology, however, this place has remained too important to look away from, because a burial ground of Yayoi people from more than 2,300 years ago was discovered there. The discovery itself goes back to 1930, and after nearly a century of investigation, some 300 skeletons have been unearthed so far, packed closely together. That has given the site an extremely important place at the forefront of research on the Yayoi people.

Here is where the Yayoi people become troublesome. They are generally thought of as the group that appeared after the Jomon people, and they stand at the juncture with the Kofun people who came after them. If the Jomon are taken as the native baseline, the Yayoi period is when large-scale migration to the archipelago first began.

Human bones do not interest most people, but they are time capsules that preserve the history of our ancestors. By examining their skeletal features and their genes, we can bring the figures of our ancestors into view with a fair degree of accuracy. And the Doigahama site is the single most important base for reconstructing what the ancient people looked like.

In anthropology, people have begun to think that while the physical traits of the Jomon were fairly consistent across the Japanese archipelago, the Yayoi were an extremely diverse population. They used to be contrasted as a pair, the Jomon people against the Yayoi people, but that view has already been abandoned. For now, we can understand them as the people who lived through the Jomon period, who were quite possibly of a relatively uniform kind, and the people who lived through the Yayoi period, who were considerably diverse.

Yet in recent years the question of who the Yayoi people really were has been thrown into fierce confusion, and we face the strange reality that their picture changes almost every year. Until a few years ago, for example, the Yayoi people of northwestern Kyushu, centered on Nagasaki, and the Yayoi people of Doigahama were thought to have been entirely different, even though they lived in the same period.

Lately, though, things have become even more complicated. In January 2026, a joint research group including the University of Tokyo and researchers on the Doigahama site published its findings. They analyzed the nuclear genome sequences of four Yayoi individuals, from about 2,300 to 2,500 years ago, unearthed at two sites in Nagasaki Prefecture in northwestern Kyushu. Two of the four turned out to carry genome components nearly identical to those of the Jomon people, while the other two carried components derived both from the Jomon and from immigrants.

Set this beside the whole-genome analysis of a single individual from the Doigahama site carried out a little earlier, in 2024, and an unexpected picture emerges. Leaving the difficult details aside and putting it simply, the Yayoi people of northwestern Kyushu around Nagasaki were found to be either Jomon or a mix of Jomon and Yayoi, and they carried plenty of components from both the Jomon and the immigrants. The individual from Doigahama, by contrast, had Jomon elements but very few of them, and was shown to be overwhelmingly of immigrant ancestry. Roughly speaking, the Yayoi of Doigahama had about 5 percent Jomon ancestry and about 20 percent Northeast Asian ancestry, and the rest, surprisingly, was made up of East Asian ancestry.

I say “surprisingly” because, as of the early 2020s, the Yayoi people were in fact thought to be of Northeast Asian origin. This is the so-called triple-structure theory of the Japanese. Before these results were announced, contact with East Asian populations was thought to have been extremely limited, and it was assumed to have had no direct relationship with the Yayoi people. That has now been turned on its head.

From this we can say that the Yayoi people who lived at Doigahama were basically of immigrant ancestry. Quite intriguingly, though, long before any genetic testing was done, it had already been pointed out that the features of these Yayoi bones almost exactly matched those of a certain ancient people.

Next time, I will turn to the mystery of the Yayoi people of Doigahama and the origin that had already been suggested.