Tracing the ancient ancestors of Europeans

An international team of researchers has compared ancient European hunter-gatherers and early farmers to present-day humans and found that modern Europeans can trace their ancestry to three ancient populations.

Dr Wolfgang Haak, a research fellow with the Australian Centre for Ancient DNA (ACAD) and co-author on the study, said recent genetic studies on ancient remains have “suggested a massive expansion of people into Europe coinciding with the spread of farming”. As hunter-gatherers were replaced by sedentary farmers, there were large increases in population size that laid the foundation for larger towns and eventually complex societies.

“However, the relative proportions and distributions of the genetic components contributing to modern Europeans remained unclear,” Dr Haak said. “This study has added significantly to our knowledge of the genetic make-up of our European ancestors.”

Writing in the journal Nature, the researchers explained that they “sequenced the genomes of a ~7000-year-old farmer from Germany and eight ~8000-year-old hunter-gatherers from Luxembourg and Sweden”. In order to compare the ancient humans to present-day people, the team also generated genome-wide data from 2435 humans from almost 200 diverse worldwide contemporary populations. Using this dataset, the researchers were able to calculate the proportion of the ancestral components in present-day Europeans.

Skull of an ~8000-year-old hunter-gatherer male, from the Loschbour rock shelter in Luxembourg, whose genome was sequenced. Credit: Dominique Delsate, Musée national d’Histoire naturelle de Luxembourg.

The team found that “most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry”.

“Northern Europeans have more hunter-gatherer ancestry - up to about 50% in Lithuanians - and Southern Europeans have more farmer ancestry,” said co-author Iosif Lazaridis from Harvard Medical School. “Even the early farmers themselves had some hunter-gatherer ancestry: they were not unmixed descendants of the original Near Eastern migrants that brought farming to Europe.”

“The surprising finding was that present-day Europeans trace their ancestry back to three and not just two ancestral groups as previously thought,” said co-author Professor Alan Cooper, ACAD director. Co-author Nick Patterson, from the Broad Institute of Harvard and MIT, added that the team had “previously found an ancient genetic link of present-day Europeans and Native Americans” but this component was “not present in the ancient hunter-gatherer from Luxembourg, nor was it present in the first European farmers”.

“It seems clear now that the third group linking Europeans and Native Americans arrives in Central Europe after the early farmers,” explained lead investigator Johannes Krause from the University of Tübingen. But how Europeans received their Northern Eurasian ancestry remains an open question; Lazaridis noted, “The Northern Eurasian ancestry is proportionally the smallest component everywhere in Europe, never more than 20%, but we find it in nearly every European group we’ve studied and also in populations from the Caucasus and Near East.”

The researchers also analysed genes with known phenotypic association and showed that some of the hunter-gatherers likely had blue eyes and darker skin, whereas the early farmers had lighter skin and brownish eyes. Both the hunter-gatherers as well as the early farmers displayed high copy numbers of amylase genes in their genomes, suggesting that both populations had already adapted to a starch-rich diet. None of the ancient humans was yet adapted to digest milk sugar into adulthood.

The researchers were also able to fit the genomic data of modern and ancient humans into a simplified genetic model to reconstruct the deep population history of modern humans outside Africa in the last 50,000 years. While the model suggests that present-day Europeans received contributions from at least three ancestral populations, it also suggests that Early Near Eastern farmers carried genetic material that falls outside the typical non-African variation.

“The finding of an ancient lineage that is present in Europeans and Near Easterners, but not elsewhere in Eurasia, was a major surprise of our study,” said co-author David Reich from the Broad Institute. “It will be exciting to carry out further ancient DNA work to understand the archaeological cultures associated with the arrival of this ancestry.”

“We are only starting to understand the complex genetic relationship of our ancestors,” said Krause. “Only more genetic data from ancient human remains will allow us to disentangle our prehistoric past.”