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Ancient human genomes suggest three ancestral populations for present-day Europeans

Artist impression of the male-hunter gatherer

This reconstruction shows the dark skin and blue eyes of a 7,000-year-old hunter from northern Spain

Europeans = Neolithic farmers, Mesolithic hunter-gatherers and “Ancient North Eurasians” (etc.)

Ancient human genomes suggest three ancestral populations for present-day Europeans

Europeans are a mixture of hunter-gatherers, agriculturalists, and also a third wave of migrants from north Eurasia – Strands of DNA taken from ancient corpses have revealed an unexpected addition to the ancestral roots of modern Europeans.

Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden.

We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans.

The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry.

West European Hunter-Gatherer (WHG): this ancestral component is based on an 8,000 year-old forager from the Loschbour rock shelter in Luxembourg (one of the individuals mentioned above belonging to I2a1b). The WHG meta-population includes the Loschbour sample and two Mesolithic individuals from the La Brana Cave in Spain. However, today the WHG component peaks among Estonians and Lithuanians, in the East Baltic region, at almost 50%.

Early European Farmer (EEF): apparently this is a hybrid component, the result of mixture between “Basal Eurasians” and a WHG-like population possibly from the Balkans. It’s based on the aforementioned LBK farmer from Stuttgart, but today peaks at just over 80% among Sardinians. Apart from the Stuttgart sample, the EEF meta-population includes Oetzi the Iceman and a Neolithic Funnelbeaker farmer from Sweden.

Ancient North Eurasian (ANE): this is the twist in the tale, a component based on a previously reported genome of a 24,000 year-old Upper Paleolithic forager from South Central Siberia, belonging to Y-hg R*, and known as Mal’ta boy or MA-1. This component was very likely present in Southern Scandinavia since at least the Mesolithic (see the summary of SHG below), but only seems to have reached Western Europe after the Neolithic. At some point it also spread into the Americas. In Europe today it peaks among Estonians at just over 18%, and, intriguingly, reaches a similar level among Scots. However, numbers weren’t given for Finns, Russians and Mordovians, who, according to one of the maps, also carry very high ANE, but their results are confounded by more recent Siberian admixture (see the discussion on the European outliers below). The ANE meta-population includes Mal’ta boy as well as a late Upper Paleolithic sample from Central Siberia, dubbed Afontova Gora-2 (AG2).

Scandinavian Hunter-Gatherer (SHG): this is a meta-population made up of Swedish Mesolithic and Neolithic forager samples from Motala and Gotland, respectively. It’s a more easterly variant of WHG, with probable ANE admixture.

We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.

The first Homo sapiens arrived in Europe around 45,000 years ago, and these hunter-gatherers were replaced by early farmers who brought agriculture to the continent more than 7,000 years ago from Anatolia and the Levant in the near east.

The arrival of the first farmers set the stage for Europeans to be the descendents of the agriculturalists and indigenous hunter-gatherers, but genetic studies found that a piece of the puzzle was missing: some European DNA came from elsewhere.

To clear up the mystery, researchers in Germany and the US sequenced the full genetic code of nine ancient humans. Among them were a 7,000-year-old farmer from Germany and 7,000- to 8,000-year-old hunter-gatherers from Luxembourg and Sweden. The scientists then compared these genomes with DNA taken from more than 2,000 modern-day people from all over the world and with other ancient genomes.

They found that nearly all modern Europeans had a mixture of western European hunter-gatherer and early European farmer DNA, but with a good measure of ancient north Eurasian ancestry thrown in.

The north Eurasian DNA was identified from the 24,000-year-old remains of a young boy buried at Mal’ta near Lake Baikal in eastern Siberia.

“It became very clear that all Europeans have hunter-gatherer as well as early farmer DNA to varying degrees, but it was also very clear that something was missing here in the makeup of modern Europeans,” said Johannes Krause, at the University of Tubingen’s Institute for Archaeological Sciences.

The findings suggest that the arrival of modern humans into Europe more than 40,000 years ago was followed by an influx of farmers some 8,000 years ago, with a third wave of migrants coming from north Eurasia perhaps 5,000 years ago. Others from the same population of north Eurasians took off towards the Americas and gave rise to Native Americans.

Modern Europeans are various mixes of the three populations. Sardinians are more than 80% early European farmer, with less than 1% of their genetic makeup coming from the ancient north Eurasians. In the Baltic states such as Estonia, some modern people are 50% hunter-gatherer and around a third early European farmer.

The modern English inherited around 50% of their genes from early European farmers, 36% from western European hunter-gatherers, and 14% from the ancient north Eurasians. According to the study, published in Nature, modern Scots can trace 40% of their DNA to the early European farmers and 43% to hunter-gatherers, though David Reich, a senior author on the study at Harvard University, said the differences were not significant.

In the absence of writings from ancient times, researchers are left with only archaeology, palaeontology and genetics to understand our distant pasts. “The genetics can tell us a bit about who these people were, how they interacted, where they came from, what their subsistence strategy was, and whether they had adaptations to their environment and diet,” said Krause.

“The neolithic revolution spread agriculture across the continent in a couple of thousand years. Suddenly you have settlements that cover square kilometres, large cemeteries, large population increases. Suddenly the whole of central Europe becomes deforested because people are clearing it to make fields and produce crops. Everything changes and we don’t have any historical information about that. We can look at the archaeology, but we can also look at the genes. They tell us how all those people are related, and you can’t tell that from staring at a skeleton.”

Ancient human genomes suggest three ancestral populations for present-day Europeans

Europeans = Neolithic farmers, Mesolithic hunter-gatherers and “Ancient North Eurasians” (etc.)

Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans

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