Examining the Science: What is Ancient DNA?

This article is awaiting additional images and will be updated in due course. It contains images of skeletal human remains, discretion is advised.

The journey into Ancient DNA began in 1984, with a groundbreaking study at the University of California, Berkeley, that proved the feasibility of extracting and analysing genetic material from ancient specimens.

In this study, Russ Higuchi and colleagues found that traces of DNA were still present in a 150 year old museum specimen of a quagga (an extinct subspecies of Plains Zebra).

Soon after, studies on both naturally and artificially mummified specimens showed that it was not just possible to find DNA in carefully preserved, comparatively recent museum specimens, but that some DNA could survive in less ideal conditions as well.

Since then, both the science and the technology of Ancient DNA have made huge advancements.

Now, the DNA used in studies on human remains is usually extracted from the petrous ear bone. This bone has a very dense structure, and provides the best possible conditions for preserving DNA. Advances have also made it faster and cheaper to analyse large numbers of samples with incredible accuracy.

Despite the advances, there are still limitations that apply to the analysis of Ancient DNA. In the introduction to his book Who We Are and How We Got Here, David Reich estimates that “...we have obtained about 75 percent success rates for ancient samples from the cold climate of Russia, but only around 30 percent for samples in the Near East.” (Reich, xxi)

Degradation

As soon as a cell dies, whether because it’s been shed by or removed from a living organism, or because the organism it belongs to has died, the DNA within it begins to break down and degrade. This process can be hastened or slowed by a number of factors - temperature, humidity, exposure to light, and even environmental acidity. Degradation can lead to the DNA being too fragmented for successful analysis.

Contamination

Ancient DNA samples are at risk of contamination, which can lead to erroneous and frustrating results. Contamination can come from a number of sources, but the two main categories are microbial - often also ancient, but not from the specimen being examined - or modern human DNA. To reduce the risk of modern contamination, extraction and processing of aDNA samples is conducted under very strict and extremely sterile conditions.

Limited Sample Availability

Ancient DNA samples are rare, and often difficult to obtain. Many ancient specimens have degraded beyond the point of analysis, while others are inaccessible due to preservation or ethical concerns. The limited availability means that researchers are restricted in the scope of their research, and also means that there are some biases in our understanding of ancient populations as often only specific groups (such as those with wealth or high status) were buried in the right conditions to preserve their DNA.

Despite these - and other - limitations, advances in technology and methodology continue to push the boundaries of ancient DNA research, offering new insights into human history, evolution, and population dynamics. By acknowledging and addressing these challenges, researchers can maximise the utility of ancient DNA analysis, while maintaining the integrity and ethical responsibility of their work.

There are a handful of more well known ancient specimens that have yielded DNA results and captured the imagination. Sometimes these cases stand out for the unusual circumstances of their death - such as Ötzi the Iceman’s violent final days - and sometimes it is because of the startling information they yield - such as Cheddar Man’s striking appearance. These are two men who lived thousands of years ago, but we know a lot about them from the evidence they left behind.

Ötzi the Iceman

One of the most iconic figures in Ancient DNA research, Ötzi was found in a remarkably preserved state in the Alps in 1991. He was initially believed to be a recently deceased individual, perhaps a hiker, but initial analysis of the axe he had carried soon showed that he was “at least four thousand years old.”

We now believe that Ötzi most likely died somewhere between 3239 and 3105 BCE, based upon further analysis of his body and belongings.

Reconstruction of Ötzi the Iceman at the South Tyrol Museum of Archaeology by Kennis & Kennis, 2011 (c) South Tyrol Museum of Archaeology / foto-dpi.com

In 2012, researchers first published Ötzi’s full genome, and in 2023 a new version was published, this time with less modern human contamination.

We know from these analyses that Ötzi’s Y-DNA haplogroup was G-L91 (although researchers haven’t yet typed him for any haplotypes downstream of this). G-L91 is now mostly found in Corsica. The main branch of his mtDNA haplogroup was K1, but no living human who has been tested so far shares his haplotype, so it has been named K1ö, after him.

Ötzi’s remains are on display at the South Tyrol Museum of Archaeology in Bolzano, Italy. You can read more about him here.

Cheddar Man

Closer to home but longer ago, Cheddar Man was discovered in Gough's Cave in Cheddar, just a 40 minute drive from Living DNA’s head office in 1903.

At the time, there were some fantastic claims made about his remains, which are still the oldest almost complete human skeletal remains ever found in Britain. He was called the ”first Englishman” and some claimed that he was 40,000 or even 80,000 years old. These sensationalist claims were proven false in the 1970s, when radiocarbon dating showed that he was much younger, closer to a sprightly 10,000 years old.

Using his petrous bone, researchers at the National History Museum where his remains are on display were able to extract his DNA, and published their findings in 2018. They found that his skin tone is likely to have been dark, with pigmentation that is more commonly associated today with sub-Saharan Africa, while his eyes are likely to have been a blue-green colour. While striking and unusual today, this combination would have been common for Europeans of the time. Pale skin and blond hair appear to have spread across the continent more slowly than light coloured eyes, appearing in the region only after the arrival of farming.

Perhaps ironically, as his resting place for 10,000 years was in an area that would become famous for its cheese, Cheddar Man would have been lactose intolerant. The variant that’s linked to lactose tolerance in European populations is estimated to only be 9000 years old, so Cheddar man and everyone he knew is likely to have had the same (somewhat explosive) reaction to a glass of milk!

Cheddar Man’s mtDNA haplogroup was U5b1, which appears to have been fairly common in Europe at the time, with an estimated 65% of western European Mesolithic hunter-gatherers carrying haplogroup U5.

His Y-DNA was I2a2, which still survives in genetic males living in the British Isles today.

You can see Cheddar Man’s remains at the National History Museum in London, where they’re on loan from the Longleat Estate, and read more about him here.

It’s not just our own ancestors that are being studied. Researchers have also delved into the genetic histories of other species. Dogs and wolves, grains such as einkorn, horses, rice, and cattle are just a few of the areas researchers are studying.

While it might be more palatable to think about discovering when dogs first became genetically distinguishable from wolves, there is also a lot of research into ancient pathogens. By tracing the DNA of Yersinia pestis, the bacteria that’s responsible for the bubonic plague or ‘Black Death,’ researchers have been able to discover that it originated in Bronze Age Eurasia (although it didn’t evolve far enough to cause bubonic plague for three thousand years).

By learning more about ancient pathogens through their genomes, researchers are able to better understand how they adapted to human hosts and predict how modern illnesses may develop.

No discussion of ancient DNA would be complete without mentioning our prehistoric cousins, the Neanderthals and the Denisovans. Through analysis of ancient DNA, scientists have discovered fascinating insights into the genetic relationship between modern humans and these long-extinct ancient hominids.

Neanderthals inhabited Europe and parts of Asia, and traces of their genome are present in the non-African population even today. Their genes may be responsible for a number of your traits - from your skin tone and hair colour, through to your sleeping patterns.

Denisovans are more elusive in the fossil record. We know more about them from their DNA than their bones, as we only have a few fragmentary remains from Denisova Cave in Siberia.

Despite the scarcity of their remains today, they were once populous enough to have left their mark on our modern-day genetics through interbreeding with our ancient ancestors. There is even evidence that they interbred with Neanderthals, with the finger bone of a 1st generation hybrid (Neanderthal mother and Denisovan father) that was sequenced in 2018. You can read more about Neanderthals and Denisovans on our blog posts about them, originally published in October 2023.

So what’s next?

As technology continues to advance and methodologies further improve, the study of ancient DNA will evolve and offer fresh avenues of exploration. From unravelling population movements to understanding the dynamics of ancient ecosystems, there are so many exciting possibilities to explore.

Ancient DNA is a powerful tool, enabling us to connect on a deeper level with our ancient roots. With Living DNA’s upgrades, you can discover how you are connected to ancient populations through your DNA, from the Neanderthals and Denisovans who walked the earth with early modern humans, through the Classical world with Ancient Greeks, Romans, and Egyptians, to the Vikings who sailed and raided the shores of Europe. Explore your upgrade options in the store today.