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, 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 BC, between the Early Dynastic period and Fourth Dynasty, with the funerary practices and related artifacts of the tomb being 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 around 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 BC.
Study
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 BC, with funerary practices archeologically attributed to the Third and Fourth Dynasty, which was excavated in Nuwayrat, in a cliff 265 km south of Cairo.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 BC to 426 AD, only three of the samples had acceptable nuclear contamination rates; two from the Pre-Ptolemaic 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.
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 2, until samplings were made for the 2025 study. 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 .
Genomic analysis
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 musculoskeletal stress suggesting intense physical labor, with characteristics possibly consistent with the professional activity of a potter.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.
Main findings
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, itself consisting of predominantly Levant Neolithic ancestry and minor Iberomaurusian ancestry, with the remaining most closely related to known genomes from Neolithic Mesopotamia. No other two-source model met the significance criteria. Two Three-source models were also consistent with the data, consisting of similar ancestry proportions, with the addition of a smaller direct contribution from populations of the Chalcolithic Levant.Ancestry modelling of ancient East African genomes with qpAdm identified the Nuwayrat genome as an equally strong candidate for the West Eurasian-related ancestry in ancient pastoralists from Kenya and Tanzania, as populations of the Chalcolithic Levant, consistent with the results of ADMIXTURE analysis of modern East African or 1st millennium Sudan Early Christians' genomes.
The Nuwayrat individual's Y-Chromosome and Mitochondrial haplogroups were identified as E1b1b1b2b, also known as E-V1515 and haplogroup I/N1a1b2, respectively. The frequency of both haplogroup peaks respectively among modern-day populations of East Africa and "a few small areas of East Africa, West Asia and Europe", consistent with the findings from the study's whole-genome analysis. The latest study however states the mitochondrial DNA and chromosome Y haplogroups of the Nuwayrat individual are most common in present-day North African and West Asian groups, not East Africa.
Neolithic North African component (77.6% ± 3.8%)
Most of the genome of the Nuwayrat individual derived from Neolithic North African ancestry, specifically matching samples from the Moroccan site of Skhirat-Rouazi. 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. 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%.According to a 2023 genetic study, the Skhirat-Rouazi ancestry actually corresponds to one of the three main genetic groups interacting and progressively intermixing in northwestern Africa during the Neolithic:
- 1) The first group, named Taforalt, going back around 15,000 years ago and whose profile persisted well into the Neolithic, represents the autochthonous Maghrebi Upper Paleolithic substrate of hunter-gatherers. However, no present-day or ancient Holocene Sub-Saharan African group was found to be a good proxy for the non-Eurasian admixture component found in Taforalt individuals. Instead, Iosif Lazaridis et al. argued that this Iberomaurusian/Taforalt lineage contributed around 13% ancestry to modern West Africans "rather than Taforalt having ancestry from an unknown Sub-Saharan African source". Finally a study in 2025 by researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig discovered that the non-Eurasian ancestry found in Taforalt was from an ancestral lineage, native to North Africa that diverged there before the Out-of-Africa migration that gave rise to Eurasians, but never left Africa and became mostly isolated. This North African lineage did "not carry sub-Saharan African ancestry, suggesting that, contrary to previous interpretations, the Green Sahara was not a corridor connecting Northern and sub-Saharan Africa."
- 2) The second group named Kaf Taht el-Ghar consists of Neolithic European agriculturists who crossed the Straight of Gibraltar and settled in North Africa around 5500 BC, bringing a Neolithic way of life and Cardium pottery, and marginally interbreeding with the TAF component The third and last group is Skhirat-Rouazi, 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 BC, and who, around 5000 BC, introduced animal husbandry and a distinct pottery style to Northwest Africa. 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.
Mesopotamian component (22.4 ± 3.8%)
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. The referenced "Mesopotamia_Neolithic" cluster consisted in a dozen samples from Nemrik 9, Boncuklu Tarla and Çayönü, all Pre-Pottery Neolithic cultures located in Upper Mesopotamia and Central Mesopotamia. 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 and agriculture developed from the 9th millennium BC.In a 2022 genetic study, the population of Çayönü 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 cattle in Upper Mesopotamian. The Çayönü population was shown to be genetically diverse, carrying both western and eastern Fertile Crescent ancestry, and best modelled by an ancestry combining about 48% Anatolian Epipaleolithic, 33% Central Zagros Neolithic and 19% South Levant Neolithic components.
Historical context
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.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 BC. 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 BC, 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.
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.