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Native American Genotyping Study Suggests First Inhabitants of the Americas Arrived in Multiple Migrations

NEW YORK (GenomeWeb News) – At least three historical migrations from Asia introduced the ancestors of Native Americans to the Americas, according to a new study in Nature, though migrants from the first of these waves made the most pronounced genetic contributions to present-day Native American populations.

"For years it has been contentious whether the settlement of the Americas occurred by means of a single or multiple migrations from Siberia," University College London genetics, evolution, and environment researcher Andrés Ruiz-Linares, the study's senior author, said in a statement. "But our research settles this debate: Native Americans do not stem from a single migration."

Ruiz-Linares led an international research team that brought together genotype data on hundreds of individuals from Native American, Siberian, and other populations to not only retrace the Asian migration events that peopled the Americas, but also the dispersal events that followed.

Genetic patterns detected in existing populations point to three periods of Asian gene flow into the Americas across the land bridge that once linked the continents. The group involved in the initial migration — dubbed the "First American" population by study authors — appears to be ancestral to all of the Native American populations tested.

In addition, a few existing Native American populations carry genes passed down from Asian populations involved in more recent migrations, Ruiz-Linares told GenomeWeb Daily News, though the precise timing of these subsequent migrations is yet to be determined.

Previous research on the population history of the Americas suggests that the first settlers arrived from Asia an estimated 15,000 years ago or more over the Beringia land bridge, the study's authors explained. There has been ongoing debate over whether this settlement occurred as the result of one migration wave or many, they added, as well as interest in understanding how populations spread out once they arrived in the Americas.

To address such questions, researchers looked at patterns for nearly 365,000 SNPs in 493 samples from 52 Native American populations, 245 samples from 17 Siberian populations, and more than 1,600 samples from 57 additional populations. Almost 300 of the samples were genotyped specifically for the study using Illumina arrays, while others had been tested for other studies done over the past few decades.

In an effort to minimize confounding genetic clues produced by admixture between Native American populations and more recently arrived populations from Europe and Africa, investigators relied on a local ancestry inference method for focusing on Native American regions of each individual's genome. They also verified findings based on this method with data for participants from 34 Native American populations that showed little or no evidence of European or African admixture.

In general, the team found that genetic patterns in the populations tested tended to cluster in ways that agreed with known language and geographical groupings. But when they looked more closely at Asian gene flow patterns, the researchers found signs of at least three ancient migrations from Asia to the Americas.

The present-day Native American populations tested all seem to have descended from members of the first migration wave, they explained, but two subsequent migrations appear to have contributed to the ancestry of Eskimo-Aleut speaking populations in the Arctic and Na-Dene speaking populations in Canada, respectively.

More than half of the Native American ancestry in the Eskimo-Aleut speaking populations can be attributed to the First American migration, researchers reported, while the remaining Native American ancestry seems to stem from a second migration.

In the Na-Dene speaking Chipewyan population, on the other hand, some 90 percent of Native American ancestry can be traced back to the First American population. The other 10 percent appears to have been introduced via a third migration from Asia.

"The Asian lineage leading to First Americans is the most anciently diverged, whereas the Asian lineages that contributed some of the DNA to Eskimo-Aleut speakers and the Na-Dene-speaking Chipewyan from Canada are more closely related to present-day East Asian populations," first author David Reich, a genetics researcher at Harvard University and the Broad Institute, explained in a statement.

The study provides clues to the course that the early Asian migrants took as they expanded into the Americas, too, with lingering genetic signatures suggesting individual populations split off and settled en route as Asian migrants moved south along the coast.

In most cases, there appears to have been relatively little mixing between populations after this separation.

Even so, the team's data indicates that at least a few populations backtracked after their early treks. For instance, genetic patterns in Chibchan-speaking populations reveal ancestry from both North and South America, suggesting that their ancestors settled in South America and moved back across the Panama land link to Central America before returning to more southern locales.

The researchers also found genetic signs suggesting relatives of Eskimo-Aleut speaking populations returned from the Americas to Siberia, carrying with them DNA from the earliest Asian First American migrants.

While the genotyping information available for the current study has provided a more refined view of Native American population history than has been possible previously, those involved in the effort noted that there is still more to be learned by studying additional participants and by assessing complete genome sequences.

In particular, Ruiz-Linares noted that whole-genome sequence data should help in estimating the timing of the three historical migrations to the Americas — something that is tough to discern using SNP data alone.

"We hope to be able to get those dates by analyzing genome sequence data," he said, "and we're working on that at the moment."

To that end, Ruiz-Linares said the team has already started doing whole-genome sequencing on a few dozen individuals from some of the same populations represented in the current study.

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