Ancient DNA Could Unravel the Mystery of Prehistoric European Migration

New research pinpoints the geographic origins of ancient Eurasians, showing how the continent’s population changed

Lorraine Boissoneault

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B098r4Ancient DNA revolutionized archaeology. Now, researchers think they can use it to create a GPS system for the remains of the long-dead. (Relaximages / Alamy

Let’s face it: Even with the modern conveniences of U-Hauls and cardboard boxes, moving is a pain. For Neolithic humans living in Europe 5,000 years ago, the obstacles—roaming predators, lack of transportation, unforgiving—must have seemed insurmountable. “Deep in the past, a few humans could have moved hundreds of kilometers, certainly, but most people at that time would not have,” says Chris Tyler-Smith, a human genetics researcher at England's Sanger Institute.

New research based on a novel mapping technique, however, suggests otherwise. By combining genetic data with archaeology, researchers analyzed the DNA of over 300 ancient Eurasians and Near-Eastern Europeans to find that these people may have roamed surprisingly far. They found that 50 percent of ancient skeletons were in graves more than 100 miles from their place of origin, 30 percent were up to 620 miles away, and the remaining people had roamed as far as 1,900 miles from their homes.

This is the first time anyone has ever been able to do anything like this,” says Eran Elhaik, one of the pioneers of the new technique and a geneticist at the University of Sheffield. “We were able to see the emergence of farming, and populations moving because they exhausted the land, and then irrigation systems. As the populations moved, they replaced all the hunter-gatherers.” Elhaik and his team presented their preliminary findings last month at the European Society of Human Genetics Conference.

Archaeologists and geneticists alike have speculated about how and where humans migrated across Europe. Based on skeletal remains, they believe Europe was populated by modern humans around 45,000 years ago as hominins moved out of Africa and into other parts of the world. Europe was then largely depopulated when the most recent ice age took hold around 25,000 years ago, except for some stalwart holdouts who found survivable conditions in southern Europe.

Archaeologists have long hypothesized that Europe was colonized by successive waves of hunter-gatherers, based on clear differences in stone tools and bone and shell ornaments recovered from sites across Europe and the Middle East,” writes Ewen Callaway for Nature.

But it’s only recently that archaeologists have been able to compare their material data to the story that genetics tells. With recent advances in analyzing ancient DNA, we’re beginning to get a much clearer—and more complex—picture about these humans and their lives.

DNA is notoriously delicate. It can only survive intact under certain environmental conditions, and prefers cold places. In human samples, the best place to find it from is the petrous bone on the skull, near the ear. But even once you’ve gotten your hands on some usable DNA, mining it for useful information comes with a series of hurdles.

Extracting ancient DNA and sequencing it with next-generation techniques results in a hodgepodge of information. The DNA isn’t just from the ancient human—it’s also from the surrounding environment, and maybe from contamination introduced by modern researchers. To sort through this tangle, researchers rely on computer assistance to identify a single mitochondrial DNA sequence (the presence of more than one indicates contamination) and pick out deterioration patterns that signal human DNA.

But once those snippets of human DNA have been plucked from the mess, they can open up a world of discoveries. We can learn about everything from what ancient humans like Ötzi the ice mummy ate and wore, to how often Neanderthals and humans were procreating. “I think it’s one of the most exciting developments in science in the last few decades,” says Tyler-Smith. “People have compared it to the development of radiocarbon dating in the middle of the 20th century in terms of its impact.”

Elhaik has expanded on the information that can be extracted from ancient DNA using a technique he pioneered with living humans, called Geographic Population Structure, or GPS. This technique relies on datasets that compare single nucleotide polymorphisms—differences in DNA nucleotides that act as biological markers among individuals. The GPS method uses the SNPs (pronounced “snips”) of populations that have been in one place for multiple generations, then contrasts it to groups that live farther away.

We didn’t just hack a cool acronym, it really works like GPS navigation,” Elhaik says. “Instead of satellites we’re using populations that are very well localized to their regions.”

In a 2014 study in Nature Communications, Elhaik and his colleagues applied the GPS method to more than 600 people around the world, and were able to correctly assign 83 percent of those individuals to their country of origin. When the same technique was applied to 200 Sardinian villagers, a quarter of them were placed in their villages and the majority of people were placed within 50 km of their homes.

The same technique is at play in their new research. “We used ancient DNA extracted from skeleton remains from 12000 BC to 500 AD," says Elhaik. "The DNA goes in and coordinates come out”—though he adds that the sample size is far smaller for ancient individuals, so there are far more gaps across the continent. Think of it as GPS for the long-dead. 

If you have perhaps 20 or 30 people who come from the same population, then there’s extra information you can get,” says Tyler-Smith, who is not involved in the GPS research. But, he adds, “bigger numbers are always better.”

But geneticists and archaeologists don’t always agree on the finer points of prehistory. For Marc Vander Linden, a professor of archaeology at University College London, using such small sample sizes to draw large conclusions is problematic.

Geneticists have suggested wide-scale processes on the basis of limited, spatially clustered samples, and then—wrongly—generalized these results for the entire corresponding archaeological cultures,” Linden said by email. “Both archaeologists and geneticists need to fully realize and consider that genes and material culture do not operate in the same spheres of action, nor do they unfold upon the same spatial and temporal scales.”

Linden does agree that geneticists’ work in ancient DNA has revolutionized the field and opened up new avenues of inquiry. “Ancient DNA research, alongside other types of data, points to the fact that the population history of prehistoric Europe was in constant flux and marked by numerous episodes of both expansion and retraction.”

If Elhaik’s technique pans out, it could answer tantalizing questions about human migration—for instance, how agriculture came to the region. Archaeologists have debated for decades whether it was transmitted by human migration, or by the movement of the idea itself. Part of the debate has recently been settled by genetics, with researchers seeing the movement of agricultural communities from the Near-East into the hunter-gatherer groups in Europe. Elhaik thinks his group’s research will further elucidate that question and show more precise movements of multiple groups of people.

For Tyler-Smith, that type of increased resolution into the broad outlines of the past is the future of the field. He’d also like to see more samples from other parts of the world—the hotter, dryer regions like Africa and southern Europe where it’s been harder to find ancient DNA still intact due to the environmental conditions. For now, though, unraveling European migration is itself helping us make sense of human ancestry—and the fact that we’re all mutts.

There’s no such thing as a European population that’s been around for 40,000 years,” Tyler-Smith says. “Mixing has been going on throughout prehistory and I think we will see that in every part of the world as we come to study it in this level of detail.”