Stories Written in Bone

Emory anthropologist Jessica Thompson was at a human origins conference years ago when she heard a presenter lament: "Of course there is no ancient DNA from Africa because of the poor preservation there." That's when it clicked in Thompson's mind: She had visited a place in Africa—the highlands of northern Malawi—that had neither extremes of heat or wetness—two main environmental factors that degrade DNA.

She also knew that scant archaeological research had been done in the region, although a team had unearthed several ancient skeletons there decades ago.

"It's a strange and fascinating landscape," says Thompson, who made that 2005 visit as a tourist and was struck by the surreal beauty of the high mountain grassland.

It's also remote and off the radar of most of the world. "We saw maybe three other tourists while we were there," she recalls.

That trip laid the groundwork for discoveries of the oldest known DNA from Africa. In September, the journal Cell published an analysis of the new discoveries, filling in thousands of years of human prehistory of hunter-gatherers in Africa, led by Harvard geneticist David Reich.

Thompson is second author of the paper. She contributed and described the cultural context for nearly half of the fifteen new DNA finds, including the oldest samples. Her fieldwork in Malawi uncovered human remains that yielded DNA ranging in age from about 2,500 to 6,100 years old. And her work is ongoing at a site where a skeleton recovered in 1950 was just dated to 8,100 years old and also yielded DNA.

The other DNA in the Cell paper ranges in age from five hundred to three thousand years ago and comes from South Africa, Tanzania, and Kenya.

"Malawi is positioned in between where living hunter-gatherers survive," Thompson says. "For the first time, we can see the distribution of ancient hunter-gatherer DNA across Africa, showing how these populations were connected in the past."

Modern-day Malawi people, shown dancing at a festival, are descendants of the iron age agriculturalists who spread across the African continent three thousand years ago.

Ancient hunter-gatherers don't have a lot of living representatives in Africa today; they occur as remnants of people scattered across the continent. The remains of Malawi hunter-gatherers that Thompson is studying may represent a population that was once thriving but subsequently was pushed into marginal areas during the expansion of agriculturalists and pastoralists during the past three thousand years. Some of this population may have survived until much more recently.

"There are legends in Malawi of the original people who came there, passed down through oral histories," Thompson says. "They are described as hunters and little people, short in stature. There is also a story of a last, epic battle, about two hundred years ago, when these people got eradicated."

Thompson was a graduate student when she spent a summer working on a dig in the Serengeti. She and two companions decided to make a road trip before returning to the United States, including a stop in Malawi.

The landlocked country is located in southeast Africa, bordered by Zambia, Tanzania, and Mozambique. It is one of the least developed and smallest countries in Africa, about the size of the state of Tennessee, and runs north to south along the Rift Valley. An enormous body of water, Lake Malawi, makes up about one-third of the country.

"My traveling companions wanted to relax by the lake in the lowlands," Thompson recalls. "I had read about the Malawi highlands and really wanted to see this unique ecosystem, so I convinced them to go there instead."

Antelope in the chilly Malawi highlands.

Her companions complained of the cold—it's windy and regularly freezes in the highlands of Malawi and summer temperatures peak at around 65 or 70 degrees Fahrenheit. Despite the cold, Thompson admired the rugged, isolated beauty of rocky outcrops and grasslands studded with orchids and fairy ferns where zebra and shaggy antelope grazed.

Thompson, who joined Emory as an assistant professor of anthropology in 2015, dug through the archaeological literature surrounding Malawi and started making exploratory trips there in 2009. She learned of two digs in the Malawi highlands—in 1950 and 1966—that revealed human skeletons alongside rich cultural evidence of an extinct hunting-and-gathering lifeway.

The 1950 dig turned out to be led by the renowned archaeologist J. Desmond Clark, who Thompson calls her "academic grandfather." Although Clark died before Thompson could meet him, he served as the mentor to her mentor, Curtis Marean.

Mount Hora

On the slopes of Mount Hora—a striking 1,500-meter peak and a major landmark in the highlands—Clark uncovered two skeletons: A woman who had died at around age twenty-two and a nearby male, who had died in his forties. The skeletons had been taken out of the country, to the Livingstone Museum in Zambia, and were never dated.

"It was impossible to accurately do radiocarbon dating on bone in 1950," Thompson explains. "The skeletons became, quite frankly, forgotten over time."

Guided by the clues from the previous excavations, Thompson began heading digs in the Malawi highlands. A site at a landmark outcrop, known as Fingira Rock, is particularly isolated, requiring the team to hike up a mountainside to more than two thousand meters on the Nyika Plateau. "Working there you feel the wind, you feel the chill," Thompson says. Poachers are a hazard in the area, along with the occasional black mamba—one of the world's deadliest snakes. The Fingira site had not been excavated since 1966.

"We were appalled to discover that it had been heavily disturbed since then," Thompson says. Her team uncovered two human leg bones from two different adult males, yielding DNA that was about 6,100 years old.

The 8,100-year-old skeleton of a hunter-gatherer woman was found on the slopes of Mount Hora.

J. Desmond Clark

In the back of a cave, they found fragments of a child's skull in a termite mound. A tiny leg bone next to it indicated that the remains were from a baby younger than age one. DNA analysis revealed that she had been a girl and radiocarbon dating showed that she had died about 2,500 years ago. The analysis also showed that the bones from the infant and the two men were from the same hunter-gatherer population—even though they were separated by thousands of years.

The archaeological sediments suggest that Fingira was a place where the dead were buried, although the skeletal material has become scattered over time. Human bones are mixed with the bones of animals that they hunted and ate, as well as with stone tools and shell beads used for ornaments.

"When you visit the site," Thompson says, "you wonder, why were these people living up here where it's not the most comfortable conditions you can imagine? What was bringing them here? Why were they burying their dead, over and over again, for many thousands of years, in the same place?"

Meanwhile, Thompson tracked down the skeletons that Clark had discovered at Mount Hora in 1950, learning that they had been moved from Zambia to the University of Cape Town in South Africa. She contacted the curator of the skeletons to ask about the possibility of sampling their DNA. Alan Morris, now professor emeritus of physical anthropology at the University of Cape Town, had had the same idea. A sample of the female skeleton was already slated to be sent to one of the top genetic labs in the world, at University College Dublin (UCD) in Ireland.

Enter Emory graduate student of anthropology Kendra Ann Sirak 18PhD, who developed a minimally invasive technique for drilling ancient skulls to recover DNA from them (see related story). Sirak was a visiting researcher at UCD and teamed up with Thompson and Morris to see if ancient DNA could be extracted from the female skeleton.

The petrous bone, which contains components of the inner ear, is the most promising site to drill for ancient DNA. The skeleton's petrous bone had already broken away from the skull, so only this tiny, triangular-shaped piece of the skeleton was sent to Dublin.

Jessica Thompson at the Malawi field site.

"It was extremely fragile," says Sirak, whose job was to drill into the petrous bone and get about two hundred millimeters of bone powder without shattering the specimen.

Sirak was successful. Her colleagues in Dublin processed the sample and then sent it to the genetics team at Harvard Medical School for DNA analysis—also successful. Meanwhile, radiocarbon dating revealed that the skeleton was 8,100 years old.

"It was like Christmas," Sirak says, "knowing that we had DNA data on such an ancient specimen."

The skeleton's genetic analysis connected her to the same population of hunter-gatherers who died thousands of years later and were found seventy kilometers away at Fingira.

Another surprise revealed by the genetics of the Malawi hunter-gatherers: They did not contribute any detectable ancestry to the people living in Malawi today, descendants of the Iron Age agriculturalists and pastoralists who began sweeping across the African continent about three thousand years ago.

"In most parts of Africa, you see quite a bit of a mixture," Thompson says. "When you take genetic samples from modern people who are living today, you find that they are a combination of the folks who were expanding into a region and also the folks who were living there before. In Malawi, we see that's not the case. It appears that there was a complete replacement of the original hunter-gatherer people. They are not just gone as a lifeway, they are actually gone as a people as well."

One of the mysteries Thompson hopes to solve is how that happened. Was it violent? Was it a sudden or a slow process? Did the entrance of strange new technologies, like pottery and iron working, play a role? "We can't use genetics to answer these questions," Thompson says. "We have to use the archaeology."

She continues to excavate in Malawi, aided by local technicians and other collaborators. This past summer, five Emory anthropology students accompanied her in the field (see related story). The team uncovered more human remains at Mount Hora—a charred bone from a human arm and parts of two legs. These bones, recently dated to between 9,500 and 9,300 years old, show that the Hora site still has many secrets to reveal.

Back in her lab at Emory, Thompson uses the data to generate three-dimensional images of the digs and pinpoint where each bone fragment, shell bead, or stone tool was found. Her digital model for this summer's Mount Hora dig uses different-colored dots to give a glimpse of how hunter-gatherers were depositing both human remains and ordinary objects from their day-to-day lives over time.

"And then at this point," Thompson says as she moves the cursor on her computer screen, "you see the introduction of pottery and iron technology. And right after that you see this fundamental change in the way that the site was used. People are no longer going there frequently. They're no longer making these big bonfires. And they're no longer interring their dead there."

Ultimately, Thompson seeks to understand how and when the earliest members of our species—Stone Age Homo sapiens—interacted with one another and with their environments in Africa.

"One thing that's really easy to forget, when we look at the way people live today, is that for most of our evolution we lived as hunter-gatherers," she says. "So, if we want to understand our own origins as a species, we have to know what those lifeways looked like in the past."

Bonding over bones, stones, and beads

I've really been into bones since I was little. I don't know why," says Alexandra Davis 18C, an anthropology major. "Not fresh bodies, though. No soft tissues or blood. Just bones."

Now Davis stands before a counter in Thompson's lab, sorting through the thousands of bone fragments the team recovered—cleaning them, categorizing them—then placing them into clear, plastic Ziploc bags. The bags labeled "Metapodial" and "Phalanx" contain bones from the hands and feet of mammals.

We think this one might be from a human," Davis says, pointing to a phalanx set aside from the other bones, which are all likely from animals. "My friends who aren't into anthropology would be like, 'Oh, no! A human toe!' But we were all really excited," she adds, indicating her fellow students at work in the lab.

Anthropology PhD candidate Grace Veatch 20PhD is passionate about taphonomy—studying bones to learn how an animal died and its remains decayed. "Ultimately, I'm trying to understand the evolution of the human diet," she says.

She opens a specimen drawer and pulls out two small, plastic boxes. One contains loose pieces of fur from a rat. The other holds a few fragments of the rat's bones, including a couple of teeth. These are the dissected parts of a modern-day owl pellet, she explains—the indigestible bits from an owl's meal that it regurgitated as a compacted mass.

After the surfaces of the ancient Malawi animal bones are cleaned, Veatch will compare them to these modern samples.

Veatch will also check the animal bones for telltale signs of cut marks from the stone tools of the hunter-gatherers.

Rock shards from the Malawi toolmakers are spread out on a nearby table where Alexa Rome 20C and Aditi Majoe 19C, both anthropology and human biology majors, pore over them with magnifying glasses. Many of the shards are barely bigger than a thumbnail—likely the flakes that shattered and fell as the hunter-gatherers shaped a tool from a stone core.

"Quartz is relatively easy to break, and you can get really sharp edges from it," Majoe says. "It's hard to examine, though, because it's clear." She eyes the edges of a luminescent flake to determine whether it is lithic—altered by human hands.

"The tools that Stone Age people used are a really important part to their story," she says. "You can learn a lot about their behavior from the things that they made."

"I'm the shell person," says Suzanne Kunitz 10C, who is majoring in anthropology and human biology and psychology. She opens a specimen drawer and brings out the shell of an African giant land snail, from the genus Achatina. The shell is a bit longer than her palm. Its brown-striped whorls decrease in size to form an elongated spear shape.

On a table nearby are Achatina shell beads recovered from Malawi—flat discs, about the size of aspirin tablets, with holes poked through their centers.

"Not much research has been done on ancient shell beads, but to me they're really interesting," Kunitz says. "I'd like to know whether all the hunter-gatherers wore the beads and why they wore them. Did they have a ritual purpose? Or were they just for decoration?"

The students stayed in tents in the Malawi highlands where it was too cold to even think about using the crude camp showers.

Kunitz and Davis teamed up to dig at one site, which was studded with termite mounds. "It was freezing—a wind tunnel," Kunitz says. "We bundled up and stuck it out."

"We pretty much dug through termites for three days," says Davis, who was disappointed to come across only one bone fragment—of a medium-sized animal. She was later buoyed when that bone turned out to be eight thousand years old.

A highlight for everyone occurred at a dig site on the slopes of a peak called Mount Hora. One of the local excavators said that he had found something interesting and called everyone over.

"It was human remains, part of an elbow joint," Veatch says. "That was a big moment."

"It was cool to find a human bone," Rome says. "I love looking at stone tool flakes, don't get me wrong. But when you find human remains it feels a little more real. That was an actual person."

Ultimately, the experience of sifting through the human past made Rome feel more connected to people in the present.

"We all got really close over the seven weeks we spent together in Malawi," she says. "Our last night there, we went out to dinner at a vegetarian Indian place. The food was really good. We had finished all the hard work and we were talking and laughing, joking around. That was one of the best times of my life."

Kendra Sirak takes her bone drill everywhere she travels. "No one at customs has ever questioned me about why I'm carrying a gigantic drill in my suitcase," she says.

Unusual Skull Set: How a grad student invented the go-to technique for drilling skulls

A PhD candidate in anthropology in Emory's Laney Graduate School, Kendra Ann Sirak 18PhD has developed a specialized technique for drilling into ancient skulls to remove DNA samples. Her skills are in demand; she's flown to more than a dozen countries and drilled more than one thousand skulls.

Sirak was the last graduate student of the late George Armelagos, Goodrich C. White Professor of Anthropology and one of the founders of the field of paleopathology. Armelagos spent decades working with graduate students to study the bones of ancient Sudanese Nubians to learn about patterns of health, illness, and death in the past. The only piece missing in studies of this population was genetic analysis. So in 2013, Armelagos sent Sirak to one of the best ancient DNA labs in the world, University College Dublin, with samples of the Nubian bones.

I had no interest in genetics," says Sirak, who was passionate about studying human bones and paleopathology. "But George believed DNA was going to become a critical part of anthropological research."

Sirak was hooked when she saw how she could combine her interest in ancient bones with insights from DNA. She formed collaborations not just in Dublin but at Harvard Medical School's Department of Genetics and elsewhere, working on unsolved mysteries surrounding deaths going back anywhere from decades to ancient times.

As genetic sequencing techniques keep improving, anthropology and DNA analysis are becoming increasingly complementary. In 2015, another breakthrough occurred when researchers realized that the petrous bone consistently yielded the most DNA from ancient skeletons.

But the way the petrous bone is wedged into the skull makes it difficult to access without shattering the cranium. Understandably, museum curators were reluctant to allow DNA researchers to tamper with fragile, ancient skulls.

So Sirak set about developing a technique to drill into a skull and reach the petrous bone in the most noninvasive way possible, while also getting enough bone powder for DNA analysis. The journal Biotechniques recently published her method, which involves drilling through the cranial base, where the spinal cord enters the skull. The drill bits she uses are a mere 3.4 to 4.8 millimeters in diameter.

Hopefully it will become the gold standard for both anthropology stewardship and DNA analysis," Sirak says.

She is now finishing up her dissertation, a bioethnography of the ancient Nubians. "Anthropological genetics is a huge and growing field," Sirak says. "[Armelagos] was a good mentor. He introduced me to something that I didn't know existed and let me run with it."