by Aparna Nathan
figures by Abagail Burrus

Superheroes aren’t the only ones with riveting origin stories. As humans, where did we come from? How did we populate six continents? For hundreds of years, archaeology has tried to provide the answers by digging up artifacts and piecing together their histories. However, shovels and brushes are now joining forces with test tubes and lab coats. Within the last decade, scientists have unraveled a new layer of the archaeological record: ancient DNA, or aDNA. Under the right circumstances, it can remain preserved within skeletal remains for over a million years.

Genetic data continues to provide new insights into how humans function, and aDNA can even shed light on our ancient predecessors. aDNA lays a trail of breadcrumbs that enables scientists to trace the migration and intermingling of different groups throughout history. By incorporating other archaeological evidence, they can piece together stories of war, technological revolutions, and disease.

Reading thousand-year-old DNA

If you want to look at your own genetic code—say, through a direct-to-consumer test like 23andMe—all you have to do is spit in a tube. Your saliva contains skin and blood cells that slough off your body’s surfaces, and these cells in turn contain the DNA to be sequenced.

But skeletons can’t spit, and any traces of saliva, skin, or blood are long gone after thousands of years of decay. The only remaining source of DNA is bone and teeth, and even this genetic material can be degraded from exposure to heat, water, air, or radiation. For this reason, some of the earliest successful ancient DNA extractions were from Nordic samples that were well-preserved in the cold soil.

Extracting DNA from bone samples is a meticulous task (Figure 1). It involves sandblasters (to clean the sample), chisels (to break down large fragments), and ultraviolet light (to destroy any contaminants). Technicians reduce a centimeter-long bone sample to a few hundred milligrams of powder, and release millions of fragments of DNA from the cells. Each DNA fragment can then be read using sequencing technology and compared to previously-decoded genomes from different geographic regions. This allows scientists to quantify the percent of the specimen’s genome that matches each ancestry of interest and piece together a theoretical origin story for the skeleton.

Figure 1: Extracting aDNA from bone samples. Technicians have to isolate a small, dense section of the skull (1), and, in a sterile environment, they clean (2) and break down the sample into a fine powder (3) that can be sequenced (4).

Writing (and re-writing) history through a genomic lens

aDNA studies don’t usually substantially re-write historic events. Instead, they fill in the gaps and provide explanations for how one group of people moved from Site A to Site B, or how two groups ever encountered each other in the first place. For example, in 2015, researchers from the lab of Harvard geneticist David Reich sequenced aDNA from 69 European specimens ranging from 3000 to 8000 years old and noticed something odd. European samples from the Late Neolithic period (or Bronze Age) shared some genetic material not only with their predecessors from the Middle Neolithic period, but also with a group of herders from the Russian steppes. This wasn’t in itself a novel observation, since previous archaeological work suggested that the two groups met.

However, the more interesting observation was how the composition of the central European genome changed. Instead of having traces of steppe ancestry—as would be expected if there was gradual interbreeding between the two groups—the steppe ancestry suddenly became a dominant feature of the Neolithic European genome. This was new evidence supporting a bold theory: Europe—its people, language, and culture—were a product of large-scale migration from the Eurasian steppes.

Discovery, but at what cultural cost?

aDNA might illuminate the people of the past, but scientists can stir up controversy when  carrying out aDNA research of an outside community, prompting debate about how to responsibly study the history of these populations.

A major question is consent: whose consent matters when you want to sequence ancient skeletal remains? The museum where the remains are held? The community from which the remains were excavated? For example, in Australia, starting with the arrival of colonists in the 1700s, aboriginal people’s remains have been studied by scientists and museums—without the groups’ consent—and often used to underpin racist “scientific” theories. Many museums are now returning these remains and other artifacts to their original communities, forcing scientists to think about who the true owners of their samples are. That’s not to mention the ethics of destroying ancient relics for genetic studies: extracting bone irreversibly disfigures the skull, which reduces the integrity of rare artifacts and may infringe on cultural beliefs regarding the proper treatment of human remains.

Beyond that, cultural identity is often built on population history, and aDNA studies add additional layers of complexity that sometimes clash with cultural paradigms. In one example, the people of the remote Oceanic nation of Vanuatu believed for centuries that they were descended from the island’s original settlers, who had journeyed from Taiwan through nearby Papua 3,000 years ago. Vanuatuans share culture and appearances with modern-day Taiwanese and Papuans, so this history seemed to make sense, and they proudly derive their heritage from their adventuring ancestors.

A burial site on the island contained remains of these first settlers, but when scientists sequenced skulls found there, the results showed that they only genetically resembled Taiwanese origin, with minimal relationship to Papuans and to modern day Vanuatuans. To the scientists, this meant that modern-day Vanuatuans were not descended from the island’s earliest settlers; instead, they were descended from a much later wave of nearby Papuan immigrants (Figure 2). This undermined tenets of Vanuatuan culture, such as their belief that their ancestors were the first people to set foot on the island. Ongoing research is using language and other cultural artifacts to piece together how Taiwanese and Papuan influences combined to shape modern Vanuatuan culture.

Figure 2: Old and new theories of Vanuatuan settlement. Originally, ancient Vanuatuan settlers were thought to have traveled from Taiwan, through Southeast Asian and Papua, to land in Vanuatu (left). Along the way, their DNA would have accumulated a mosaic of small changes that add up to the patterns found in the modern Vanuatuan genome. But with aDNA evidence, the new theory posits that the ancient settlers (solid line) came straight from Taiwan, and later settlers (dashed line) joined them from Papua (right).

To gain cultural context for their findings, some aDNA studies engage members of the subject community as collaborators and consultants — or even as leaders of the study, empowering them to use genetics as a tool to dissect their own cultural histories. A group of researchers led by Maria Nieves-Colón—who is of Puerto Rican descent—extracted and analyzed DNA from 124 ancient Puerto Rican specimens and confirmed that modern-day islanders are genetically descended from the island’s ancient indigenous populations. Meanwhile, in Australia, collaborations between scientists and indigenous communities to sequence ancient (and more recent) DNA has enabled the repatriation of ancestral remains and artifacts that were taken from these communities.

With modern advances in genomic analysis, aDNA is the newest tool to illuminate ancient life. But the past is the foundation for our present, and as aDNA researchers (literally) dig into the long-sealed historical archives contained within the genome, they are becoming entangled in the roots of modern cultures and nations. Both the subjects and the scientist have valuable perspectives to shape this work, and together, they can ensure that aDNA research is fair to both parties and fulfills its promise of clarifying the murky past and expanding our present understanding of the human genome.

Aparna Nathan is a third-year Ph.D. student in the Bioinformatics and Integrative Genomics program at Harvard University. Follow her on Twitter at @aparnanathan.

Abagail Burrus is a fourth-year Organismic and Evolutionary Biology Ph.D. candidate who studies elaiophore development at Harvard University.

Cover image: “Xaibe, Coba” by williamaveryhudson is licensed under CC BY-NC-ND 2.0 

For more information:

  • Linguists, geneticists, and anthropologists have followed up on the Vanuatu findings, as summarized here.
  • This in-depth feature from the New York Times explores the controversy behind aDNA research (and one of the major researchers in the field responded).
  • To ensure that samples are obtained ethically, a set of standards has been proposed for museums and other repositories of ancient remains.
  • A summer research program (profiled here) is getting indigenous students involved in genomic research to prepare them to lead and collaborate on genomic studies in their communities.

2 thoughts on “Digging for DNA: Ancient genomes can illuminate the past and reframe the present

  1. I like this article about Ancient genomes can illuminate the past and reframe the present, thanks for sharing this great info, it has a lot of info I need to know

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