Researchers sequence first genome from Ancient Egypt

Researchers from the Francis Crick Institute and Liverpool John Moores University (LJMU) have extracted and sequenced the oldest Egyptian DNA to date from a man who lived around 4,500 to 4,800 years ago, the age of the first pyramids, in research published today (July 2) in Nature.

The man’s ancestry links back to the Middle East – the first anthropological evidence of migration to the growing empire from the East.

Although his remains suggest a life of hard labour – possibly a potter – he had been buried elaborately in a ceramic vessel in a tomb cut into the hillside.

Joel Irish, Professor of Anthropology and Archaeology and second author, who extracted the DNA, said the find suggest a degree of meritocracy in the country at that time: “His higher-class burial is not expected for a potter, who would not normally receive such treatment. Perhaps he was exceptionally skilled or successful to advance his social status.”

DNA extracted from a tooth

The research team extracted the DNA from the tooth of the man from Nuwayrat, a village 265km south of Cairo. The individual had been donated by the Egyptian Antiquities Service to the University of Liverpool in the early 20th century and then resided in the Museum of Liverpool.

He died at some point in the overlap between two periods in Egyptian history, the Early Dynastic and Old Kingdom periods, a time when archaeological evidence has suggested trade and cultural connections existed with the Fertile Crescent – an area of the Middle East encompassing modern-day Iraq, Iran and Jordan, among other countries.

Researchers believed that objects and imagery, like writing systems or pottery, were exchanged, but genetic evidence has been limited due to warm temperatures preventing DNA preservation.

By analysing his genetic code, the researchers showed that most of his ancestry mapped to individuals who lived in North Africa. The remaining 20% of his ancestry could be traced to ancient individuals who lived in the Fertile Crescent, particularly an area called Mesopotamia (roughly modern-day Iraq).

Egypt-born with ancestry from the East

This finding is genetic evidence that people moved into Egypt and mixed with local populations at this time, which was previously only visible in archaeological artefacts. However, the researchers caution that many more individual genome sequences would be needed to fully understand variation in ancestry in Egypt at the time.

By investigating chemical signals in his teeth relating to diet and environment, the researchers showed that the individual had likely grown up in Egypt.

They then used evidence from his skeleton to estimate sex, age, height, and information on ancestry and lifestyle. These signs suggested he could have worked as a potter or in a trade requiring comparable movements, as his bones had muscle markings from sitting for long periods with outstretched limbs.

Added Professor Irish: “The markings on the skeleton are clues to the individual’s life and lifestyle – his seat bones are expanded in size, his arms showed evidence of extensive movement back and forth, and there’s substantial arthritis in just the right foot. Though circumstantial these clues point towards pottery, including use of a pottery wheel, which arrived in Egypt around the same time.”

'Extraordinary journey'

Adeline Morez Jacobs, Visiting Research Fellow and former PhD student at Liverpool John Moores University, former postdoctoral researcher at the Crick Institute and first author, said: “Piecing together all the clues from this individual’s DNA, bones and teeth have allowed us to build a comprehensive picture. We hope that future DNA samples from Ancient Egypt can expand on when precisely this movement from the Middle East started.”

Linus Girdland Flink, Lecturer in Ancient Biomolecules at the University of Aberdeen, Visiting Researcher at LJMU and co-senior author, said: “This individual has been on an extraordinary journey. He lived and died during a critical period of change in Ancient Egypt, and his skeleton was excavated in 1902 and donated to the Museum of Liverpool, where it then survived bombings during the Blitz that destroyed most of the human remains in their collection. We’ve now been able to tell part of the individual’s story, finding that some of his ancestry came from the Fertile Crescent, highlighting mixture between groups at this time.”

Pontus Skoglund, Group Leader of the Ancient Genomics Laboratory at the Crick and co-senior author, said: “Forty years have passed since the early pioneering attempts to retrieve DNA from mummies without successful sequencing of an ancient Egyptian genome. Ancient Egypt is a place of extraordinary written history and archaeology, but challenging DNA preservation has meant that no genomic record of ancestry in early Egypt has been available for comparison. New and powerful genetic techniques have allowed us to cross these technical boundaries and rule out contaminating DNA, providing the first genetic evidence for potential movements of people in Egypt at this time.”

More information 

Reference: Morez Jacobs, A. et al. (2025). Whole-genome ancestry of an Old Kingdom Egyptian. Nature. DOI.

1.            The Old Kingdom of Egypt, also known as the ‘Age of the Pyramids’, refers to the period from the Third Dynasty to the Sixth Dynasty (2686 to 2181 BCE). This period has fascinated archaeologists for decades, as there was a boom of progress, including the construction of the first pyramid of Egypt, the ‘step’ pyramid at Saqqara. The individual in this research lived at some point during the bridge between the Early Dynastic period and the Old Kingdom.

2.            The technique used was called ‘whole genome sequencing’ where the entire DNA sequence is sequenced. This is different to previous methods which involved looking for specific markers in the DNA.

3.            The researchers took evidence from the skeleton that the individual habitually sat on or near the hard ground, with arms and legs extended, though also often kneeling, and looking down a lot as he had severe arthritis in his neck. Though circumstantial, this is consistent with work as a potter. This theory is supported further by unusual wear on several toe and arch bones in his right foot only, potentially guiding a pottery wheel, which was invented in the Middle East and spread into Egypt at this time. These skeletal markings match the positions that potters took as depicted in tomb paintings. This evidence for constant physical labour is at odds with his high-status tomb burial.

Images: A reconstruction of the man's face was made by maxillofacial experts at Face Lab at Liverpool John Moores University, led by Professor Caroline Wilkinson.