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Ancient DNA Sheds New Light on Human Migrations in the Americas

NEW YORK (GenomeWeb) – Three studies published today are offering a new look at the multifaceted population movements and expansions that marked the peopling of the Americas.

For the first of the studies, published online today in Science, researchers from the University of Copenhagen, the University of California, and elsewhere considered ancient genome sequence data for 15 individuals found at sites that stretched from present-day Alaska to Patagonia and that dated as far back as 10,000 years or more.

Through comparisons with genomic data for hundreds of individuals from modern-day populations, the team teased out rapid, but patchy, population spread following initial migrations into North and South America.

"We find that once south of eastern Beringia, Native Americans radiated and gave rise to multiple populations, some of which are visible in the genetic record only as unsampled populations, and who at different times expanded to different portions of the continent, though not as extensively as the initial peopling," the authors wrote.

Although all of the ancient individuals shared genetic features with Native Americans, the researchers saw more subtle relationships pointing to past population migrations and diversifications. For example, the sample set included a tooth from a toddler on Alaska's Seward Peninsula, dated at roughly 9,000 years ago, with genetic profiles resembling those in Beringian individuals.

"This one small tooth is a treasure trove of information about Alaska's early populations, not only their genetic affinities but also their movements, interactions with other people and diet," co-author Jeffrey Rasic, a researcher with the US National Park Service, said in a statement.

Meanwhile, using "Paleoamerican" samples and a sample from a 19th century individual from the Andaman Islands, the team saw signs of a population with genetic ties to Australasia that was present in South America roughly 11,700 years ago, but has not been detected in North America.

"Overall, our findings suggest that soon after arrival, South Americans diverged along multiple geographic paths," the authors wrote. "That process was further complicated by the arrival of a second independent migration and gene flow in Middle to Late Holocene times. Later admixture potentially reduced the Australasian signature that might have been carried by earlier inhabitants."

A related study published online today in Science Advances focused on ancient population adaptations to cold, low oxygen environments with high exposure to ultraviolet light at high-altitude sites in the South American Andes. There, an Emory University- and University of Chicago-led team did whole-genome shotgun sequencing on seven samples dating back 1,400 years to nearly 7,000 years, spanning three distinct archeological periods.

"Contact with Europeans had a devastating impact on South American populations, such as the introduction of disease, war, and social disruption," first author John Lindo, an anthropology and human genetics researcher affiliated with Emory and the University of Chicago, said in a statement. "By focusing on the period before that, we were able to distinguish environmental adaptations from adaptations that stemmed from historical events."

Based on their ancient genome data, new sequences for dozens of individuals from present-day populations, and available population genotyping profiles, the researchers estimated that permanent populations have occupied the Andean highlands since roughly 9,000 years ago, remaining more robust after European arrivals that dramatically affected lowland populations in South America.

When it came to high-altitude adaptations in the region, the team found evidence of alterations affecting heart-related genes rather than at hypoxia-associated genes implicated in low oxygen-response elsewhere.

The researchers also saw signs of selection affecting genes such as the intestinal enzyme-coding gene MGAM that appear to contribute to starch digestion, likely reflecting potato-rich diets in the area. And they detected more recent signs of positive selection in the Andes involving genes known to respond to the types of infectious diseases introduced by Europeans.

Finally, in a paper published online today in Cell, researchers from Harvard Medical School, the Max Planck Institute for the Science of Human History, and elsewhere described three main migrations from a related ancestral source population into South America based on genome-wide sequence data for 49 ancient individuals in the Central Andes, southern South America, Brazil, and Belize going back almost 11,000 years.

"This broader dataset reveals a common origin of North, Central, and South Americans as well as two previously unknown genetic exchanges between North and South America," co-senior author David Reich, a genetics researcher at Harvard, said in a statement.

While the spread of Clovis culture from North America into South America has not been documented, the team's latest genetic results revealed shared ancestry between Clovis individuals and individuals who lived in what is now Brazil more than 9,000 years ago. Samples from parts of Central and South America that were dated at less than 9,000 years old pointed to a population replacement that ousted individuals with Clovis-related genetic ancestry and was followed by ongoing population continuity.

The researchers also described another previously unappreciated relationship between populations with shared ancestry in the southern Peruvian Andes and California's Channel Islands. 

Reich noted that that study lacked ancient representatives from several important locations, including Amazonia, northern South America, and the Caribbean. Consequently, he said, "[f]illing in these gaps should be a priority for future work."