The study of genomes of ancient remains is writing the story of early Americans.
Nearly 11,000 years ago, a man died in what is now Nevada. Wrapped in a rabbit-skin blanket and reed mats, he was buried in a place called Spirit Cave.
On Nov. 8, a team of scientists reported that they had successfully recovered the man’s entire genome — by itself an important scientific development. But the man from Spirit Cave is not alone.
Last week, three international teams of scientists have published studies of DNA recovered from 70 other ancient people in the Americas.
Five years ago, scientists had retrieved just one ancient human genome from the entire Western Hemisphere: that of a 4,000-year-old man discovered in Greenland. With the latest batch, the total has reached 229.
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The genomes were obtained from the teeth and bones of people who lived from Alaska to Chile, from the coastal tropics of Belize to the high Andes. Hidden in this DNA are important discoveries about how humans spread through the Americas thousands of years ago.
Earlier studies had indicated that people moved into the Americas at the end of the last ice age, traveling from Siberia to Alaska across a land bridge now under the Bering Sea. They spread southward, eventually reaching the tip of South America.
But the new genetic findings have given researchers a much sharper picture. The earliest known Americans were already splitting off into recognizably distinct groups.
Some of these groups thrived, becoming the ancestors of indigenous people throughout the Western Hemisphere. Some died out entirely, leaving no trace save for what can be discerned in ancient DNA.
The new research hints at dramatic chapters in the people of the Americas that archaeology has not yet documented.
“Now, this is the grist for archaeologists,” said Ben Potter of the University of Alaska, who was not involved in the new papers. “Holy cow, this is awesome.”
Earlier studies pointed to Siberia as the origin of all living people in the Americas.
In January, Eske Willerslev and colleagues at the University of Copenhagen published an analysis of the genome of a 11,500-year-old girl found in eastern Alaska. She belonged to an early group of migrants, now called the Ancient Beringians, who split off 20,000 years ago from the ancestors of living indigenous people in the Americas.
In their latest study, published in the journal Science, the team reported discovering DNA from a second Ancient Beringian, an individual who lived 9,000 years ago in western Alaska.
The Ancient Beringians seem to have endured for several thousand years. But then they disappeared, leaving no known genetic trace in living people.
But another wave of migrants from Siberia did not stop in Alaska. They kept moving, eventually reaching south of the ice age glaciers. They split into two branches between 17,500 and 14,600 years ago.
One group turned and headed north, following the retreating glaciers into Canada and back to Alaska.
The other branch took a remarkable journey south. The genetic data suggest that this group spread swiftly across much of North America and South America about 14,000 years ago. The expansion may have taken only centuries.
“It’s basically an explosion,” Willerslev said.
The man from Spirit Cave in Nevada belonged to this southern branch of migrants. Willerslev also found that the man was closely related to a 12,700-year-old boy found on the other side of the Rocky Mountains in Montana.
But the man from Spirit Cave also turned out to have a close genetic link to 10,400-year-old skeletons found in Brazil, on the other side of the equator.
David Reich of Harvard University and his colleagues found a similar pattern in their own research, published Nov. 8 in the journal Cell. They uncovered a link between the ancient Montana boy and another group of ancient South Americans, including a 10,900-year-old skeleton in Chile.
Like Willerslev’s work, the kinship suggests that migrants moved quickly from North America to South America. “We agree that this must be a rapid radiation,” Reich said.
Starting about 9,000 years ago, both teams found, waves of people from North America or Central America moved southward. Willerslev’s research suggests the new arrivals mixed with older South American populations already present.
Reich, on the other hand, sees evidence for two waves of migrants that completely replaced the people who had lived in South America.
The new research also revealed instances of remarkable continuity, kinships that spanned thousands of years.
Willerslev and his colleagues compared the genome of the man from Spirit Cave to those of four sets of remains found nearby in Nevada’s Lovelock Cave, who lived as recently as 600 years ago.
All of these people were closely related, his team found, despite being separated by 10,000 years of history.
A similar bond was found in the Andes. John Lindo of Emory University and his colleagues analyzed DNA from seven people who lived at high elevations between 6,800 and 1,400 years ago.
The researchers estimate that people who lived above 7,500 feet in the mountains were separated from the lowland populations between 9,200 and 8,200 years ago. Today, the mountain people still show a strong genetic link to the ancient remains.
“This is not something that you see in most other regions of the world,” Reich said.
In 2015, Reich and his colleagues found that some living people in the Amazon carry some DNA that’s most similar to that of people who live today in Australia and New Guinea.
The researchers speculated that their ancestry included an unknown group, which the scientists called Population Y, who separately made their way into the Americas.
In their new study, Reich and his colleagues found no trace of Population Y — but Willerslev’s team succeeded in identifying their DNA in some of the 10,400-year-old skeletons in Brazil.
“The million-dollar question obviously is, how did this happen?” Willerslev said.
Perhaps another group of Asians entered the Americas long before the ancestors of the man from Spirit Cave and other early Native Americans. Maybe they interbred with people in the Amazon before disappearing altogether.
Or perhaps a few of the early members of the southern branch happened to have some odd genes that survived through the generations.
The new rush of genetic samples reflects a growing working relationship between scientists and indigenous peoples. For decades, many tribes rejected requests for DNA from researchers.
The man from Spirit Cave, for example, was dug up by archaeologists in 1940 and stored in a museum. The local tribe, the Fallon Paiute-Shoshone, didn’t learn of the body till 1996. For years they fought for its repatriation.
Initially, the tribe was opposed to looking for DNA in the skeleton, because scientists would have to destroy much of it. Willerslev met with the tribe and explained that he would require only a tooth and a small piece of ear bone.
The tribe agreed to give him one shot at finding DNA in the Spirit Cave remains.
Willerslev’s results led the Bureau of Land Management to turn over the skeleton to the tribe. They buried the man from Spirit Cave at an undisclosed location in 2017.