The genetic history of Egypt reflects its geographical location at the crossroads of several major biocultural areas: North Africa, the Sahara/Sahel, the Middle East, the Mediterranean and sub-Saharan Africa.
Genetic studies on ancient Egyptians
Egyptologist Barry Kemp has noted that DNA studies can only provide firm conclusions about the population of ancient Egypt if the sample results are of a significant number of individuals and represent a broad geographical and chronological range. According to historian William Stiebling and archaeologist Susan N. Helft, conflicting DNA analysis on recent genetic samples such as the Amarna royal mummies has led to a lack of consensus on the genetic makeup of the ancient Egyptians and their geographic origins.
2012 study of Ramesses III In 2012, two mummies of two 20th dynasty individuals, Ramesses III and "Unknown Man E" believed to be Ramesses III's son Pentawer, were analysed by Albert Zink, Yehia Z Gad, and a team of researchers under Zahi Hawass. Genetic kinship analyses revealed identical haplotypes in both mummies; using the Whit Athey's haplogroup predictor, the Y chromosomal haplogroup E1b1a was predicted.
In another study by the same authors in 2020, which once again deals with the paternal lineage of Ramesses III and the "Unknown Man E" (possibly Pentawer), E1b1a shows its highest frequencies in modern West African populations (~80%) and Central Africa (~60%).
2017 DNA study of Mummies at Abusir el-Meleq A study published in 2017 by Schuenemann et al. extracted DNA from 151 Egyptian mummies, whose remains were recovered from Abusir el-Meleq in Middle Egypt. The samples are from the time periods: Late New Kingdom, Ptolemaic, and Roman. Complete mtDNA sequences from 90 samples as well as genome-wide data from three ancient Egyptian individuals were successfully obtained and were compared with other ancient and modern datasets. The study used 135 modern Egyptian samples. The ancient Egyptian individuals in their own dataset possessed highly similar mtDNA haplogroup profiles, and cluster together, supporting genetic continuity across the 1,300-year transect. Modern Egyptians shared this mtDNA haplogroup profile, but also carried 8% more African component. A wide range of mtDNA haplogroups was found including clades of J, U, H, HV, M, R0, R2, K, T, L, I, N, X and W. In addition three ancient Egyptian individuals were analysed for Y-DNA, two were assigned to Middle Eastern haplogroup J and one to haplogroup E1b1b1a1b2. Both of these haplogroups are carried by modern Egyptians, and also common among Afroasiatic speakers in Northern Africa, Eastern Africa and the Middle East. The researchers cautioned that the examined ancient Egyptian specimens may not be representative of those of all ancient Egyptians since they were from a single archaeological site from the northern part of Egypt. The analyses revealed that Ancient Egyptians had higher affinities with Near Eastern and European populations than modern Egyptians do, likely due to the 8% increase in the African component found in modern Egyptians. However, comparative data from a contemporary population under Roman rule in Anatolia, did not reveal a closer relationship to the ancient Egyptians from the Roman period. "Genetic continuity between ancient and modern Egyptians cannot be ruled out despite this more recent sub-Saharan African influx, while continuity with modern Ethiopians is not supported".
The absolute estimates of sub-Saharan African ancestry in these three ancient Egyptian individuals ranged from 6 to 15%, and the absolute estimates of sub-Saharan African ancestry in the 135 modern Egyptian samples ranged from 14 to 21%, which show an 8% increase in African component. The age of the ancient Egyptian samples suggests that this 8% increase in African component occurred predominantly within the last 2000 years. The 135 modern Egyptian samples were: 100 from modern Egyptians taken from a study by Pagani et al., and 35 from el-Hayez Western Desert Oasis taken from a study by Kujanova et al. The 35 samples from el-Hayez Western Desert Oasis, whose population is described by the Kujanova et al. study as a mixed, relatively isolated, demographically small but autochthonous population, were already known from that study to have a relatively high sub-Saharan African component, which is more than 11% higher than the African component in the 100 modern Egyptian samples.
Verena Schuenemann and the authors of this study suggest a high level of genetic interaction with the Near East since ancient times, probably going back to Prehistoric Egypt although the oldest mummies at the site were from the New Kingdom: "Our data seem to indicate close admixture and affinity at a much earlier date, which is unsurprising given the long and complex connections between Egypt and the Middle East. These connections date back to Prehistory and occurred at a variety of scales, including overland and maritime commerce, diplomacy, immigration, invasion and deportation".
Responses to the 2017 DNA study
The 2017 study has generated academic responses from scholars from other related disciplines, remarking on the conclusions of the study from a multi-disciplinary approach.
In 2020, Stuart Tyson Smith, professor of anthropology at UC Santa Barbara, stated: "Additionally, they are oblivious to the fact that the mouth of the Faiyum Oasis, where the sample was located, is well known, through historical documents, as an area where Middle Eastern people, like the Sherden, were settled as a reward for military service, during the late New Kingdom, about 1300 to 1070 BCE. This provides a far more likely explanation for any stronger affinity to Middle Eastern populations, and weaker ties to Sub-Saharan populations than modern Egyptians in their sample, but was not even considered."
In 2021, Gourdine et al disputed Scheunemann et al's claim, in an unpublished article, that the increase in the sub-Saharan component in the modern Egyptian samples resulted from the trans-Saharan slave trade. Instead they argued that the sub-Saharan "genetic affinities" may be attributed to "early settlers" and "the relevant sub-Saharan genetic markers do not correspond with the geography of known trade routes".
In 2022, biological anthropologist S.O.Y. Keita argued that there were problems with the study's approaches and conclusions such as over-generalizations and a failure to consider alternative explanations. Particularly, he raised issues with the comparative samples from West Africa as a proxy group and generalisations about geographical Egypt and population origins from the sample results. He also drew attention to the fact that the authors draw inference on migrations in line with their Bayesian statistical approach rather than integrate other data into their explanations about the population history.
In 2022, archaeologist Danielle Candelora stated that there were several limitations with the 2017 Scheunemann et al. study such as "new (untested) sampling methods, small sample size and problematic comparative data".
In 2023, Stiebling and Helft acknowledged that the 2017 study had performed the largest study on ancient Egyptians but noted that the findings still derived from a small sample of mummies from one site in Middle Egypt dating to the New Kingdom and later periods. They also stated that this study could not represent earlier populations or Egyptians from Upper Egypt who were geographically closer to Sub-Saharan populations.
In 2023, Christopher Ehret argued that the conclusions of the 2017 study were based on insufficiently small sample sizes, and that the authors had a biased interpretation of the genetic data. Ehret also criticised the Schuenemann article for asserting that there was "no sub-Saharan genetic component" in the Egyptian population and cited previous genetic analysis which had identified the Horn of Africa as the origin of the E-M35 paternal haplogroup.
In 2025, UNESCO scholars Augustin Holl and Jean Gourdine both presented similar forms of criticisms, in the international General History of Africa Volume IX publication, of the 2017 Scheunemann study in terms of its geographical coverage, general conclusions on the population of Egypt and methodological approach. Gourdine argued that there were a number of biases in the interpretation and the conclusions conflicted with other analysis such as the Amarna STR analysis, and evidence of identifiable African haplogroups such as E1b1b1, JK2955 (haplogroup L3) and JK2963 (haplogroup M1a1i), which preceded the trans-Saharan slave trade in Egypt.
Later findings A 2020 study was conducted on ancient samples from Lebanon. Two individuals who lived in Lebanon around 500 BCE did not cluster with their contemporary Lebanese population. The study used the same Egyptian samples from the 2017 Schuenemann et al. study to further test these two individuals. One of these two individuals was a female who formed a clade with the three ancient Egyptian individuals from Schuenemann et al., implying that she shared all of her ancestry with them or a genetically equivalent population. The other one was a male who derived ~70% of his ancestry from a population related to the female and ~30% from a population related to ancient Levantines. Further testing suggests that the female was an Egyptian woman and the male was her son from a man who himself had both Egyptian and Lebanese ancestries.
2018 study of Nakht-Ankh and Khnum-Nakht The tomb of two high-status Egyptians, Nakht-Ankh and Khnum-Nakht, was discovered by Egyptian workmen directed by Sir William Flinders Petrie and Ernest Mackay in 1907. Nakht-Ankh and Khnum-Nakht lived during the 12th Dynasty (1985–1773 BCE) in Middle Egypt and were aged 20 years apart. Their tomb has been called Tomb of Two Brothers because the mummies were buried adjacent to one other and inscriptions on the coffins mention the female name Khnum-Aa, who is described as 'lady of the house' and referred to as the mother of both Nakht-Ankh and Khnum-Nakht. The Y-chromosome sequences were not complete, but the Y-chromosome SNPs indicated that they had different fathers, suggesting that they were half-brothers. The SNP identities were consistent with mtDNA haplogroup M1a1 with 88.05–91.27% degree of confidence, thus "confirming the African origins of the two individuals" according to the study authors, based on their maternal lineage.
2018 study of Djehutynakht In 2018 the mummified head of Djehutynakht was analysed for mitochondrial DNA. Djehutynakht was the nomarch of the Hare nome in Upper Egypt during the 11th or 12th Dynasty in the early Middle Kingdom period, c. 2000 BC. Two laboratories independently analysed Djehutynakht's DNA and found that he belonged to the mtDNA haplogroup U5b2b5, described by the lead author Odile Loreille as "a European haplogroup". U5 is thought to have originated in Europe, and U5b2b5 has been found in ancient European samples dating from the Neolithic onwards. U5b2b5 has also been found in 10 samples from Christian Period Nubia, and a related European sequence (U5b2c1) has been observed in an ancient sample from Carthage (6th century BC). Among ancient Egyptian samples the Djehutynakht sequence resembles a U5a lineage from sample JK2903, a 2000-year-old skeleton from the Abusir el-Meleq site in Egypt. Haplogroup U5 is found in modern Egyptians, and is found in modern Egyptian Berbers from the Siwa Oasis in Egypt. A 2009 study by Coudray et al. recorded haplogroup U5 at 16.7% in the Siwa Oasis in Egypt, whereas haplogroup U6 is more common in other Berber populations to the west of Egypt.
2020 study on two Egyptian child mummies