How do researchers study DNA that is more than 1,000 years old?

In the 2000s, an exhibit of the infamous man-eating lions of Tsavo from Kenya that chowed down on 35 construction workers in the late 1890s was revived at Chicago’s Field Museum of Natural History. The museum’s assistant collections manager, Thomas Gnoske, wanted to decode their prey history.

To do this, the DNA extracted from the tooth cavities of these maneless male lions became Gnoske’s best friend — as did scientists analyzing prey dynamics. Years later, they have managed to chalk out the macabre dining habits of the lions using hair samples that Gnoske excavated from their teeth.

“Who would have thought even five years ago that we would be able to sequence an animal that is more than a million years old,” says Alida de Flamingh, a postdoctoral researcher at the University of Illinois, Urbana-Champaign and one of the authors of the study.

While this work is just one such example, ancient DNA has been elemental in unravelling historical mysteries of animal-human interactions and our evolutionary dynamics.

But how do researchers extract DNA from aged samples fraught with decay? Gently, and while bracing for failure, researchers say. 

“By the time it gets to us, because it’s been in the bone, ground or in a museum for a very long time, there might be some DNA left — but more often than not, [there’s] no DNA at all,” says Greger Larson, an evolutionary geneticist who conducts paleogenomic research at the University of Oxford. Despite this challenge, researchers like Emily Johana Ruiz Puerta have embarked on this arduous journey of working with ancient DNA. 

What does ancient DNA tell us?

When Ruiz Puerta drilled into a bone, she didn’t think she could paint a distinct picture of how 500 years ago, Norse hunters in Greenland roamed deep into the high Arctic hunting walruses to near-extinction and trading their prized tusks throughout Europe.

But the postdoctoral student at the University of Copenhagen, who relied on data from artifacts made out of walrus tusks, mentions how she looked for repetitive distinctive patterns in the genes, using what she called a “fingerprinting method.” This approach, which her recently published findings outline, relies on a color-coding process to determine whether the walrus lived in the waters of Iceland, close to the main Norse settlements, or 1,500 miles away in a distant region of northwestern Greenland far above the Arctic Circle known as North Water Polynya.

But ancient DNA is critical, not only because it offers important insight into how we came to be — but also to rebuke colonial narratives. “Human populations today are mosaics of different ancestry — which is a result of varied and complex genetic admixture in the past,” said Maanasa Raghavan, an assistant professor at the University of Chicago whose work has contributed to refuting radicalized claims of “pure populations.”

Raghavan — utilizing long bones, teeth, petrous bones and hair available from archaeological excavations — interspersed present-day genomic data with ancient human groups, investigating where the originating populations came from. Using these techniques, she was also able to track the number of migration waves and other historical aspects of the Indigenous peoples of the Americas.

How do the researchers extract the DNA?

This process, they say, depends on the kind of samples they are working with, citing how a “one fits all’ approach does not work. Separating DNA from the rest of the bone or hair matter requires them to put it in a chemical solution that removes everything that isn’t DNA, Larson explains.

But for Flamingh, her team had to be extra cautious during this step. After her team took the hair samples from the Field museum, they had to ensure they did not cross-contaminate the samples with their own DNA. 

“You put on a bodysuit with disposable sleeves, double gloves, hearing aids, hair masks and everything and then decontaminate,” she says.  The ancient genetics lab, ironically labeled a “DNA-free zone”, is protected by high air pressure, restricting air inflow. 

The researchers then dunk the hair samples in a low lead solution, separating any other strands of DNA mixed in with the hair. They run the DNA concentrate through a silica membrane that is specifically used for extracting and purifying highly degraded ancient DNA fragments. “This specific extraction technique is very helpful for extracting very low quality or low amounts of DNA,” Flamingh says.

Next, she matched the extracted DNA with an existing repository of genetic information in a gene bank in order to trace the animals that were hunted by the Tsavo lions. While the lore of their man-eating diets was popular, this analysis informed Flamingh and her team about something that they hadn’t known before — these lions also feasted on wildebeests. “There were historically no wildebeests in that region, so their presence indicates that these lions roamed in a much larger area than we had previously thought,” she says.

What hurdles did they encounter during extraction? 

There was a high chance of failure in this process, as Raghavan attests that petrous or pyramid-shaped bones or teeth often preserve DNA much better than others. “Because it is one of the densest bones in the body, [it] can encapsulate and protect DNA from environmental factors, like microbes and humidity, that degrade DNA.” 

DNA degradation, Larson says, happens immediately upon the death of the organism. But factors such as humidity in the tropics tend to accelerate the degradation. In a surprising turn of events, melting glaciers have been able to successfully unearth historical animals that were once inaccessible to palaeontologists. “As the climate is warming up, [in] places where there is no longer permafrost, people have been discovering baby mammoths and rhinos,” Flamingh points out, hinting at a world of ancient DNA that global warming is slowly revealing.