The history of ancient Egypt has fascinated historians and archaeologists for more than a thousand years. The genetic history of the early Egyptians remains unclear despite a wealth of cultural and archaeological knowledge, primarily because deoxyribonucleic acid (DNA) has not been well preserved in Egypt’s hot and arid climate. This lack of knowledge regarding the preservation has limited insights into the origins and migrations of early populations in the formative phases of Egyptian civilization, as most genetic research has been limited mostly to post-Dynastic periods.
This study presents the first whole-genome sequence of an Egyptian person from the Old Kingdom era (circa 2855–2570 BCE). During this period, the expanding Sumerian civilization in Mesopotamia continued to grow cultural interchange into the latter part of the fourth millennium BCE. The individual analysed in this study was discovered at Nuwayrat, located approximately 265 kilometers south of Cairo, and it is close to the settlement of Beni Hasan. According to the skeletal remains’ radiocarbon dating, the Nuwayrat person lived between 2855 and 2570 calibrated BCE.
The body was preserved in a big jar inside a rock-cut tomb, which was a burial custom prevalent at the time for people with high social status. According to osteological examination, the individual is genetically male, with a height estimated between 157.4 and 160.5 cm. The various types of physical activities are regularly involved in the patterns of osteoarthritis and stress indicators. An Illumina sequencing platform was used to evaluate seven cementum-enriched DNA extracts, which were synthesized into single-stranded DNA sequencing libraries. With evidence of increased rates of cytosine-to-thymine (C-to-T) substitutions at the beginning of the sequence alignments, five of these libraries exhibited typical ancient DNA degradation patterns.
The Nuwayrat individual’s mitochondrial DNA and chromosome Y haplogroups are most prevalent in modern-day West Asian and North African populations. Following the influx of the Mesopotamian Late Uruk era into the Nile Valley during the late Predynastic era, trade persisted throughout the fourth millennium BCE. Principal component analysis (PCA) and ADMIXTURE clustering were used to compare the Nuwayrat genome with more than 4,000 ancient and modern genomes. The Nuwayrat individual’s ancestry was modelled using qpAdm, a statistical technique used to model genetic contributions from various source populations.
The discovery of lineage from Mesopotamia is consistent with archaeological records documenting extensive cultural interactions between Egypt and Mesopotamia, including early writing systems and shared technology. This study supported findings of population migration from Mesopotamia into North Africa during the Neolithic period, which confirms a strong genetic connection between the Nuwayrat person and ancient Neolithic Mesopotamians. The Nuwayrat genome showed no significant ancestry from central, eastern, or southern Africa, including the “Mota” genome from a 4,500-year-old Ethiopian genome.
The number of alignments to the Y chromosome divided by the total number of alignments to both sex chromosomes is known as the Ry parameter. This is used to confirm the individual’s male genetic sex. This research highlighted the complex interplay between migration, cultural progress, and local continuity in ancient Egypt. The interaction between population mobility and continuity in the area was highlighted by the Nuwayrat genome, which explores the origins of the early Bronze Age period in Egypt.
Reference: Morez Jacobs A, Irish JD, Cooke A, et al. Whole-genome ancestry of an Old Kingdom Egyptian. Nature. 2025. doi:10.1038/s41586-025-09195-5
