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Agriculture Linked to DNA Changes in Ancient Europe
New York Times, November 23, 2015

The agricultural revolution was one of the most profound events in human history, leading to the rise of modern civilization. Now, in the first study of its kind, an international team of scientists has found that after agriculture arrived in Europe 8,500 years ago, people’s DNA underwent widespread changes, altering their height, digestion, immune system and skin color.

Researchers had found indirect clues of some of these alterations by studying the genomes of living Europeans. But the new study, they said, makes it possible to see the changes as they occurred over thousands of years.

“For decades we’ve been trying to figure out what happened in the past,” said Rasmus Nielsen, a geneticist at the University of California, Berkeley, who was not involved in the new study. “And now we have a time machine.”

Before the advent of studies of ancient DNA, scientists had relied mainly on bones and other physical remains to understand European history. The earliest bones of modern humans in Europe date to about 45,000 years ago, researchers have found.

Early Europeans lived as hunter-gatherers for over 35,000 years. About 8,500 years ago, farmers left their first mark in the archaeological record of the continent.

By studying living Europeans, scientists had already found evidence suggesting that their ancestors adapted to agriculture through natural selection. As tools to sequence DNA became more readily available, researchers even discovered some of the molecular underpinnings of these traits.

But these studies couldn’t help determine exactly when the changes occurred, or whether they resulted from natural selection or the migrations of people into Europe from other regions.

Scientists are now tackling these questions in a much more direct way, thanks to a rapidly growing supply of DNA from ancient skeletons. These studies have revealed that the DNA of Europeans today comes from three main sources.

Before the rise of agriculture, Europe was home to a population of hunter-gatherers. Then a wave of people arrived whose DNA resembles that of people in the Near East. It’s likely that they brought agriculture with them.

Finally, about 4,500 years ago, a nomadic population from the steppes of Russia, known as the Yamnaya, swept into Europe.

The analyses that revealed these migrations were based on dozens of ancient European genomes. But in a study published Monday in Nature, David Reich, a geneticist at Harvard Medical School, and his colleagues analyzed the genomes of 230 people who lived between 8,500 and 2,300 years ago.

The enormous sample size has provided enough data to track individual genetic variations as they become more or less common through the history of ancient Europe.

The remains that Dr. Reich and his colleagues analyzed DNA from span the entire continent of Europe. They also include the Yamnaya as well as 21 people who lived in a region of Turkey called Anatolia 8,500 years ago. The study marks the first time scientists have been able to analyze the DNA of the people who brought farming to Europe.

The researchers compared these ancient genes to those of living humans. Their analysis confirmed earlier hypotheses based on living Europeans, but also revealed that other genes have evolved, too.

Previous studies had suggested that Europeans became better able to digest milk once they began raising cattle. Dr. Reich and his colleagues confirmed that LCT, a gene that aids milk digestion, did experience intense natural selection, rapidly becoming more common in ancient Europeans. But it didn’t happen when farming began in Europe, as had been supposed. The earliest sign of this change, it turns out, dates back only 4,000 years.

While agriculture brought benefits like a new supply of protein in milk, it also created risks. Early European farmers who depended mainly on wheat and other crops risked getting low doses of important nutrients.

So a gene called SLC22A4 proved advantageous as soon as Europeans started to farm, Dr. Reich and his colleagues found. It encodes a protein on the surface of cells that draws in an amino acid called ergothioneine. Wheat and other crops have low levels of ergothioneine, and the new variant increases its absorption. That would have increased the chances of survival among the farmers who had the gene.

Yet this solution created a problem of its own. The same segment of DNA that carries SLC22A4 also contains a variation that raises the risk of digestive disorders like irritable bowel syndrome. These diseases, then, may be an indirect consequence of Europe’s pivot toward agriculture.

Dr. Reich and his colleagues also tracked changes in the color of European skin.

The original hunter-gatherers, descendants of people who had come from Africa, had dark skin as recently as 9,000 years ago. Farmers arriving from Anatolia were lighter, and this trait spread through Europe. Later, a new gene variant emerged that lightened European skin even more.

Why? Scientists have long thought that light skin helped capture more vitamin D in sunlight at high latitudes. But early hunter-gatherers managed well with dark skin. Dr. Reich suggests that they got enough vitamin D in the meat they caught.

He hypothesizes that it was the shift to agriculture, which reduced the intake of vitamin D, that may have triggered a change in skin color.

The new collection of ancient DNA also allowed Dr. Reich and his colleagues to track the puzzling evolution of height in Europe. After sorting through 169 height-related genes, they found that Anatolian farmers were relatively tall, and the Yamnaya even taller.

Northern Europeans inherited a larger amount of Yamnaya DNA, making them taller, too. But in southern Europe, people grew shorter after the advent of farming.

Dr. Reich said it wasn’t clear why natural selection favored short stature in the south and not in the north. Whatever the reason, this evolutionary history still shapes differences in height across the continent today.

Dr. Reich and other researchers are gathering even more ancient European DNA, which will allow them to uncover more effects of natural selection. Indeed, other researchers are doing the same on other continents.

One day, they may be able to track historic changes in the human genome across the globe over tens of thousands of years.

“I think in the future we can do this everywhere in the world, not just in Europe,” Dr. Reich said.

Copyright 2015 The New York Times Company. Reproduced with permission.
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