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Ancient Alaskan Genome Shows Common Founding Population of Native Americans

NEW YORK (GenomeWeb) – Ancient Beringians and the ancestors of other Native Americans descend from a single founding population, according to a genomic analysis of an ancient Alaskan genome.

The first human settlers of the Americas crossed from Asia through Beringia, which connected northwestern North America and northeastern Asia, but when and how the settlers spread through the Americas has been unclear.

By sequencing the genome of an individual who lived in Beringia, dubbed USR1, about 11,500 years ago, researchers led by the University of Copenhagen's Eske Willerslev began to tease out how this individual is related to other Native American groups. As they reported in Nature today, the researchers found that ancient Beringians and the ancestors of other Native Americans split from East Asians about 36,000 years ago.

"The USR1 results provide direct genomic evidence that all Native Americans can be traced back to the same source population from a single Late Pleistocene founding event," the researchers wrote in their paper.

The remains of two infants who lived about 11,500 years ago were recently uncovered in Upward Run River in Alaska in eastern Beringia. Willerslev and his colleagues sequenced one of the two samples — the other didn't contain enough DNA for analysis — to 17X coverage. They then compared the USR1 sequence to a panel of global populations at more than 199,000 SNPs using multiple statistical approaches.

From this, the researchers found that USR1 is most closely related to modern-day Native Americans, followed by Siberians and East Asians, than any other population in the panel. Additionally, comparisons of USR1 to a set of modern and ancient Native Americans found that they were similarly related to Eurasians, Australasians, and Africans.

However, they noted that USR1 does not cluster with any one Native American group, suggesting that it belongs to an unknown Native American population not included in the panel.

Additionally, Willerslev and his colleagues found that USR1 forms a clade with other Native American populations and that USR1 and present-day Native Americans are equally related to the ancient north Eurasian population to which the 24,000-year-old Mal'ta individual belongs. This, they said, confirms that USR1 and present-day Native Americans descend from the same ancestral source population.

A phylogenetic tree the researchers constructed placed USR1 basal to other Native American groups, indicating that it is a branch within the Native American clade, but equally related to Northern and Southern Native Americans.

Willerslev and his colleagues then pieced together how the peopling of the Americans might have occurred. They estimated that the founding population of Native Americans — including both Northern and Southern Native Americans and Beringians — diverged from ancestral Asians about 36,000 years ago, though with a high level of gene flow until about 25,000 years ago. Ancient Beringians then diverged from the common ancestor of other Native Americans about 20,900 years ago. This, they noted, is in agreement with the Beringian standstill model, which says that the people moving from Asia to the Americas were isolated in Beringia for a period of time before moving southward.

But where that split occurred remains unclear. One possibility is that Ancient Beringians and other Native American split while in northeast Asia, while another is that they split in northwest North America, the researchers said. Willerslev and his colleagues noted that the first scenario is more consistent with archaeological evidence, while the second is in line with genetic evidence.

Both those scenarios, they added, are still consistent with the Northern and Southern Native American populations splitting about 15,000 years ago, south of eastern Beringia, with some populations like the Athabascans returning north some 11,500 years ago.