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Two Genomic Analyses of Native Americans Come to Differing Conclusions

NEW YORK (GenomeWeb) – A pair of genomic studies published today has come to conflicting conclusions as to how the Americas were peopled.

One study, appearing in the online early version of Science from the University of Copenhagen's Eske Willerslev and his colleagues, reported that the ancestors of all present-day Native Americans came to the Americas in a single wave from Siberia no earlier than 23,000 years ago. The other study, published in the advanced online version of Nature from Harvard Medical School's David Reich and his colleagues, concluded that two migration streams were more likely, one of which was more closely related to ancestors of Australasian populations.

Modern-day Native Americans are thought to be the descendants of people from Siberia who crossed the Bering land bridge sometime in the late Pleistocene  then spread, diversifying into two basal genetic branches about 12,000 years ago — one branch found in North America and the other throughout North and South America. But, both groups of researchers noted, questions remain regarding whether this peopling occurred in one or more waves and when the ancestors of modern-day Native Americans diverged from their Eurasian ancestors.

In particular, the studies differed in their interpretation of genomic data suggesting that some Native American groups in South America, such as the Suruí of Brazil, were more closely related to ancestors of present-day Australasians.

Previous archaeological and morphological findings had suggested that some skeletons dating from the Pleistocene and early Holocene fell outside the variation seen within modern-day Native Americans and were more similar to modern-day indigenous Australasians. This, both teams noted, has led to a theory that a 'Paleoamerican' pioneer population had been present in the Americas, and then mostly replaced by the population arriving from Northeast Asia.

The Reich team said a separate population, which they called Population Y for Ypykuéra, or ancestor in the Tupi language family, was likely the source of this apparent Australasian DNA, while the Willerslev team reported no support for the migration of people directly related to Australasians into the Americas and instead suggested that apparent relatedness came from later gene flow.

Reich and his team examined SNP genotyping data from 63 people of Native American descent without any apparent European or African ancestry. They examined the allele frequencies between these individuals, representing seven Central and South America groups, and 24 outgroups. Their analysis suggested that Native American populations do not all descend from a homogenous ancestor.

Instead, they found that the Amazonian groups, the Suruí and Karitiana, were similar to Australasian groups like the Onge, Papuans, and New Guineans, among others. They found similar results even after extending their analysis to include 197 non-American populations and when using other statistical approaches.

They added that their analysis also argued that this shared genetic signal between South Americans and Australasians couldn't be due to post-Columbian gene flow.

Instead, they suggested that Population Y contributed the Australasian-related ancestry, and was likely already mixed with a lineage related to First Americans when it reached the Amazon.

This — in addition to their findings that this signal isn't present in other Native American populations in Central and South America nor in the 12,600 year-old Clovis individual — suggests that the genetic ancestry of Native Americans in Central and South America isn't due to a single migration wave, but rather to at least two waves of migration.

At the same time, Willerslev and his team sequenced the genomes of 31 modern-day individuals from the Americas, Siberia, and Oceania as well and 23 genomes from ancient individuals from North and South America.

Through ADMIXTURE and TreeMix-based analyses, the researchers found that all Native Americans form a monophyletic group that then diversifies into two branches, one representing Amerindians and one Athabascans. They also reported that all Native American populations diverged from the Koryak of Siberia some 20,000 years ago. This, they noted, indicates a common, Siberian origin for all Native Americans.

The Willerslev team also examined the apparent genetic relatedness between some Native American groups and Australasians.

They tested the Paleoamerican model by sequencing 17 ancient individuals who belonged to the now-extinct Pericúes from Mexico and Fuego-Patagonians from Chile and Argentina, groups that, based on their skull morphologies, have been proposed to be related to Paleoamericans. They also sequenced two pre-Columbian mummies from Northern Mexico.

Their analyses, though, indicated low shared ancestry between these ancient groups and Oceanians, and they found no evidence of gene flow from them to the Pericúes and Fuego-Patagonians. In addition, they were unable to reproduce earlier cranial morphology studies that suggested this link between Paleoamericans and Oceanians.

This, they concluded, doesn't support a model of early migration of a population directly related to Oceanians to the Americas.

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