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Complex Early Farmer, Hunter-Gatherer Interactions Identified With Ancient European Samples

NEW YORK (GenomeWeb) – An international team led by investigators in the US and Budapest has retraced population interactions going back to the Neolithic and Chalcolithic periods between early farmer and hunter-gather groups in parts of Europe.

As they reported online today in Nature, the researchers used solution capture sequencing to characterize genome-wide variant patterns in more than 100 samples dated at roughly 4,200 to more than 8,000 years old from sites in present-day Hungary, Germany, and Spain. They then compared them to existing genome sequences and new hunter-gatherer sequences from samples that were more than 7,700 to 14,000 years old, found at sites in Hungary, Spain, Luxembourg, and northeastern Italy.

At each of the sites, the team saw admixture between local hunter-gatherer groups and early farming populations migrating into the area, leading to distinct ancestry patterns. Those interactions were somewhat more complicated than might have been anticipated, however, and were often marked by multiple instances of gene flow involving hunter-gather groups.  

"In each of our three study regions, the arrival of farmers prompted admixture with local hunter-gatherers: almost all sampled populations have more hunter-gatherer ancestry and more recent dates of admixture than their local predecessors, suggesting recurrent changes in genetic composition and substantial hunter-gatherer gene flow beyond initial contact," senior author David Reich, a genetics researcher affiliated with Harvard Medical School and the Broad Institute, and his colleagues wrote.

For the analysis, the team focused on 180 European samples, including 100 samples from Hungary dated between 2,200 and 6,000 years B.C.E., 42 samples from German sites traced back to between 3,000 and 5,500 B.C.E., and 38 slightly younger samples from Spain from around 2,200 to 5,500 B.C.E. While 50 samples had been profiled previously, 130 of the ancient samples were newly sequenced.

After screening for sequencing libraries with relatively low contamination, DNA damage, and off-target sequence levels with in-solution hybridization using baits synthesized with CustomArray, the researchers enriched the samples for SNPs at roughly 1.23 million sites across the genome.

They then sequenced the samples and settled on sequences for 104 individuals from 15 populations that met the quality control criteria, which were considered alongside available Neolithic sequences, sequences from early Anatolian farmers, and four hunter-gatherer sequences.

In particular, the team saw an uptick in hunter-gatherer ancestry in the early farming populations present at each site over time — admixture that appeared to be somewhat more rapid in populations in Germany and Spain than those sampled from Hungary. 

And based on their subsequent analyses of the timing and nature of the admixture events, the researchers concluded that ongoing gene flow from hunter-gatherer groups after the original meeting and mixing with early farmers "left distinct signatures in each region, implying that they resulted from a complex web of local interactions rather than from a uniform demographic phenomenon," Reich and co-authors noted.

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