We decoded the oldest genetic data from an Egyptian, a man buried around 4,500 years ago – what it told us

A group of scientists has sequenced the genome of a man who was buried in Egypt around 4,500 years ago. The study offers rare insight into the genetic ancestry of early Egyptians and reveals links to both ancient north Africa and Mesopotamia, which includes modern day Iraq and parts of Syria, Turkey and Iran.

Egypt’s heat and terrain made it difficult for such studies to be conducted but lead researcher Adeline Morez Jacobs and team made a breakthrough. We spoke to her about the challenges of sequencing ancient remains, the scientific advances that made this discovery possible, and why this genome could reshape how we understand Egypt’s early dynastic history.

What is genome sequencing? How does it work in your world?

Genome sequencing is the process of reading an organism’s entire genetic code. In humans, that’s about 3 billion chemical “letters” (A, C, T and G). The technology was first developed in the late 1970s, and by 2003 scientists had completed the first full human genome. But applying it to ancient remains came much later and has been far more difficult.

DNA breaks down over time. Heat, humidity and chemical reactions damage it, and ancient bones and teeth are filled with DNA from soil microbes rather than from the individual we want to study. In early attempts during the 1980s, scientists hoped mummified remains might still hold usable DNA. But the available sequencing methods weren’t suited to the tiny, fragmented molecules left after centuries or millennia.

To sequence DNA, scientists first need to make lots of copies of it, so there’s enough to read. Originally, this meant putting DNA into bacteria and waiting for the colonies to grow. It took days, demanded careful upkeep and yielded inconsistent results. Two breakthroughs changed this.

In the early 1990s, PCR (polymerase chain reaction) allowed millions of DNA copies to be made in hours, and by the mid-2000s, new sequencing machines could read thousands of fragments in parallel. These advances not only sped up the process but also made it more reliable, enabling even highly degraded DNA to be sequenced.

Since then, researchers have reconstructed the genomes of extinct human relatives like Neanderthals, and more than 10,000 ancient people who lived over the past 45,000 years. But the work is still challenging – success rates are low for very old remains, and tropical climates destroy DNA quickly.

What’s exceptional about the sequencing you did on these remains?

What made our study unusual is that we were able to sequence a surprisingly well-preserved genome from a region where ancient DNA rarely survives.

When we analysed the sample, we found that about 4%-5% of all DNA fragments came from the person himself (the rest came from bacteria and other organisms that colonised the remains after burial). The quantity of DNA of interest (here, human) is usually between 40% and 90% when working with living organisms. That 4%-5% might sound tiny, but in this part of the world, it’s a relatively high proportion, and enough to recover meaningful genetic information.

We think the individual’s unusual burial may have helped. He was placed inside a ceramic vessel within a rock-cut tomb, which could have shielded him from heat, moisture and other damaging elements for thousands of years.

To make the most of this rare preservation, we filtered out the very shortest fragments, which are too damaged to be useful. The sequencing machines could then focus on higher-quality pieces. Thanks to advanced facilities at the Francis Crick Institute, we were able to read the DNA over and over, generating about eight billion sequences in total. This gave us enough data to reconstruct the genome of what we call the Nuwayrat individual, making him the oldest genome from Egypt to date.

Does this open new frontiers?

We did not develop entirely new techniques for this study but we combined some of the most effective methods currently available into a single optimised pipeline. This is what palaeogeneticists (scientists who study the DNA of ancient organisms) often do: we adapt and refine existing methods to push the limits of what can be recovered from fragile remains.

That’s why this result matters. It shows that, with the right combination of methods, we can sometimes retrieve genomes even from places where DNA usually doesn’t survive well, like Egypt.

Egypt is also a treasure trove for archaeology, with remains that could answer major questions about human history, migration and cultural change.

Our success suggests that other ancient Egyptian remains might still hold genetic secrets, opening the door to discoveries we couldn’t have imagined just a decade ago.

What was your biggest takeaway from the sequencing?

The most exciting result was uncovering this man’s genetic ancestry. By comparing his DNA to ancient genomes from Africa, western Asia and Europe, we found that about 80% of his ancestry was shared with earlier north African populations, suggesting shared roots within the earlier local population. The remaining 20% was more similar to groups from the eastern Fertile Crescent, particularly Neolithic Mesopotamia (present-day Iraq).

This might sound expected, but until now we had no direct genetic data from an Old Kingdom (2686–2125 BCE) Egyptian individual. The results support earlier studies of skeletal features from this period, which suggested close links to predynastic populations, but the genome gives a far more precise and conclusive picture.

This genetic profile fits with archaeological evidence of long-standing connections between Egypt and the eastern Fertile Crescent, dating back at least 10,000 years with the spread of farming, domesticated animals and new crops into Egypt. Both regions also developed some of the world’s first writing systems, hieroglyphs in Egypt and cuneiform in Mesopotamia. Our finding adds genetic evidence to the picture, suggesting that along with goods and ideas, people themselves were moving between these regions.

Of course, one person can’t represent the full diversity of the ancient Egyptian society, which was likely complex and cosmopolitan, but this successful sequencing opens the door for future studies, building a richer and more nuanced picture of the people who lived there over thousands of years.