How ancient DNA—from Neanderthals to the Black Plague—has transformed archaeology

In 2010, geneticists in Denmark passed a remarkable milestone. Extracting fragments of DNA from 4,000-year-old strands of hair from Greenland that had been stored in a Copenhagen museum for decades, they reconstructed the first complete ancient human genome.

The study was the culmination of decades of work by researchers around the world, beginning with faltering attempts to get genetic material from Egyptian mummies in the 1980s. As recently as 2013, the number of ancient human genomes could still be counted on two hands. In the last five years, the numbers have increased exponentially: In April 2023, the 10,000th ancient human genome was published, with thousands more on their way.

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The remarkable growth of ancient DNA research—the focus of an entirely new discipline called paleogenomics—may be the biggest thing to hit archaeology since the development of radiocarbon dating in the 1950s. Last year, pioneering researcher Svante Pääbo, a geneticist at the Max Planck Institute for Human Evolution in Leipzig, Germany, won a Nobel Prize for his work on the genes of extinct Neanderthals. Now, ancient DNA has become a tool to better understand where we came from—and a way to glimpse where we’re going.

Perfecting the process

To recover ancient DNA from ancient samples, researchers take a tiny bit of bone, tooth or hair from a skeleton using a dentist’s drill or similar tool and extract DNA fragments from them. By duplicating the DNA fragments multiple times and then using computers to match and reassemble the tiny strands, as if in a billion-piece puzzle, geneticists can reconstruct entire genomes.

The process took decades to perfect. The first attempts to get DNA from ancient bones in the 1980s were plagued by problems. The biggest was contamination: Every living organism has DNA, and early research struggled to separate ancient genetic material from modern DNA. Samples could be tainted by anything from soil bacteria that infiltrates buried bones to a lab technician’s stray dandruff. Early claims that dinosaur DNA could be recovered from Cretaceous-era amber proved to be overly optimistic, for example, and mostly the result of contamination—putting the entire field in doubt.

Pääbo and others persisted, developing ways to eliminate contamination and prove the DNA they were looking at indeed belonged to ancient specimens. As a result, today ancient DNA samples are taken under tightly controlled conditions, in clean rooms flooded with ultraviolet light, which is capable of destroying bacteria and their DNA. Results are compared to databases of DNA from modern species or other ancient samples, helping sort and isolate the genetic material from different sources.

Early on, the procedures were also wildly expensive—far more than most archaeologists and paleontologists could afford. But as costs have dropped and the number of samples increased, the method has become a powerful tool for understanding the past. Ancient DNA studies are shifting from headline-grabbing one-offs to a standard part of the archaeologist’s toolkit. That’s already led to better understandings of ancient migrations and how societies functioned in the distant past.

On the move across time

By comparing the DNA of people buried in different time periods but the same geographic region, for example, geneticists and archaeologists can identify shifting populations. Dozens of studies in the last decade from all around the world show that migration and movement have always been part of the human story. We now know that Europe’s population has been dynamic for many millennia, with dramatically different populations entering the continent, mixing and mingling multiple times since the first modern humans arrived around 50,000 years ago. And ancient DNA has helped show when the first people arrived in the Americas and link them to ancestral populations in Asia.

Some discoveries go even further back. By comparing Neanderthal DNA to that of modern people, for instance, Pääbo and his team were able to show modern Europeans and Asians get a small fraction—up to 5 percent—of their ancestry from Neanderthals, suggesting that our distant ancestors encountered and mated with Neanderthals at some point in the distant past.

DNA even makes it possible to figure out when: The genes of people in sub-Saharan Africa today contain no Neanderthal DNA. That suggests modern humans met our Neanderthal cousins after migrating out of Africa 50,000 years ago.

Ancient DNA has even revealed the existence of entirely new species of human ancestors. In 2008, archaeologists recovered a fragment of knuckle bone from a cave in western Siberia. They estimated it was more than 50,000 years old, but the fragment was too small to say much more using traditional archaeological methods.

Thanks to cool conditions in the Siberian cave, researchers were able to extract DNA from the bone—revealing it was neither Neanderthal nor modern human, but something else entirely: a previously unknown ancestral human species now referred to as Denisovans, after the cave in which their remains were initially discovered.

Human DNA is just the tip of the iceberg. The same techniques used to investigate long-gone humans have also allowed researchers to sequence the DNA of extinct species. The genes of wooly mammoths, cave bears and dodo birds have offering unprecedented glimpses into the past—and a better understanding of the biology of their living relatives.

Meanwhile millennia-old bacterial DNA make it possible to track the origins and evolution of diseases like tuberculosis and yersinia pestis, better known as the Black Plague. And scientists have isolated and identified bacteria trapped in plaque on the teeth of ancient skeletons, showing what people ate, what diseases they had, and how the modern microbiome differs from that of our ancestors.

New frontiers and ethical questions

The next frontier? Extracting DNA from dirt. In a recent study, scientists were able to reconstruct the environment of Greenland before it was covered in ice, identifying the DNA of mammoths, reindeer and geese that roamed the island more than two million years ago. Researchers hope dirt may soon provide information about people, too. The floor of caves occupied in the past, for example, might contain enough DNA to identify their long-gone occupants.

Particularly when it comes to human DNA, research is concentrated on Europe and Russia, which represent two-thirds of the samples published so far. That’s partly because early studies focused on places where cool conditions preserved DNA well. A decade ago, many researchers doubted ancient DNA would ever be recovered from Africa, or even the shores of the Mediterranean. But as techniques improve, researchers are increasingly turning to sites in Africa and Asia to answer important questions about human origins and history.

These advances in genetic and archaeological knowledge have also brought up new ethical questions and pushback. While living people can volunteer a cheek swab or blood sample containing their DNA, analyzing the genes of the dead requires a few hundredths of an ounce of powdered bone or tooth. Such “destructive” analysis of human remains violates the religious beliefs of some groups. It also destroys part of an ancient skeleton, the ultimate non-renewable resource.

Geneticists, archaeologists, and descendant communities don’t always see eye-to-eye when it comes to deciding who can give permission to study such remains. Over the past decade, critics have pushed geneticists to engage more with the communities their samples come from. Sampling and publishing the genes of long-dead people, they argue, should require permission from their descendants before research begins. Many skeletons in museum collections, meanwhile, were acquired under circumstance that wouldn’t be considered ethical today.

Archaeologists say relying on ancient DNA risks oversimplifying prehistory: Genes can’t tell you what language people spoke, what gods they worshipped or how they thought of themselves—just who their parents, grandparents and more distant ancestors were. But combined with more traditional archaeological techniques, DNA from ancient skeletons is a powerful way to study the past.