Old Kingdom individual (NUE001)

NUE001 is the genetic code name of an Old Kingdom adult male Egyptian of relatively high-status who was excavated in Nuwayrat (Nuerat, نويرات), in a cliff 265 km south of Cairo, and whose whole-genome ancestry was published in 2025 in an article in the journal Nature. The individual was radiocarbon-dated to 2855–2570 BCE, with funerary practices and related artifacts archeologically attributed to the Third and Fourth Dynasty.

NUE001 is remarkable in that it represents the first successfully sequenced Early Dynastic Egyptian to date, and for the resulting discovery that about 20% of his genetic ancestry can be traced to the Eastern Fertile Crescent, including Mesopotamia, which suggests early human migrations from Mesopotamia to Egypt, in addition to the already known cultural flows starting from at least the 6th millennium BCE.^[2]

For the first time in 2025, a study was able to give insights into the genetic background of Early Dynastic Egyptians, by sequencing the whole genome of an Old Kingdom adult male Egyptian of relatively high-status, radiocarbon-dated to 2855–2570 BCE, with funerary practices archeologically attributed to the Third and Fourth Dynasty, which was excavated in Nuwayrat (Nuerat, نويرات), in a cliff 265 km south of Cairo.^[2][3]

Before this study, whole-genome sequencing of Ancient Egyptians from the earliest periods of Egyptian Dynastic history had not yet been accomplished, primarily because of the unforgiving DNA preservation conditions in Egypt. Although previous archaeogenetic research had managed to study the partial DNA of ancient Egyptian individuals from 1388 BCE to 426 CE, only three of the samples had acceptable nuclear contamination rates; two from the Pre-Ptolemaic Period (New Kingdom to Late Period), and one from the Ptolemaic Period. These samples were dated to millennia after the Old Kingdom period, well after Egypt had experienced multiple pivotal upheavals, which may or may not have resulted in substantial genetic turnover within the Egyptian population. As a result, the genetic structure of Early-Dynastic Ancient Egyptians remained unclear. ^[2]

The body was initially excavated in 1902 and stored in the World Museum in Liverpool, where it survived the bombings during the Blitz in World War Two, until samplings were made for the 2025 study.^[4] The discoverer, John Garstang of the University of Liverpool, published a short account of the discovery in The burial customs of ancient Egypt as illustrated by tombs of the Middle Kingdom; being a report of excavations made in the necropolis of Beni Hassan during 1902-3-4 (pp.26-28).^[5]

The corpse had been placed intact in a large circular clay pot without embalming or mummification, which were not standard practice at the time, and then installed inside a cliff tomb, which accounts for the comparatively good level of conservation of the skeleton and its DNA. This special mortuary treatment suggests that the individual had a relatively higher social status. However his skeleton revealed important muscoloskeletal stress suggesting intense physical labor, with characteristics possibly consistent with the professional activity of a potter.^[2]

The DNA was extracted from the cementum at the root of a tooth, an excellent source for DNA preservation. Shotgun sequencing was used, giving full coverage across the whole genome.^[3]

The genetic profile of the Nuwayrat individual was most closely represented by a two-source model, in which 77.6% ± 3.8% of the ancestry corresponded to genomes from the Middle Neolithic Moroccan site of Skhirat-Rouazi (SKH, dated to 4780–4230 BCE), itself consisting of predominantly (76.4 ± 4.0%) Levant Neolithic ancestry and (22.4 ± 3.8%) minor Iberomaurusian ancestry, with the remaining (22.4% ± 3.8%) most closely related to known genomes from Neolithic Mesopotamia (dated to 9000-8000 BCE).^[2][6] No other two-source model met the significance criteria (P>0.05). A total of two Three-source models also emerged, but had similar ancestry proportions, with the addition of a much smaller third-place component from the Neolithic/Chalcolithic Levant.^[2] According to Lazardis, “What this sample does tell us is that at such an early date there were people in Egypt that were mostly North African in ancestry, but with some contribution of ancestry from Mesopotamia". According to Girdland-Flink, the fact that 20% of the man’s ancestry best matches older genomes from Mesopotamia suggests a fairly substantial diffusion of Mesopotamian-related people into Egypt.^[3]

Most of the genome of the Nuwayrat individual (about 78%) derived from Neolithic North African ancestry, specifically matching samples from the Moroccan site of Skhirat-Rouazi (SKH, dated to 4780–4230 BCE).^[2] This seems to reflect shared Neolithic ancestry across North Africa during this period, and its specific genetic contribution to the Early Dynastic and Old Kingdom people.^[2] However this shared Neolithic North African ancestry itself has been previously shown to be a combination of Levant Neolithic ancestry for about 76%, probably reflecting one or several pre-Bronze Age Levantine migration events, and Iberomaurusian ancestry for about 24%.^[2]

According to a 2023 genetic study, the Skhirat-Rouazi (SKH) ancestry actually corresponds to one of the three main genetic groups interacting and progressively intermixing in northwestern Africa during the Neolithic:^[7]

• 1) The first group (■), named Taforalt (TAF), going back to circa 15,000 BP and whose profile persisted well into the Neolithic, represents the autochthonous Maghrebi Upper Paleolithic substrate of hunter-gatherers (their genetic makeup is modelled as intermediate between contemporary Levantine foragers and sub-Saharan African populations).^[8]
• 2) The second group (■) named Kaf Taht el-Ghar (KTG, dated 5400–4900 BCE) consists of Neolithic European agriculturists who crossed the Straight of Gibraltar and settled in North Africa around 5,500 BCE, bringing a Neolithic way of life and Cardium pottery, and marginally interbreeding with the TAF component (their genetic makeup is modelled at 72% Anatolian Neolithic, since Neolithic Europeans are the result of the demic expansion from Anatolia that accompanied the introduction of agriculture in Europe, 10% WHG and 18% Maghrebi.^[9]
• 3) The third and last group (■) is Skhirat-Rouazi (SKH, dated 4,700–4,100 BCE), a population whose principal ancestry was introduced to Northwestern Africa during the Middle Neolithic through a westward expansion of pastoralists originating in the Levant, who entered Northeast Africa via the Sinai around 6,000 BCE,^[10] and who, around 5000 BCE, introduced animal husbandry and a distinct pottery style to Northwest Africa.^[6] This group correlates closely with the introduction of southwest Asian domesticates such as sheep, goats, and cattle, coinciding with the rise of Saharan cattle pastoralism and the appearance of Ashakar Ware pottery in the Maghreb, and may have contributed to the early dispersal of Afro-Asiatic languages across North Africa. They also admixed with local Maghrebi groups (their genetic makeup is modelled at 76% Levant Neolithic and 24% Maghrebi).^[6]

This Skhirat-Rouazi (SKH) population is the one which forms the bulk (~77.6%) of the ancestry of the Egyptian Old Kingdom individual from Nuwayrat NUE001.

Nemrik 9

Çayönü

Boncuklu

Nuwayrat

Göbekli Tepe

Nuwayrat (), together with locations and dates of the reference samples for Mesopotamia_Neolithic (): Nemrik 9 (9500-8000 BCE), Boncuklu Tarla (9000-8500 BCE), Çayönü (8300-7500 BCE).^[11]

The remaining ~22% of the Nuwayrat individual's genetic ancestry derived from Neolithic Mesopotamian-related populations, likely originating from the eastern Fertile Crescent, including Mesopotamia.^[2] The referenced "Mesopotamia_Neolithic" cluster consisted in a dozen samples from Nemrik 9 (9500-8000 BCE), Boncuklu Tarla (9000-8500 BCE) and Çayönü (8300-7500 BCE), all Pre-Pottery Neolithic cultures (Pre-Pottery Neolithic A or Pre-Pottery Neolithic B) located in Upper Mesopotamia and Central Mesopotamia.^[11] These sites, such as Çayönü or Boncuklu Tarla, developed from the Taş Tepeler cultural tradition of Gobekli Tepe, and a site such as Çayönü is where some of the first animal domestication occurred (the pig may have first been domesticated there in 8,500 BCE) and agriculture developed from the 9th millenium BCE.^[12][13][14]

In a 2022 genetic study, the population of Çayönü (8300-7500 BCE) was analyzed as a representative of the earliest known hunter-gatherer sedentary populations who built the monumental structure of Gobekli Tepe and domesticated various plants and animals, such as the einkorn, emmer, sheep, goats, pigs and cattles in Upper Mesopotamian.^[15] The Çayönü population was shown to be genetically diverse, carrying both western and eastern Fertile Crescent ancesty, and best modelled by an ancestry combining about 48% Anatolian Epipaleolithic, 33% Central Zagros Neolithic and 19% South Levant Neolithic components.^[16]

A 2022 DNA study had already shown evidence of gene flow from the Mesopotamian and Zagros regions into surrounding areas, including Anatolia, during the Neolithic, but not as far as Egypt yet.^[7]

In terms of chronology, Egypt was one of the first areas to adopt the Neolithic package emerging from West Asia as early as the 6th millennium BCE. Population genetics in the Nile Valley observed a marked change around this period, as shown by odontometric and dental tissue changes. Cultural exchange and trade between the two regions then continued through the 4th millennium BCE, as shown by the transfer of Mesopotamian Late Uruk period features to the Nile Valley of the later Predynastic Period. Migrations flows from Mesopotamia accompanied such cultural exchanges, possibly through the sea routes of the Mediterranean and the Red Sea or through yet un-sampled intermediaries in the Levant, which could explain the relative smallness of genetic influence from known Chalcolithic/Bronze Age Levantines populations. According to the DNA analysis, the Mesopotamian genetic contribution to Egypt was essentially direct, and was not a secondary effect of the Mesopotamian expansion in the Levant.^[2]

The analysis also excluded any substantial ancestry in the Nuwayrat genome related to a previously published 4,500-year-old hunter-gatherer genome from the Mota cave in Ethiopia, or other individuals in central, eastern, or southern Africa.

The Nuwayrat individual is predicted to have had brown eyes, brown hair, and skin pigmentation ranging from dark to black. The further osteological examination revealed that he would have stood 157.4–160.5 cm tall. These physical features are broadly consistent with those observed among present-day Egyptians and North Africans.

The authors acknowledged limitations to the study, such as the reliance on a single Egyptian genome and the limited accuracy of phenotypic predictions in understudied populations. For reference, the HIrisPlex-S phenotype analysis featured in the study established probabilities for various eye, hair and skin colours as follows: for the eyes, ~98.79% for brown, ~1.19% for intermediate and ~0.02% for blue; for the hair, ~52.89% for black, ~0.14% for red, ~45.04% for brown and ~1.92% for blond; for the skin, ~37.84% for dark to black, ~56.78% for dark, ~5.28% for intermediate and ~0.1% for pale.^[17]

Regarding the supplemental facial reconstruction, the researchers noted that while the DNA analysis is indicative of population origin, there is no definitive data for skin colour, eye colour or hair colour; therefore, the reconstruction was produced in black and white without head hair or facial hair.^[2]

The timing of the admixture event cannot be calculated directly from the 2025 genetic study.^[18] The 2025 study showed that the Nuwayrat sample had the greatest affinity with samples from Neolithic Mesopotamia dating to 9000-8000 BCE (composed of individuals from Nemrik 9, Boncuklu Tarla and Çayönü, from the Pre-Pottery Neolithic A and Pre-Pottery Neolithic B periods).^[11][18] Concurrently, other studies have shown that during the Neolithic, in the 10,000-5,000 BCE period, populations from Mesopotamia and the Zagros expanded into the Near-East, particularly Anatolia, bringing with them the Neolithic package of technological innovation (domesticated plants, pottery, greater sedentism). Egypt may also have been affected by such migratory movements.^[18][20] Futher changes in odontometrics and dental tissues have been observed in the Nile Valley around 6000 BCE.^[18] Subsequent cultural influxes from Mesopotamia are documented into the 4th millenium (3999-3000 BCE) with the appearance of Late Uruk features during the Late Pre-dynastic period of Egypt.^[18]

Further Mesopotamian expansions into the Near-East are dated to the Chalcolithic (5000–3300 BCE) and subsequent Bronze age periods, with high proportions of Mesopotamian ancestry found in human samples of this period in the Anatolian and Levantine regions.^[18] However, the present 2025 study also showed through follow-up qpAdm analysis that these Chalcolithic Near-Eastern populations could not be a potential source of the Nuwayrat sample.^[18] This suggests that the proposed Copper Age arrival of the Mesopotamian ancestry in Egypt must have occurred through either an as-yet-unknown migration path across the Near-East, or by way of maritime trade-routes over the Mediterranean or Red Sea.^[18]

Overall, the 2025 study "provides direct evidence of genetic ancestry related to the eastern Fertile Crescent in ancient Egypt". This genetic connection suggests that there had been ancient migration flows from the eastern Fertile Crescent to Egypt, in addition to the exchanges of objects and imagery (domesticated animals and plants, writing systems...) already observed. This suggests a pattern of wide cultural and demographic expansion from the Mesopotamian region, which affected both Anatolia and Egypt during this period.^[2]

The 2025 study re-analysed previously published genetic data from Third Intermediate Period mummies (787-544 BCE).^[18][22] It showed marginal continuity from the Nuwayrat sample, complemented by a significant Levantine ancestry influx, its main source being Bronze Age Levant ancestry, appearing at around 64% in the main model (P=0.32).^[18] The best-fit three-source model showed 46% for Levantine, 18% for Mesopotamian, and 36% for Moroccan-type ancestry (P=0.24).^[21] This shift towards majoritary Levantine ancestry could have originated in the proposed Bronze Age Canaanite expansion of the end of the Middle Kingdom and the advent of the Second Intermediate Period of Egypt, associated with the rise of the Hyksos and the Late Bronze Age collapse.^[18]

Genetic modelling suggests that most present-day Egyptians derive their ancestry from a combination of five ancient populations. Up to ~75% traces back to groups related to either the Old Kingdom individual from Nuwayrat or to Middle Neolithic populations from Morocco, which itself contributed approximately 80% of the Nuwayrat individual's ancestry. Additional components include ancestry related to the Bronze Age Levant, which the researchers note as the second most prevalent ancestry component, as well as more recent admixture from sub-Saharan Africa (East and West African ancestries) that the authors noted was suggested from previous published analysis and their models.

• DNA history of Egypt
• Ancient Egyptian race controversy
• Population history of Egypt
• Dynastic race theory