Uncovering a new history of humanity

Only David Reich's eyes were visible as he inspected the batch of bones. Reich, a geneticist at Harvard Medical School, wore a hooded white clean room suit, cream-coloured clogs, and a blue surgical mask. On a counter in front of him lay a row of bone fragments. He pointed out a strawberry-size chunk: "This is from a 4,000-year-old site in Central Asia - from Uzbekistan, I think."

He moved down the row. "This is a 2,500-year-old sample from a site in Britain. This is Bronze Age Russian, and these are Arabian samples. These people would have never met each other in time or space." Reich hopes that his team of scientists and technicians can find DNA in these bones. Odds are good that they will.

In less than three years, Reich's laboratory has published DNA from the genomes of 938 ancient humans - more than all other research teams working in this field combined. The work in his lab has reshaped our understanding of human prehistory.

"They often answer age-old questions and sometimes provide astonishing unanticipated insights," said Svante Paabo, the director of the Max Planck Institute of Paleoanthropology in Leipzig, Germany.

Reich, Paabo and other experts in ancient DNA are putting together a new history of humanity, one that runs in parallel with the narratives gleaned from fossils and written records. In Reich's research, he and his colleagues have shed light on the peopling of the planet and the spread of agriculture, among other momentous events.

In the book Who We Are and How We Got Here, Reich, 43, explains how advances in DNA sequencing and analysis have helped this new field take off. "It's really like the invention of a new scientific instrument, like a microscope or a telescope," he said. "When an instrument that powerful is invented, it opens up all these horizons, and everything is new and surprising."

Reich oversees a team with many different skills, from genetics to mathematics. But the "clean lab" is where the raw material for all their work - ancient DNA - is recovered. The head-to-toe suits that the researchers don in an airlock each morning ensure that no stray flake of skin or bead of sweat contaminates the bones with modern DNA. Each night the entire lab is bathed in gene-destroying ultraviolet light.

The clean lab feels as if it belongs in a computer chip factory. But Reich has not forgotten that these are human remains, not widgets on a conveyor belt. "This is a bone from a person's body who lived 4,000 years ago, and we're destroying it," he said, gazing down at the Uzbek remains. "I think we need to do well by the individuals we're studying." Doing well means understanding who these people were, and how they were linked to one another - and to us.

Reich began studying sociology as a Harvard undergraduate, but later he turned to physics and then to medicine. After graduating, he went to Oxford to prepare for medical school. There he met Dr David B Goldstein, who at the time was comparing the DNA of living people for clues to what their distant ancestors were like.

Abandoning medical school, Reich continued with genetics research and was hired by Harvard Medical School in 2003. By then, he had developed a close partnership with a mathematician named Neil Patterson, who had come late in life to genetics, after 20 years working as a cryptographer in British intelligence and then joining a hedge fund.

Reich appointed Patterson deputy head of the newly formed genetics lab, and together they began developing new statistical techniques to plumb genetic data for hidden patterns. The two researchers devised a way to determine whether a single population descended from two or more distinct groups. Collaborating with researchers at the Centre for Cellular and Molecular Biology, Hyderabad they put their method to first big test.

Analysing DNA from hundreds of villages, they discovered that just about every living Indian descends from two distinct groups. One, which the researchers called Ancestral North Indians, is related to Central Asians, Near Easterners and Europeans.

The second group, Ancestral South Indians, is a mysterious population that is not closely related to any living people outside of India. The two populations mixed together, Reich estimated, 2,000 to 4,000 years ago.

As Reich and his colleagues gained attention for their new methods, they got an extraordinary invitation: to study the DNA of Neanderthals.

The invitation came from Paabo. In the 1990s, he had pioneered methods to extract ancient DNA from fossils dating back tens of thousands of years. While he studied many extinct species - such as cave bears, mastodons and ground sloths - Neanderthals were his deepest passion.

In 2006, he invited Reich's team to help figure out how modern humans and Neanderthals were related. Reich threw himself into the project, and over the next few years, the scientists made a series of landmark discoveries.

The DNA of Neanderthals indicates that their ancestors split from our own about 600,000 years ago. But Reich's tests revealed that living humans outside of Africa still carry traces of Neanderthal DNA. How is that possible? Before Neanderthals became extinct in Europe, they encountered and interbred with the ancestors of modern humans as they departed Africa.

As the scientists searched in more fossils for Neanderthal DNA, they got another surprise. In 2010, a nondescript pinkie bone recovered in a Siberian cave called Denisova yielded the entire genome of a previously unknown, and extinct, lineage of humans. The Denisovans, as they came to be known, split off from Neanderthals about 400,000 years ago, genetic analysis revealed.

Denisovan DNA has turned up only in a few additional teeth discovered in that Siberian cave. The oldest such fossils date to over 100,000 years old; the pinkie bone belonged to a Denisovan who lived 48,000 to 60,000 years ago. Reich and his colleagues discovered that Denisovans, like Neanderthals, left a genetic legacy in living people, mostly in Australia, New Guinea and Asia.

Ancient DNA has summoned the genetic shadows of a long-vanished people, one that fossils alone could not reveal. Many scientists now suspect that ancient DNA will reveal other extinct kinds of humans. "The discovery of Denisovan DNA was a landmark in my thinking about ancient DNA," Reich said. "It can reveal things about the past that are completely unexpected, that are not dreamed of in our philosophy."

Reich's voyage through prehistory left him wondering about what DNA could reveal about more recent events. Museums around the world were loaded with bones of people who lived within the last 20,000 years, after all. Since those remains were younger, they would be more likely to still have some DNA in them. To begin retrieving it, Reich retooled his laboratory, copying Paabo's facility in Germany to the last detail.

In 2015, the first results emerged from Reich's new research pipeline. He and his colleagues published DNA from 69 ancient Europeans who lived 3,000 to 8,000 years ago. According to their results, farmers with Near East ancestry displaced hunter-gatherers already living in Europe. Then, about 4,500 years ago, another wave of people arrived, descended from the horse-riding nomads of what are now the Russian steppes.

As of last month, Reich's team has published about three-quarters of all the genome-wide data from ancient human remains in the scientific literature. But the scientists are only getting started. They have retrieved DNA from 3,000 more samples. And lab refrigerators are filled with bones from 2,000 more denizens of prehistory.

Reich's plan is to find ancient DNA from every culture known to archaeology everywhere in the world. Ultimately, he hopes to build a genetic atlas of humanity over the past 50,000 years. "I try not to think about it all at once, because it's so overwhelming," he said.