The Jomon people lived in Japan for more than 10,000 years. They hunted, fished, and gathered nuts. Scientists read DNA from old Jomon bones found in shell mounds. They learned that the Jomon split from other East Asian groups very long ago.

Today, Japanese people still have some Jomon DNA. A new idea says that modern Japanese people have three groups of ancestors, not two.

Many textbooks say that modern Japanese people come from two groups: the Jomon hunter-gatherers and Yayoi people who brought rice farming from the continent. Ancient DNA is changing this story. Because Japan's soil is often acidic, old bones usually dissolve, but shell mounds help protect them. In 2017, researchers analyzed DNA from 3,000-year-old Jomon people in Fukushima and found that the Jomon line split off before other East Asian groups did.

Then in 2021, a study of 12 ancient genomes proposed a third source: people who arrived during the Kofun period. Today, people on Honshu carry less than 20 percent Jomon ancestry, while the Ainu and Okinawans carry more.

Japan's acidic volcanic soil dissolves bones, so ancient DNA is hard to recover there. Shell middens help, because the shells neutralize the acid. In 2017, researchers analyzed 3,000-year-old individuals from a shell midden in Fukushima and found that the Jomon lineage split off before modern East Asian populations divided. For decades, Japanese origins had been explained by a dual-structure model, in which Jomon hunter-gatherers mixed with rice-farming migrants of the Yayoi period.

Ancient genomes have refined it. A 2021 study of 12 ancient genomes estimated that the Jomon parted from continental groups 20,000 to 15,000 years ago, as rising seas were cutting the archipelago off, and then kept a small effective population of about 1,000 for thousands of years. The same study proposed a tripartite model, with a third wave of migrants of East Asian ancestry arriving in the Kofun period.

The samples behind these conclusions are tiny. Each period is represented by only a handful of individuals, and ancestry percentages shift with the statistical model chosen. A 2024 study, though, combined ancient genomes with data from about 170,000 modern Japanese, supported the tripartite model across the country, and found that the share of Jomon ancestry varies by region.