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Ancient DNA Sequencing Sheds Light on Ice Age European Population History

NEW YORK (GenomeWeb) – An international team led by investigators in the US, Germany, and China has used ancient genome sequencing to garner clues about Europe's population history during the Ice Age, before farming became prevalent on the continent.

The researchers sequenced dozens of ancient human samples from sites across Europe, as old as 45,000 years ago and as recent as around 7,000 years ago. They found genetic patterns in the genomes that suggest the presence of a founder human population in Europe from 37,000 years ago until 33,000 years ago. This population was then temporarily displaced, and re-appeared from southwest Europe roughly 19,000 year ago, after the Ice Age peak.

A few thousand years later — about 14,000 years ago — another population appears to have moved into Europe from the Near East on the heels of a warmer climate that followed the Ice Age, the team reported today in Nature.

"[W]hat we see is a population history that is no less complicated than that in the last 7,000 years, with multiple episodes of population replacement and immigration on a vast and dramatic scale, at a time when the climate was changing dramatically," co-senior author David Reich, a genetics researcher affiliated with Harvard Medical School and the Broad Institute, said in a statement. He and his co-authors also noted that past studies suggest modern humans made their way to Europe roughly 45,000 years ago, weathering Ice Age glaciation that covered much of the continent from about 25,000 years ago until around 19,000 years ago.

To look into the population dynamics before, during, and after the Ice Age, the researchers performed Illumina sequencing on human SNP-enriched DNA libraries prepared from samples collected at sites from Spain in the west to the Caucasus region in the east. Radiocarbon dating put the samples at between 7,000 and 45,000 years old.

After using mitochondrial sequences, X chromosome patterns, and cytosine deamination profiles to root out instances of contamination with present-day human DNA, they were left with genome-wide information for 38 of the ancient individuals. To that, the team added published sequence data for ancient and contemporary humans, bringing the tally of ancient Europeans up to 51 individuals, including 16 ancient individuals successfully profiled at 790,000 SNPs, or more, apiece.

Along with Y chromosome and mitochondrial DNA analyses, the team garnered hints about the origins and migration histories of the populations at hand by clustering the ancient individuals into five main groups based on genetic drift ascertained from autosomal variants. Contrary to past findings, the researchers did not see evidence for ancestry from a basal Eurasian group or from a group related to Siberia's Mal'ta1 individual in the genomes of Upper Paleolithic European populations. Rather, their results appeared to be consistent with a single founder population that appeared around 37,000 years ago and has contributed to the ancestry of present-day European populations.

Aside from identifying this group, and the population with Near Eastern ties that began arriving in the post-Ice Age period, the team also found that the proportion of Neanderthal DNA appears to have been in decline in human populations in Europe, even before the beginning of the Ice Age. While the researchers saw nearly 6 percent Neanderthal sequence in the genomes of the oldest modern humans tested, Neanderthal sequences now make up just 2 percent or so of the sequences in European genomes, highlighting potential selection against certain ancient hominin alleles.