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ASHG Panelists Discuss New Insights into European Population Structure

SAN DIEGO (GenomeWeb) – Ancient human samples and additional genetic analyses are giving researchers a deep look into the structure of human populations.

During one session at the American Society of Human Genetics annual meeting, researchers discussed how folding in genetic data from ancient human samples as well as deeper analysis has given them a more refined picture of European populations. One group, for instance, traced an ancient ancestor of modern-day Europeans to a group called the Yamnaya while another examined finer population structure in modern-day Europeans and another investigated how immigrants to a region may affect population structure.

A recent Nature paper found that three ancestral populations likely contributed the genetic makeup of modern-day Europeans: western European hunter-gatherers, ancient north Eurasians, and early European farmers who themselves were of Near Eastern origin, but also related to western European hunter-gatherers.

As he recounted at ASHG, Harvard Medical School's Iosif Lazaridis, the lead author of that paper, has extended that study and homed in on the Yamnaya population as that likely third source.

Lazaridis and his colleagues targeted more than 350,000 SNPs in 65 ancient humans, including early Neolithic hunter-gatherers, early farmers, and late Neolithic Bronze Age populations from Europe, and compared them to SNPs from 2,345 present-day humans.

By examining admixture levels in these groups, they found that an early European farmer split off from the rest of the European farmers early on and mixed with eastern European hunter-gatherers to form the Yamnaya population, which lived on the Steppes, Lazaridis said. Meanwhile, a middle Neolithic population mixed with Yamnaya to form the late Neolithic Corded Ware population of central Europe.

"[The] major finding was that many admixture events occurred in Europe even after the advent of farming, and some of them were quite substantial," Lazaridis said.

Variation in ancestry, of course, persists into modern human populations. While broad-scale principal components analysis can largely separate out European populations, Stephen Leslie from Murdoch Children's Research Institute noted that it can't do the same on the individual level.

To examine fine-scale population structure in Europe, he and his colleagues used fineSTRUCTURE, an algorithm for identifying population structure, to analyze genome-wide SNP data from 6,209 Western Europeans. FineSTRUCTURE, which draws on haplotype information, divvied Europe into 150 clusters. Those gene-based clusters were then superimposed onto a map.

For instance, Leslie said that the algorithm first split Finland off from the rest of Europe, a move that would be expected given the history of Finland. It then separated Norway and Sweden from other parts of Europe, before splitting the Irish off from the rest of Europe. The splitting, he added, continued as Northern and Southern Europe separated and Norway separated from Sweden, and so on.

The researchers were also able to generate detailed fine-scale structure of Norway, Leslie said. For instance, one group, dubbed Group 96, was only found in very northern parts of Norway, while Group 78 was in the northwest and Group 85 at the very tip of northwest Norway. Additionally, other clusters were found in western Norway, the south coast, and the central regions.

Population structure can also be influenced by immigrants into a particular area. During a renovation at the Wellcome Trust Sanger Centre, five ancient human skeletons were unearthed — two dating to the Iron Age and three to the Anglo-Saxon period.

As the Sanger Centre's Stephen Schiffels said during a talk at ASHG, DNA from those skeletons were sequenced to between about 1x coverage to 12x coverage. With the 1,000 Genome Project data as a modern reference set, he and his colleagues found that in a PCA analysis of the data, the ancient samples fell squarely in with other Northern Europeans.

By focusing on rare variants, Schiffels said they were able to get an even more fine-grain picture that indicated that the Iron Age samples clustered more closely with modern-day Britons than the Anglo-Saxon samples, and the Anglo-Saxon samples appeared to cluster closer to Spanish and Finnish samples.

"This came as a surprise, because I would have thought the younger samples would look like present-day Britain, but the opposite is true," Schiffels said.

From this, he said, it seems as if the Anglo-Saxon immigrants to England didn't leave behind much of a genetic footprint.

He added that he and his colleagues are seeking additional samples from Europe, especially from the Netherlands and Denmark, the likely source of those Anglo-Saxon immigrants to Britain.