Early inhabitants of the Americas split into two populations over 13,000 years ago, according to a new study of ancient DNA, and remained separated for thousands of years.
Eventually, somewhere, the two groups met again and began commingling. Today, their descendants inhabit a vast region stretching from Mexico to the southern tip of South America.
The research, published on Thursday in the journal Science, paints a complex picture of human migrations through the Americas. When people arrived in the Western Hemisphere from Asia, they didn’t just move to new territories and settle down.
“This study is important because it begins to move us away from overly simplistic models of how people first spread throughout the Americas,” said Deborah A. Bolnick, a geneticist at the University of Texas at Austin, who was not involved in the study.
The findings emerged from a study of 91 ancient genomes of people who lived as long as 4,800 years ago in what are now Alaska, California and Ontario. They represent a major addition to the catalog of ancient DNA in the Western Hemisphere.
Until the 1990s, archaeological sites provided much of the evidence for the spread of people across the Americas. There’s firm archaeological evidence that people had reached southern Chile by 14,5000 years ago, for example; some researchers even argue that people arrived several thousand years earlier.
Yet archaeology alone has left many questions unanswered, such as who exactly lived in those early sites and how they were related to each other. Geneticists are seeking to answer some of those questions by looking at the DNA of living Native Americans.
Early studies on small fragments of genes suggested that all Native Americans south of the Arctic descended from the same group of migrants, who may have traveled across the Bering Land Bridge connecting Asia to what is now Alaska at the end of the last ice age.
But the pace of this research slowed in the early 2000s, thanks in part to the distrust that many Native American communities felt toward scientists after a long history of abuse.
In a 2004 lawsuit, the Havasupai Tribe sued the University of Arizona for misleading members about what their DNA would be used to study. That conflict left many researchers reluctant to get embroiled in similar controversy.
As scientists learned how to extract DNA from ancient human remains, a similar conflict arose.
Many museums store Native American skeletons, often exhumed without consent from burial grounds. Native American communities reclaimed many of these remains and often turned down research requests.
In recent years, however, these strains have started to ease.
Each summer, Ripan Malhi, a geneticist at the University of Illinois and co-author of the new study, and his colleagues run a workshop at the University of Illinois to train Native American students in genetics, focusing on research that can help their communities.
He also has established long-running relationships with Native American communities in Canada and Alaska.
Christiana Scheib, another co-author on the new study, traveled to California to meet with tribal representatives. She explained why she wanted to study Native American remains in California museums.
“Some of them were surprised,” said Dr. Scheib, who now heads the ancient DNA research group at the University of Tartu in Estonia. “They said, ‘You’re the first researcher to talk to us and ask our opinion.’”
In the new study, Dr. Scheib, Dr. Malhi and their colleagues searched for DNA in remains they had gained permission to study. They succeeded in finding genetic material in the teeth and ear bones of 91 individuals.
In some cases, they were only able to retrieve fragments of DNA; in other instances, they found enough material for an accurate reconstruction of the entire genome.
The researchers then compared the new data to publicly available genetic information about other people — both living and ancient — in North and South America. The scientists also looked at DNA from communities in Asia for close relatives.
At first, the family tree that emerged was baffling, suggesting close genetic connections between distantly related people. “We kept getting results that didn’t make sense,” Dr. Scheib said.
A closer look resolved some of the mystery.
From their data, the researchers concluded that living Native Americans descended from a population of Asians who moved into Alaska and then expanded southward, likely along the coast.
Soon afterward, that original population split into two groups, which Dr. Scheib and her colleagues call ANC-A and ANC-B.
The oldest genome yet found in the Americas, from a 13,000-year-old boy in Montana, belongs to ANC-A. By then, the groups already must have split in two.
The oldest evidence of ANC-B, on the other hand, comes from an 8,500-year-old skeleton discovered in Washington State known as Kennewick Man, or the Ancient One.
At some point, at least a few ANC-B people must have moved far to the east: Dr. Scheib and her colleagues found that people as old as 4,800 years in what is now southern Ontario belonged to ANC-B.
Once they arrived, these people put down roots. Algonquin-speaking people living today in Ontario also belong to ANC-B.
But when the scientists looked at DNA from people in California and further south, they were surprised to discover mixtures of ANC-A and ANC-B ancestry.
The oldest evidence for this mixture comes from people who lived 4,500 years ago on what are now the Channel Islands, off the coast of California. These people were 58 percent ANC-A and 42 percent ANC-B.
The researchers found similar DNA mixtures in living people in Mexico and South America.
Dr. Scheib and her colleagues put forward a few scenarios that might explain these results.
It’s possible that ANC-A people moved down the western coast of the Americas, establishing fishing communities along the way. Thousands of years later, a lineage of people descending from the ANC-B group also expanded southward, making contact with those communities.
Another possibility is that the two groups came together somewhere in North America. Only later did their descendants expand through the two continents.
Dr. Malhi said that there may well have been other massive migrations in the Americas. In the new study, for example, the researchers found that ancient people in what is now Ontario, as well as living Native Americans in places like Alaska, had ancestry related to the Inuit of Greenland.
It’s possible, then, that Arctic people moved south in the past few thousand years, mixing their genes with those of ANC-B people.
One way to explore these hypotheses is to find more ancient DNA from other parts of the Americas. But first Dr. Malhi said that he and his colleagues also want to talk with living Native Americans about their histories.
Their stories may preserve information about contacts between distantly related peoples in the far past.
“By not just looking at genes but also talking with communities, we might be able to find something,” said Dr. Malhi.