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Ancient North American Genome Offers Look at Native American History

NEW YORK (GenomeWeb News) – A new study supports the notion that the ancestors of Native-American populations were the first to settle in the Americas.

Members of an international team led by investigators at the University of Copenhagen's Centre for GeoGenetics sequenced and analyzed the more than 12,500-year-old remains of an infant who belonged to North America's historical Clovis population — work they described in today's issue of Nature.

The Clovis culture, which existed in North America some 12,600 to 13,000 years ago, is known for its particular brand of technology, including blades and bone-based tools. But there had been some debate over whether the group was descended from Europeans or from ancestors shared with present-day Native Americans.

Based on the new genetic analysis, the team concluded that the sequenced Clovis boy carried genes from Siberia's Mal'ta population, similar to Native-American populations today. The findings also indicate that the individual was part of a population ancestral to an estimated 80 percent of present-day Native Americans.

"We found that the genome of this boy is more closely related to Native Americans of today than any other population around the world," the study's corresponding author Eske Willerslev, with the University of Copenhagen, told reporters during a press briefing this week. "As such, it has settled a long-lasting debate about the origins of Clovis."

"The Solutrean theory, for example, that suggests Clovis originated from peoples in Europe doesn't fit our results," he said. "We can also see from the genome study that this ancient population … is the direct ancestor to many Native Americans today. As such, our study is in agreement with the view that present-day Native Americans are direct descendants from the first peoples in the Americas."

After using a combination of PCR and Sanger sequencing to determine the mitochondrial haplogroup of the infant, known as Anzick-1, the researchers turned to shotgun sequencing to generate 14.4-fold coverage of the individual's nuclear genome.

"It is actually the first high-coverage genome for a really poorly preserved sample," Willerslev told reporters.

"Other [ancient] samples where high-coverage genomes have been obtained have been extremely good quality, with 40 to 60 percent endogenous DNA," he added. "For the majority of the samples here, we had around 1 to 2 percent endogenous DNA."

An analysis of both the mitochondrial and nuclear sequence data suggested that the infant, found at a Clovis burial site in western Montana, was part of a population that carried genes passed down from a population that lived in Siberia during the Upper Paleolithic period, the study's authors found.

Their findings suggest that the Clovis population, in turn, was ancestral to many present-day Native-American populations, though it also points to a split in populations coming from Siberia prior to the establishment of the Clovis culture.

"We found … very early divergence among Native-American groups that actually predates the ancient [Clovis] ancestor — probably going back to pre-Clovis times," Willerslev said. "One of the [resulting] lineages resulted in the Anzick family, in Clovis.

"The other lineage is going somewhere else. We don't quite know where," he added. "But we can see that some of the modern Canadian groups where we have DNA for comparison belong to the other lineage, while the lineage of the Anzick family is represented by most [Native] South Americans and Mexicans."