Ancient DNA confirms Native Americans' deep roots in North and South America

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The Suruí from the Brazilian Amazon carry traces of Australasian ancestry, now confirmed to have arrived in South America more than 10,400 years ago.

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For decades, scientists could describe the peopling of the Americas only in broad strokes, leaving plenty of mysteries about when and how people spread across the continents. Now, state-of-the-art ancient DNA methods, applied to scores of new samples from around the Americas, are filling in the picture. Two independent studies, published in Cell and online in Science, find that ancient populations expanded rapidly across the Americas about 13,000 years ago. They also emphasize that the story continued in the thousands of years since, revealing previously undocumented, large-scale movements between North and South America.

The data include 64 newly sequenced ancient DNA samples from Alaska to Patagonia, spanning more than 10,000 years of genetic history. “The numbers [of samples] are just extraordinary,” says Ben Potter, an archaeologist at the University of Alaska in Fairbanks. Prior to these studies, only six genomes older than 6000 years from the Americas had been sequenced. As a result, says Jennifer Raff, an anthropological geneticist at the University of Kansas in Lawrence, “The [genetic] models that we’ve been using to explain the peopling of the Americas have always been oversimplified.”

Eske Willerslev, an evolutionary geneticist at the University of Copenhagen who led the Science team, worked closely with the Fallon Paiute-Shoshone Tribe in Nevada to gain access to some of the new samples. The tribe had been fighting to repatriate 10,700-year-old remains found in Nevada’s Spirit Cave and had resisted destructive genetic testing. But when Willerslev visited the tribe in person and vowed to do the work only with their permission, the tribe agreed, hoping the result would bolster their case for repatriation.

It did. Willerslev found that the remains from Spirit Cave are most closely related to living Native Americans. That strengthened the Fallon Paiute-Shoshone Tribe’s claim to the bones, which were returned to them in 2016 and reburied. Willerslev’s study validates that “this is our homeland, these are our ancestors,” says Rochanne Downs, the tribe’s cultural coordinator.

Willerslev added the Spirit Cave data to 14 other new whole genomes from sites scattered from Alaska to Chile and ranging from 10,700 to 500 years old. His data join an even bigger trove published in Cell by a team led by population geneticist David Reich of Harvard Medical School in Boston. They analyzed DNA from 49 new samples from Central and South America dating from 10,900 to 700 years old, at more than 1.2 million positions across the genome. All told, the data decisively dispel suggestions, based on the distinctive skull shape of a few ancient remains, that early populations had a different ancestry from today’s Native Americans. “Native Americans truly did originate in the Americas, as a genetically and culturally distinctive group. They are absolutely indigenous to this continent,” Raff says.

A trail of DNA

Two new papers add DNA from 64 ancient individuals to the sparse genetic record of the Americas. They show that people related to the Anzick child, part of the Clovis culture, quickly spread across both North and South America about 13,000 years ago.

Sample sizeOneEightTeam leaderPreviously publishedEske WillerslevDavid ReichUpward Sun River11,500 years agoAncient BeringianSpirit Cave10,700 years agoLovelock Cave2000–600 years agoAnzick12,700 years agoMonte Verde14,500+ years agoLapa do Santo9600 years agoLagoa Santa10,400–9600 years agoAustralasian ancestryNorthernNative AmericansSouthernNative Americans


The two studies also provide an unprecedented view of how ancient Americans moved across the continent beginning about 13,000 years ago. Previous genetic work had suggested the ancestors of Native Americans split from Siberians and East Asians about 25,000 years ago, perhaps when they entered the now mostly drowned landmass of Beringia, which bridged the Russian Far East and North America. Some populations stayed isolated in Beringia, and Willerslev sequenced one new example of such an “Ancient Beringian,” 9000-year-old remains from Alaska’s Seward peninsula. Meanwhile, other groups headed south. At some point, those that journeyed south of the ice sheets split into two groups—”Southern Native Americans” and “Northern Native Americans” (also sometimes called Ancestral A and B lineages), who went on to populate the continents.

By looking for genetic similarities between far-flung samples, both papers add detail—some of it puzzling—to this pattern. The 12,700-year-old Anzick child from Montana, who is associated with the mammoth-hunting Clovis culture, known for their distinctive spear points, provided a key reference point. Willerslev detected Anzick-related ancestry in both the Spirit Cave individual—who is associated with western stemmed tools, a tradition likely older than Clovis—and 10,000-year-old remains from Lagoa Santa in Brazil. Reich’s team found an even closer relationship between Anzick and 9300- to 10,900-year-old samples from Chile, Brazil, and Belize.

Those close genetic affinities at similar times but across vast distances suggest people must have moved rapidly across the Americas, with little time to evolve into distinct genetic groups. Reich’s team argues that Clovis technology might have spurred this rapid expansion. But anthropological geneticist Deborah Bolnick of the University of Connecticut in Storrs notes the Anzick-related ancestry group may have been broader than the Clovis people, and doubts that the culture was a driver.

Willerslev also finds traces of this Anzick-related ancestry in later samples from South America and Lovelock Cave in Nevada. But in Reich’s data it fades starting about 9000 years ago in much of South America, suggesting “a major population replacement,” he says.

After that population turnover in South America, both teams see striking genetic continuity in many regions. But that doesn’t mean no one moved around. Reich’s group sees a new genetic signal entering the central Andes about 4200 years ago, carried by people who are most closely related to ancient inhabitants of the Channel Islands, off Southern California. Meanwhile, Willerslev’s team detects ancestry related to the present-day Mixe, an Indigenous group from Oaxaca in Mexico, spreading to South America about 6000 years ago and North America about 1000 years ago. Neither of these migrations replaced local communities, but rather mixed with them. Both teams say they could be seeing the same signal, but “without comparing the data, it’s really hard to tell,” says archaeogeneticist Cosimo Posth of the Max Planck Institute for the Science of Human History in Jena, Germany, the first author of the Cell paper.

Just as mysterious is the trace of Australasian ancestry in some ancient South Americans. Reich and others had previously seen hints of it in living people in the Brazilian Amazon. Now, Willerslev has provided more evidence: telltale DNA in one person from Lagoa Santa in Brazil, who lived 10,400 years ago. “How did it get there? We have no idea,” says geneticist José Víctor Moreno-Mayar of the University of Copenhagen, first author of the Willerslev paper.

The signal doesn’t appear in any other of the team’s samples, “somehow leaping over all of North America in a single bound,” says co-author and archaeologist David Meltzer of Southern Methodist University in Dallas, Texas. He wonders whether that Australasian ancestry was confined to a small population of Siberian migrants who remained isolated from other Native American ancestors throughout the journey through Beringia and the Americas. That suggests individual groups may have moved into the continents without mixing.

Delighted as they are with the data in the new studies, scientists want more. Meltzer points out that none of the new samples can illuminate what’s happening at pre-Clovis sites such as Chile’s Monte Verde, which was occupied 14,500 years ago. And Potter notes that, “We have a huge, gaping hole in the central and eastern North American [sampling] record. … These papers aren’t the final words.”

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