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Ancient Siberian Sequences Offer a Refined Look at Native American Ancestry, Migration

NEW YORK (GenomeWeb News) – The genome sequencing study of an ancient Siberian individual, described online today in Nature, suggests that a population with ties to present-day western European populations that once lived in the region contributed ancestry to early Native American populations prior to their arrival in the New World.

University of Copenhagen Centre for GeoGenetics researcher Eske Willerslev led an international team that sequenced the draft genome and mitochondrial genome of a 24,000-year-old individual from the south central region of the Russian territory.

Within the mitochondrial sequences, the group saw genetic relationships between the ancient Siberian and hunter-gatherer populations living in Europe prior to the advent of agriculture.

Meanwhile, Y chromosome and autosomal chromosome sequences suggested the individual — known as MA-1 for the Mal'ta site where he was discovered — is related to both current western European populations and to Native American populations in ways that point to Native American migration through the region en route to the Americas.

"Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans," Willerslev and his colleagues wrote.

Present-day Native American populations show genetic ancestry from East Asia, the study authors noted. But there had been some debate about additional sources of Native American ancestry in the Old World as well as the route that the early Americans used to reach the New World.

For their current study, researchers decided to turn to extremely old human remains housed at Russia's Hermitage State Museum in an effort to better understand past population and migration patterns.

Using Illumina HiSeq and MiSeq instruments — and DNA extracted from a 24,000-year-old skeleton belonging to a juvenile male from Mal'ta, near Siberia's Lake Baikal — they generated enough sequence data to cover the MA-1 individual's genome to an average depth of one-fold.

In the process, the team also sequenced the long-deceased man's mitochondrial genome to a depth of nearly 77-fold coverage — information that placed MA-1 in the mitochondrial haplogroup U.

That haplogroup, while common to European hunter-gatherer groups during the Upper Paleolithic and Mesolithic periods, is not typically detected in East Asian populations, the researchers explained.

And that was not the last of the data pointing to ties between the ancient Siberian and populations from western Eurasia. The group found that MA-1 also carried Y chromosome and autosomal sequences that clustered with both western Eurasians and Native Americans, but were more distant from modern-day East Asian populations.

Together with existing population data and genome sequences for four Eurasian individuals sequenced for the study, investigators determined that the ancient Siberia belonged to a population that contributed some 14 to 38 percent of the ancestry detected in Native American populations today.

Based on data available at this point, the study's authors suspect that gene flow from the ancient Siberian population into ancestral Native Americans took place before Native American populations branched out in the New World, but after divergence from East Asians.

Such findings may explain the presence of non-Asian features in early Native-American populations, the team noted, while supporting the notion that early Native-American populations traversed a land mass that once crossed the Bering Strait to reach the Americas.

Moreover, when they did low-coverage genome sequencing on a slightly "younger" Siberian individual who lived only 17,000 years ago, after the Last Glacial Maximum, researchers saw sequences that resembled those in the individual from Mal'ta. That suggests a lengthy stay in Siberia by the western Eurasian and Native American-related that spanned a period before and after that chilly period of glacial growth.

"Most scientists have believed that Native-American lineages go back about 14,000 years ago, when the first people crossed Beringia into the New World," co-first author Pontus Skoglund, an evolutionary biology researcher at Uppsala University, said in a statement. "Our results provide direct evidence that some of the ancestry that characterizes Native Americans is at least 10,000 years older than that, and was already present in Siberia before the last Ice Age."