Invisible Artifacts

Off the coast of New York City, in the middle of the Hudson River, sits Ellis Island, a monument to one of the largest migrations in human history. At the museum on the island are documents, photographs, even a list of every family name that once spilled off of a ship and was reinvented on American soil. For the 1.8 million people who visit the island each year, it is important to remember the wave of migration that Ellis Island chronicles. The island, and its documented history, helps them tease apart the narratives hidden within the tangled branches of their family trees, and it connects them to their roots.

Most human migrations do not have an entire island devoted to their memory. Often, very little is left to indicate where a particular people came from and where it was going, especially if the migration happened a long time ago. In order to reconstruct these historical movements, anthropologists grasp at the smallest shreds of evidence. Increasingly, they are relying on an artifact so small it cannot even be seen with the naked eye: ancient DNA.

The genetic material extracted from old fragments of bone, scraps of hair, and even preserved flesh can often reveal more about human migrations than do cultural artifacts — tools, books, and jewelry — that are found at the same archaeological sites. New technology is making this work faster and cheaper, allowing scientists to solve some of archaeology’s most impenetrable mysteries and even unearth new chapters in history.

“It’s like photographing the situation in the past,” said Barbara Bramanti, a molecular anthropologist at Johannes Gutenberg University in Mainz, Germany, who works with ancient DNA.

By sequencing ancient DNA — that is, finding the exact combination of letters that makes up a portion of an ancient individual’s genetic code — scientists can learn how closely related a man or woman was to other groups of people, both ancient and contemporary. Knowing that two groups of people are closely related indicates that they were united at some point in history until their two gene pools were separated, perhaps by a migration event.

Bramanti and her colleagues recently used this principle to help solve a long-standing quandary in archaeology — one that cultural artifacts and modern genetic studies were unable to resolve.

In a study published in Science last fall, she used ancient DNA to help determine the origins of farming in Central Europe. Archaeologists have found cultural evidence of farming in the Near East from as far back as 9,000 B.C.E., marked by the remains of permanent dwellings, surrounded by fields of staple crops, like wheat. The people who built these homes were not traveling widely in pursuit of food, like hunter-gatherers.

In Central Europe, on the other hand, hunter-gatherers were the only people living in the region until about 6400 B.C.E., when evidence of farming first appears in the archaeological record. For years, archaeologists have debated how farming got to the region. Did farmers actually migrate to Central Europe from the Near East, bringing farming with them? Or did only the knowledge of farming spread to Central Europe, where the hunter-gathers then adopted it? Until now, there was no way to resolve the debate, since the uncovered ruins only tell archaeologists that farms were built, not who built them.

To answer these questions, Bramanti and her colleagues sequenced the ancient DNA from the bones of both hunter-gatherers and farmers from Central Europe. Then they compared the genetic sequences, and found that the farmers’ DNA was significantly different from that of the hunter-gatherers, indicating that they were people of separate lineages. While the scientists still do not know exactly where the farmers came from, they can say that the Neolithic farmers were not merely hunter-gatherers who had learned how to grow crops and raise animals.

Ancient DNA studies like this one can help us solve long-standing mysteries about human migrations from a time before people kept records of their actions. But working with ancient DNA can also inform us about the gaps in our understanding of the more recent past, from times when we have relatively detailed accounts of history.

For example, a group of archaeologists analyzing the DNA of skeletons from ancient Rome recently discovered that one of the bodies belonged to a woman of East Asian descent. This finding, which will be published in the September supplement to the Journal of Roman Archaeology, is surprising, as no known literature from ancient Rome exists that acknowledges the presence of East Asians in Italy.

“You’ve got Rome, and you’ve got a really amazing civilization existing in China. And there are some historical asides in the historical literature about being aware of this other great civilization. But there’s no clear connection between Rome and China,” said Tracy Prowse, a physical anthropologist from McMaster University in Canada who worked at the site.

Prowse cautioned that one body cannot tell us whether there was a substantial East Asian presence in ancient Rome, or when the two civilizations made contact. In fact, because the scientists sequenced a portion of the woman’s mitochondrial DNA, which children inherit from their mothers, it is possible that the woman’s great-great-grandmother was from East Asia, while the woman’s family may have been living in Rome for generations. However, the DNA does offer evidence that there was a connection at some point between Rome and China over 2,000 years ago.

Jodi Barta, a molecular anthropologist at Washington State University who sequenced the East Asian woman’s DNA, said that it is especially remarkable to have this genetic data because it allows us to learn about average people in ancient times, rather than the elite men who actually recorded history.

“You know, I’m just an average person,” said Barta. “What could they tell about average me if they dug me up 2,000 years later?”

The discoveries being made from ancient DNA are the result of technical bravado. Working with the molecule is always difficult — often even impossible — because ancient DNA is prone to contamination from modern genetic material. It is also fragile, degrading and breaking into tiny pieces over time. At that point, it becomes tricky to sequence.

Contamination has been the major enemy of this type of work since scientists first interpreted ancient DNA in 1984. In fact, in the 1990s, there was a slew of claims that scientists had sequenced DNA from insects trapped in amber, dinosaur bones, and magnolia leaves that were many millions of years old. However, later analyses showed that these sequences were all the result of bacterial contamination.

Scientists can even contaminate samples with their own genetic material — a particular problem when the ancient DNA under examination is human. People constantly shed DNA from their skin and hair, Barta explained, so when researchers work with ancient DNA, they have to make sure that no hairs or skin cells have gotten into their samples. They wear gloves, caps, and masks, but often DNA, trapped in their clothing or suspended in the air around them, still floats into their test tubes.

To detect contamination, any scientists who handle the ancient samples must sequence their own DNA as well. If the sequences match their own genetic code, then they will know that they’ve accidentally sequenced themselves and not the ancient genes.

After sequencing, scientists often have to throw out some of the data because the samples sequenced too easily and the resulting sequences were too long — a clear sign of contamination with intact, modern DNA.

Another problem: Minute fragments of DNA slip through the cracks of traditional sequencing methods. However, new laboratory techniques, known as next-generation sequencing, are allowing scientists to sequence minuscule pieces of DNA rapidly.

Classical sequencing works by running strands of DNA through a gel. The strands leisurely make their way up to a laser beam, which reads the genetic code. The process is a slow one, and classical sequencing machines can only handle about 100 samples at a time. Next-generation sequencing speeds up this process by harnessing many small pieces of DNA to tiny platforms, and then sequencing the pieces right where they are anchored. The new sequencing machines can process millions of these platforms at one time.

Recently, scientists used next-generation technology to sequence the first entire genome of an ancient human. The sequence was from a member of the Saqqaq Culture, the earliest known Paleo-Eskimo culture, which existed in Greenland around 4,000 years ago. The research, published in the February 11 issue of Nature, was completed in only one and a half months and cost less than $500,000. Ten years ago, when the first modern human genome was sequenced using the traditional methods, it took a decade and cost billions of dollars.

According to Eske Willerslev, a biologist from the Centre for GeoGenetics at the Natural History Museum of Denmark who led the research, next-generation sequencing is so sensitive that scientists may now be able to do genetic work on old bone or hair samples that they had previously set aside, believing the samples contained no usable DNA.

“There’s a very big chance that these samples will work today,” he said. “So that’s fantastic.”

The benefits of next-generation sequencing are tantalizing, but for many, cost is still an obstacle. Barta looks forward to the day when she can afford to have a next-generation sequencing machine in her lab.

In the coming years, ancient DNA studies using next-generation technology may help us better understand how people have moved about the globe. And, while we may never have an island devoted to each of these historical journeys, we will soon be able to reconstruct the lives of many ancient people for whom there is no other record.

“They have a story to tell,” said Barta, “and ancient DNA is a way to get at these stories.”