Was this ancient person from China the offspring of modern humans and Neandertals?

When scientists excavated a 40,000-year-old skeleton in China in 2003, they thought they had discovered the offspring of a Neandertal and a modern human. But ancient DNA now reveals that the “Tianyuan Man” has only traces of Neandertal DNA and none detectable from another type of extinct human known as a Denisovan. Instead, he was a full-fledged member of our species, Homo sapiens, and a distant relative of people who today live in East Asia and South America. The work could help scientists retrace some of the earliest steps of human migration.

“The paper is very exciting because it is the first genome to fill a really big gap, both geographically and temporally, in East Asia,” says paleogeneticist Pontus Skoglund of Harvard Medical School in Boston, who was not involved in the work.

The first modern humans arose in Africa about 300,000 years ago. By 60,000 years ago, a subset swept out of Africa and mated with Neandertals, perhaps in the Middle East. After that, they spread around the world—DNA from ancient humans in Europe, western Asia, and the Americas has revealed the identity of those early migrants and whether they were related to people living today, especially in Europe. But the trail grows cold in eastern Asia, where warmer climates have made it hard to get ancient DNA from fossils.

The new genome sheds some light on those missing years. In the first genome-wide study of an ancient East Asian, researchers led by Qiaomei Fu, a paleogeneticist at the Chinese Academy of Sciences in Beijing, extracted DNA from the thighbone of the Tianyuan Man—so named because he was found in Tianyuan Cave, 56 kilometers southwest of Beijing.

The team calculated that the Tianyuan Man inherited about as much Neandertal DNA—4% to 5%—as ancient Europeans and Asians of similar age. That’s a bit higher than the 1.8% to 2.6% of Neandertal DNA in living Europeans and Asians. The Tianyuan Man did not have any detectable DNA from Denisovans, an elusive cousin of Neandertals known only from their DNA extracted from a few teeth and small bones from a Siberian cave and from traces of their DNA that can still be found in people in Melanesia—where they got it is a major mystery.

A big surprise is that the Tianyuan Man shares DNA with one ancient European—a 35,000-year-old modern human from Goyet Caves in Belgium. But he doesn’t share it with other ancient humans who lived at roughly the same time in Romania and Siberia—or with living Europeans. But the Tianyuan Man is most closely related to living people in east Asia—including in China, Japan, and the Koreas—and in Southeast Asia, including Papua New Guinea and Australia.

All of this suggests that the Tianyuan Man was not a direct ancestor, but rather a distant cousin, of a founding population in Asia that gave rise to present-day Asians, Fu’s team reports today in Current Biology . It also shows that these ancient “populations moved around a lot and intermixed,” says paleoanthropologist Erik Trinkaus of Washington University in St. Louis in Missouri, who is not a co-author.

And some left offspring whereas others did not. “I find it interesting that … some of the early modern colonizers of Eurasia were successful while others were not,” says co-author Svante Pääbo, a paleogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The Tianyuan Man also was a distant relative of Native Americans living today in the Amazon of South America, such as the Karitiana and Surui peoples of Brazil and the Chane people of northern Argentina and southern Bolivia. They inherited about 9% to 15% of their DNA from an ancestral population in Asia that also gave rise to the Tianyuan Man. But he is not an ancestor to ancient or living Native Americans in North America, which suggests there were two different source populations in Asia for Native Americans.

This is welcome news to Skoglund, who found in a separate study in 2015 that the Karitiana and Surui peoples are closely related to indigenous Australians, New Guineans, and Andaman Islanders. At the time, he predicted that they came from the same “ghost” source population in Asia, which was separate from another Asian population that gave rise to Native Americans in North America. “It’s fascinating that a prediction of a ‘ghost population’ based on modern-day populations alone can be confirmed in this way,” he says.