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Ancient Human Genome Points to Ancestral Meta-European Population

NEW YORK (GenomeWeb) – The genome sequence of a modern human man who lived in western Russia some 36,200 to 38,700 years ago is serving as a source of information on European population origins.

"I think this is, in many ways, changing our view of how the genetic diversity found in present-day Europeans came about," Eske Willerslev, an evolutionary biologist with the University of Copenhagen's Centre for GeoGenetics, told GenomeWeb Daily News.

As they reported online today in Science, Willerslev and his colleagues sequenced DNA from the leg bone of an ancient Kostenki 14 (K14) individual, who was nicknamed for the Russian region where his remains were found in the 1950s. Their comparisons with modern-day Europeans and other ancient samples suggested that K14 was descended from a "meta-European" group that carried much of the genetic structure found on the continent today.

"The traditional or common view has been that the genomic diversity of Europeans was formed by a number of migrations into Europe," Willerslev said. "What was really surprising was that basically all of the genetic components you find in present-day Europeans are actually present in Kostenki already."

For the new study, researchers used Illumina shotgun sequencing to tackle seven libraries made with DNA from the K14 individual's tibia bone that had been captured with a new approach targeting ancient DNA damage signatures. In the process, they generated more than 175 million sequence reads, which were aligned to the human reference genome at an average depth of 2.84-fold coverage.

When the team compared K14's nuclear and mitochondrial sequences to genetic patterns present in almost 2,100 ancient and contemporary European individuals, it found features consistent with European ancestry.

For instance, the researchers saw especially close genetic ties between K14 and a previously sequenced individual from central Siberia, called the "Mal'ta boy," who died roughly 24,000 years ago.

The ancient Russian was also quite closely related to Mesolithic hunter-gatherers sequenced for other studies and to individuals from populations found in northern Europe, eastern Europe, and western Siberia today.

More broadly, though, the K14 individual's genome contained sequences that the team suspects were present in a so-called "meta-European" population from the Upper Paleolithic period onward, spanning a glaciation event that occurred after the Stone Age.

"[O]ur findings show the existence of a meta-population structure in Europe from the Upper Paleolithic [period] onwards," the study's authors wrote, "remnants of which are still found today, despite migrations to and from Europe since the [Upper Paleolithic]."

These meta-European signatures included sequences resembling those found in some Middle Eastern populations today, which appear to reflect early European ancestry from a group that went on to mix with Europeans again thousands of years later during the spread of agriculture.

"One of the really big surprises was that the Middle Eastern genetic signature, that people normally say was introduced to Europe with the arrival of farming 8,000 years ago, was already present in the Kostenki individual," Willerslev said.

"I don't think there's any question that there was a movement of people from the Middle East into Europe 8,000 years ago," he explained. "But what it does show is that most likely this Middle Eastern population was part of this meta-population that stretched from Europe to Central Asia."

On the other hand, the K14 individual did not seem to share ancestry with East Asian populations, pointing to a divergence between Eurasian and East Asian populations that occurred more than 36,000 years ago. As such, the study "puts a minimum date on the split between Europeans and East Asians after people left Africa," according to Willerslev.

Together with patterns in the genome of a 45,000-year-old man from western Siberian man — reported in Nature last month by Svante Pääbo and his colleagues — the latest findings provide bookends for the European-East Asian split.

While the 36,000-year-old individual was clearly European, Willerslev explained, the 45,000-year-old Siberian individual apparently came from a period at or before the populations diverged from one another.

As expected, stretches of Neanderthal DNA in the K14 genome were longer than those found in individuals from present-day European populations. Using those remnants of past human-Neanderthal interbreeding events, the researchers calculated mixing between the hominin groups that went back about 54,000 years.

That estimate matches the date proposed by another team that sequenced a 45,000-year-old modern human, Willerslev noted, though it also stretches back well before Neanderthals ultimately disappeared, prompting questions about why mixing between the groups may have ceased while their populations apparently overlapped in time and space.

"From the archaeological record, it appears that Neanderthals and humans in Europe actually co-existed after this period," he said. "But, for whatever reason, it doesn't seem like they admixed again."

Based on their findings so far, the researchers are keen to see additional ancient genome sequencing on skeletons from Europe, a place where many fossilized skeletons have been found.

Willerslev noted that it may eventually be possible to apply emerging epigenetic analyses to this and other ancient samples, though there are still challenges associated with making appropriate comparisons of ancient samples, since epigenetic marks can vary by tissue, an individual's age, and so on.

"Such a comparison is by no means simple, but I think it will certainly be very interesting," Willerslev said, noting that such studies might make it possible to explore the role that epigenetic changes played in human evolution.