2,300-Year-Old Skeleton Reveals Secrets About Origins of the Japanese

Where did the Japanese come from? We might have just found the answer to this question that has been ruining the sleep of archaeologists and rabid Japanese nationalists for decades.

There are three main native ethnic groups in modern Japan: the Ainu, Ryukyuan, and Yamato. All three are thought to be descendants of the Jōmon, the earliest known culture of Japan. Most modern Japanese are Yamato, so researchers usually focus on them. The Yamato are a delicious ramen bowl of Jōmon, East Asian, and Northeastern Siberian DNA.

Since the 1980s, the most common belief has been that people came to Japan in two big migrations.

1. The first wave was the Jōmon, who came over during the last ice age, when there was a land bridge to Asia and when Google Maps directions were still hella dodgy. The Jōmon were hunter gatherers who lived mostly isolated from about 20,000 BC to 1,000 BC, but they were pretty advanced: they developed some cool pottery, may have grown chestnuts and beans, and took good care of their Tamagotchi.

2. The second migration wave started flowing in between 1,000 BC and 300 BC, at the beginning of the Yayoi period. They did magical things the Jōmon had never dreamed of, like rice farming. They also brought exciting, new killing technologies like bronze, iron, and Death Notes. This wave may have lasted into the Kofun period (300 AD to 538 AD), the period after Yayoi.

The (surviving) Jōmon and their advanced guests made many babies together, who became the Yayoi and eventually the Yamato (and maybe Ainu and Ryukyuan, but their stories are more complicated and are left as an exercise for the reader).

However, in 2021, some researchers surprised everyone when they looked at the DNA of several Jōmon, Yayoi, and Kofun skeletons. What they found seemed to break the accepted two-wave theory. As expected, the Kofun remains were similar to modern Yamato and contained Jōmon, East Asian, and Northeastern Siberian DNA. But the Yayoi remains did not contain any East Asian DNA!

The rebel researchers concluded that there must have been three waves of migration: the first was the Jōmon, the second was a Northeastern Siberian wave during the Yayoi period, and the third consisted of East Asian people during the Kofun period.

The three-wave theory was all the rage for a while, but like a revolting TikTok food hack, it didn’t last. Because a brand new 2025 study just dropped.

It sequenced the entire genome of a Yayoi skeleton. This study found DNA from all three sources: Jōmon, Northeastern Siberian, and East Asian. It shows you don’t need a third migration wave to explain the genetics of the modern Yamato people.

The researchers think that the remains examined in 2021 were from an isolated area and not representative of the Yayoi, then stuck out their tongues at the 2021 researchers. They also believe that the Yayoi wave came from the Korean Peninsula because the DNA of the Yayoi skeleton is similar to that of modern Koreans.

Figuring out ancient DNA is tricky, and future studies will likely shake things up again. For now, though, it seems like all the ingredients for the modern Yamato broth were in Japan by the end of the Yayoi period and the two-wave migration theory is still king, er, emperor.