DNA history of Egypt

The genetic history of Egypt's demographics reflects its geographical location at the crossroads of several major biocultural areas: North Africa, the Sahara, the Middle East, the Mediterranean and Sub-Saharan Africa.

See also: Population history of Egypt
Main article: Genetic history of the Middle East

Ancient DNA

Contamination from handling and intrusion from microbes create obstacles to the recovery of ancient DNA.[1] Blood typing and ancient DNA sampling on Egyptian mummies is scant. However, blood typing of Dynastic period mummies found their ABO frequencies to be most similar to that of modern Egyptians and northern Haratin populations in Western Africa.[2][3] Consequently, most DNA studies have been carried out on modern Egyptian populations with the intent of learning about the influences of historical migrations on the population of Egypt.[4][5][6][7] A study published in 1993 was performed on ancient mummies of the 12th Dynasty, which identified multiple lines of descent.[8]However, DNA grouping methods and classifications have attracted criticism in the view of some scholars for excluding data on African populations.[9]Barry Kemp has noted that DNA studies could only provide firm conclusions about the population of Ancient Egypt if the sample results featured a significant number of individuals, which represented a broad geographical and choronological range.[10]

2012 Ramesses III

In 2012 the 20th dynasty mummies of Ramesses III and another mummy "Unknown Man E" believed to be Ramesses III's son Pentawer were analyzed by Albert Zink, Yehia Z Gad and a team of researchers under Zahi Hawass, then Secretary General of the Supreme Council of Antiquities, Egypt. Genetic kinship analyses revealed identical haplotypes in both mummies using the Whit Athey's haplogroup predictor, the Y chromosomal haplogroup E1b1a (E-M2) was predicted.[11]

2017 DNA study
PCA and Admixture analysis of Ancient Egyptian samples and other modern and ancient populations.[12]

A study published in 2017 by an international team of scientists led by researchers from the University of Tuebingen and the Max Planck Institute for the Science of Human History in Jena described the extraction and analysis of DNA from 151 mummified ancient Egyptian individuals, whose remains were recovered from Abusir el-Meleq in Middle Egypt. Obtaining well-preserved, uncontaminated DNA from mummies has been a problem for the field of archaeogenetics and these samples provided "the first reliable data set obtained from ancient Egyptians using high-throughput DNA sequencing methods". The specimens were living in a period stretching from the late New Kingdom to the Roman era (1388 BCE–426 CE). Complete mitochondrial DNA (mtDNA) sequences were obtained for 90 of the mummies and were compared with each other and with several other ancient and modern datasets. The scientists found that the ancient Egyptian individuals in their own dataset possessed highly similar mitochondrial profiles throughout the examined period (pre Ptolemaic, Ptolemaic and Roman) and cluster close to each other in their analyses, supporting genetic continuity across the 1,300-year transect. Modern Egyptians generally shared this maternal haplogroup pattern, but also carried more African clades than Ancient Egyptians. A wide range of mtDNA haplogroups were found including clades of J,U,H,HV,M,R0,R2,K,T,L,I,N,X,W. The mtDNA analyses revealed higher affinities with modern populations from the Near East compared to modern Egyptians, possibly due to the increase in African lineages. 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.

Results from the limited 2017 study of 30 Egyptian mummies and their genetic affinity with other regional population groups in the Near East

Additionally, three of the ancient Egyptian mummified individuals were analysed for Y-DNA, two were assigned to West Asian J and one to haplogroup E1b1b1 both common in modern day Egyptians. The researchers cautioned that the affinities of the examined ancient Egyptian specimens may not be representative of those of all ancient Egyptians since they were from a single archaeological site.[12] Autosomal DNA analyses of these ancient Egyptian mummies did not find significant differences between the three ancient samples, supporting continuity across time. The analyses revealed a high affinity to near eastern populations. Modern Egyptians in comparison are more shifted toward sub-Saharan African populations.[12] "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".[12]

Estimations of the sub-Saharan African ancestry reveal that modern Egyptians inherit 8% more ancestry from sub-Saharan African ancestors than did the three ancient Egyptians. The absolute estimates of sub-Saharan African ancestry in these three individuals ranged from 6 to 15%, which is significantly lower than the level of sub-Saharan African ancestry in the modern Egyptians from Abusir el-Meleq, who "range from 14 to 21%." However, the study's authors cautioned that the mummies may be unrepresentative of the Ancient Egyptian population as a whole, since they were recovered from the northern part of Egypt.[12]

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"[12]

Later findings

In a 2020 ancient Genome wide DNA study on ancient samples from Lebanon, two individuals who lived around 500 BCE were found to be of Egyptian origin, sharing the genetic profile of Abusir el-Meleq ancient Egyptian samples. One of them formed a clade with ancient Egyptians, which implies sharing all ancestry with them or a genetically equivalent population. The other was found to have some local Levantine ancestry (~25%).[13]

2018 Nakht-Ankh and Khnum-Nakht

The tomb of two high-status Egyptians, Nakht-Ankh and Khnum-Nakht was discovered 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 was completely undisturbed prior to its excavation. 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. However, the inscriptions were less informative regarding the paternal filiation. Each mummy has a different physical morphology and in the DNA analysis by the University of Manchester differences between the Y chromosome SNPs indicate different paternal lineages concluding that Nakht-Ankh and Khnum-Nakht were half-brothers but Y chromosome sequences were not complete enough to determine paternal haplogroup. 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.[14]

2018 mitochondrial DNA of Djehutynakht

In 2018 an undated mummified head of Djehutynakht was discovered in Middle Egypt at Deir el-Bersha in 1915. Djehutynakht was a governor in the Middle Kingdom Egypt of the 11th or 12th Dynasty was analyzed for mitochondrial DNA. The sequence of the mummy most closely resembles a U5a lineage from sample JK2903, a much more recent 2000-year-old skeleton from the Abusir el-Meleq site in Egypt although no direct matches to the Djehutynakht sequence have been reported. The exact Djehutynakht's mitDNA haplogroup is U5b2b5, that before Djehutynakht has been only found in ancient DNA from Europe, although without any full match between the sequences of the ancient samples and Djehutynakht.[15] Haplogroup U5 is also found in modern-day Berbers from the Siwa Oasis in Egypt. A 2008 article by C. Coudray, The complex and diversified mitochondrial gene pool of Berber populations, recorded haplogroup U5 at 16.7% for the Siwa[16] whereas haplogroup U6 is more common in other Berber populations to the west of Egypt.

2020 Tutankhamun and other mummies of the 18th Dynasty

In 2020 Yehia Z Gad and other researchers of the Hawass team published results of an analysis of the mitochondrial and Y-chromosomal haplogroups of several mummies of 18th Dynasty Including Tutankhamun in the journal Human Molecular Genetics, Volume 30, Issue R1, 1 March 2021, Pages R24–R28,[17] Results were used to provide information about the phylogenetic groups of his family members and their presence among the reported contemporary Egyptian population data. The analysis confirmed previous data of the Tutankhamun's ancestry with multiple controls authenticating all results. However, the specific clade of R1b was not determined. Because the profiles for Tutankhamun and Amenhotep III were incomplete, the analysis produced differing probability figures despite having concordant allele results. Because the relationships of these two mummies with the KV55 mummy had previously been confirmed in an earlier study, the haplogroup prediction of both mummies could be derived from the full profile of the KV55 data. The proposed sibling relationship between Tutankhamun's parents, Akhenaten and the mummy known as the "younger lady" (KV35YL) is further supported. Genetic analysis indicated the following haplogroups:

2020 Paleogenetic Study of Ancient Mummies at the Kurchatov Institute

In 2020 three mummies, dating to the 1st millennium BCE, from the Pushkin Museum of Arts collection were tested at the Kurchatov Institute of Moscow for their mitochondrial and Y-chromosomal haplogroups. Two of the mummies were found to belong to Y-chromosomal haplogroups R1b1a1b and E1b1b1a1b2a4b5a and mtDNA haplogroups L3h1 and N5, respectively. The third mummy was found to belong to mtDNA haplogroup N.[18]

DNA studies on modern Egyptians

Genetic analysis of modern Egyptians reveals that they have paternal lineages common to other indigenous Afroasiatic-speaking populations in North Africa, West Asia, Anatolia and Horn of Africa; Some studies have proposed the view that these lineages would have spread into North Africa and Horn of Africa from Western Asia during the Neolithic Revolution and were maintained by the predynastic period.[19][20]

A study by Krings et al. (1999) on mitochondrial DNA clines along the Nile Valley found that a Eurasian cline runs from Northern Egypt to Southern Sudan and a Sub-Saharan cline from Southern Sudan to Northern Egypt derived from a sample size of 224 individuals. The study also found Egypt and Nubia have low and similar amounts of divergence for both mtDNA types, which is consistent with historical evidence for long-term interactions between Egypt and Nubia.[21]

Luis et al. (2004) found that the male haplogroups in a sample of 147 Egyptians were E1b1b (36.1%, predominantly E-M78), J (32.0%), G (8.8%), T(8.2%), and R (7.5%). E1b1b subclades are characteristic of some Afro-Asiatic speakers and are believed to have originated in either the Middle East, North Africa, or the Horn of Africa. Cruciani et al. (2007) suggests that E-M78, E1b1b predominant subclade in Egypt, originated in "Northeastern Africa", with a corridor for bidirectional migrations between northeastern and eastern Africa (at least 2 episodes between 23.9–17.3 ky and 18.0–5.9 ky ago), trans-Mediterranean migrations directly from northern Africa to Europe (mainly in the last 13.0 ky), and flow from northeastern Africa to western Asia between 20.0 and 6.8 ky ago.[22][23][24]

Other studies have shown that modern Egyptians have genetic affinities primarily with populations of North Africa, the Middle East and the Horn of Africa,[25][26][20][19] and to a lesser extent European populations.[27]

Some genetic studies done on modern Egyptians suggest a more distant relationship to sub-Saharan Africans[28] and a closer link to other North Africans.[20] In addition, some studies suggest lesser ties with populations in the Middle East, as well as some groups in southern Europe.[19] A 2004 mtDNA study of 58 upper Egyptians from Gurna found a genetic ancestral heritage to modern Northeast Africans such as the Ethiopian population, characterized by a high M1 haplotype frequency and a comparatively low L1 and L2 macrohaplogroup frequency of 20.6%. Another study links Egyptians in general with people from modern Eritrea and Ethiopia.[26][29]

Though there has been much debate of the origins of haplogroup M1 a 2007 study had concluded that M1 has West Asia origins not a Sub Saharan African origin, although the majority of the M1a lineages found outside and inside Africa had a more recent eastern Africa origin.[30] However, some authors have proposed the view that the M haplogroup developed in Africa before the 'Out of Africa' event around 50,000 years ago, and dispersed in Africa from East Africa 10,000 to 20,000 years ago.[31][32]A 2003 Y chromosome study was performed by Lucotte on modern Egyptians, with haplotypes V, XI, and IV being most common. Haplotype V is common among all North Africans and has a low frequency outside the North African region. Haplotypes V, XI, and IV are all predominantly North African/Horn of African haplotypes, and they are far more dominant in Egyptians than in Middle Eastern or European groups.[6]

Y-DNA haplogroups

A study using the Y-chromosome of modern Egyptian males found similar results, namely that sub-Saharan African haplogroups are much more predominant in the South, but the haplogroups in the North are characteristic of African as well as West Eurasian populations.[33]

Population Nb A/B E1b1a E1b1b1

(M35)

 E1b1b1a

(M78)

 E1b1b1b

(M81)

 E1b1b1c

(M123,M34)

 F K G I J1 J2 R1a R1b Other Study
Egyptians (sample includes people labeled as “berber” and people from the oases) 370 1.35% 2.43% 3.24% 21.89% 11.89% 6.76% 1.08% 0.27% 5.68% 0.54% 20.81% 6.75% 2.16% 5.94% 9.21% Bekada et al. (2013)[34]
Egyptians (sample includes people labaled as “berber”)1472.7%2.7%018.4%5.4%008.2%8.8%019.7%12.2%3.4%4.1%2.1%Luis et al. (2004)[22]
Egyptians from El-Hayez Oasis (Western Desert)3505.70%5.7%28.6%28.6%0000031.4%0000Kujanová et al. (2009)[35]
Berbers from Siwa Oasis (Western Desert)9328.0%6.5%2.2%6.5%3.3%0003.2%07.5%6.5%028.0%8.3%Dugoujon et al. (2009)[36]
Northern Egyptians442.3%04.5%27.3%11.3%06.8%2.3%009.1%9.1%2.3%9.9%6.8%Arredi et al. (2004)
Southern Egyptians290.0%0017.2%6.8%017.2%10.3%03.4%20.7%3.4%013.8%0Arredi et al. (2004)
Distribution of E1b1b1a (E-M78) and its subclades
Population N E-M78 E-M78* E-V12* E-V13 E-V22 E-V32 E-V65 Study
Egyptians (sample includes people labeled as “berber” and people from the oases) 370 21.89% 0.81% 7.03% 0.81% 9.19% 1.62% 2.43% Bekada et al. (2013)[34]
Southern Egyptians7950.6%44.3%1.3%3.8%1.3%Cruciani et al. (2007)[37]
Egyptians from Bahari4141.4%14.6%2.4%21.9%2.4%Cruciani et al. (2007)
Northern Egyptians (Delta)7223.6%5.6%1.4%13.9%2.8%Cruciani et al. (2007)
Egyptians from Gurna Oasis3417.6%5.9%8.8%2.9%Cruciani et al. (2007)
Egyptian from Siwa Oasis936.4%2.1%4.3%Cruciani et al. (2007)
Frequency of haplogroup E and proposed migration according to Cole et al. 2020 and Bergström et al. 2021.

Mitochondrial DNA

In 2009 Mitochondrial data was sequenced for 277 unrelated Egyptian individuals[38] by Jessica L Saunier et al. in the journal Forensic Science International, as follows

  • R0 and its subgroups (31.4%)
  • L3 (12.3%); and Asian origin (n = 33)

including M (6.9%)

  • T (9.4%)
  • U (9.0%)
  • J (7.6%)
  • N (5.1%)
  • K (4.7%)
  • L2 (3.6%)
  • L1 (2.5%)
  • I (3.2%)
  • W (0.7%)
  • X (1.4%); African origin (n = 57) including L0 (2.2%)

Autosomal DNA

In a 2019 study that analyzed the autosomal make-up of 21 modern North African genomes and other populations using Ancient DNA reference populations, this sample of Egyptian genomes were found to share more affinity with Middle Eastern populations compared to other North Africans. Egyptians carry more of the Caucasus hunter gatherer / Iran Neolithic component compared to other North Africans, more of the Natufian related component and less of the Iberomaurusian related component than other North Africans, and also less of the Steppe / European hunter gatherer component. consistent with Egypt's geographical proximity to southwest Asia.[39]

Mohamed, T et al. (2009) in their study of nomadic Bedouins featured a comparative study with a worldwide population database and a sample size of 153 Bedouin males. Their analysis discovered that both Muslim Egyptians, and Christians (Copts) showed a distinct North African cluster at 65%. This is their predominant ancestral component, and unique to the geographic region of Egypt.[40]

Babiker, H et al. (2011) examined the genotypes of 498 individuals from 18 Sudanese populations and featured comparative genotype data with Egypt, Somalia and the Karamoja population from Uganda. Overall, the results showed that the genotypes of individuals from northern Sudan clustered with those of Egypt, the Somali population was found to be genetically distinct and individuals from southern Sudan clustered with those from the Karamoja population. The study determined that similarity of the Nubian and Egyptian populations suggested that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.[41]

Coptic Christians of Sudan

According to Y-DNA analysis by Hassan et al. (2008), 45% of Copts in Sudan (of a sample of 33) carry haplogroup J1. Next most common was E1b1b, the most common haplogroup in North Africa. Both paternal lineages are common among other regional Afroasiatic-speaking populations, such as Beja, Ethiopians, and Sudanese Arabs, as well as non-Afroasiatic-speaking Nubians.[42] E1b1b reaches its highest frequencies among North African and Horn of Africa populations such as Amazighs and Somalis.[43] The next most common haplogroups borne by Copts are R1b (15%), most common in Europe, and the widespread African haplogroup B (15%). According to the study, the presence of haplogroup B may also be consistent with the historical record in which southern Egypt was colonized by Nilotic populations during the early state formation.[42]

Maternally, Hassan (2009) found that the majority of Copts in Sudan (of a sample of 29) carried descendants of the macrohaplogroup N; of these, haplogroup U6 was most frequent (28%), followed by T1 (17%). In addition, Copts carried 14% M1 and 7% L1c.[44]

A 2015 study by Dobon et al. identified an ancestral autosomal component of West Eurasian origin that is common to many modern Afroasiatic-speaking populations in Northeast Africa. Known as the Coptic component, it peaks among Egyptian Copts who settled in Sudan over the past two centuries. Copts also formed a separated group in PCA, a close outlier to other Egyptians, Afroasiatic-speaking Northeast Africans and Middle East populations. The Coptic component evolved out of a main North African and Middle Eastern ancestral component that is shared by other Egyptians and also found at high frequencies among other Afroasiatic-speaking populations in Northeast Africa (~70%), who carry a Nilo-Saharan element as well. The scientists suggest that this points to a common origin for the general population of Egypt.[45] They also associate the Coptic component with Ancient Egyptian ancestry, without the later Arabic influence that is present among other Egyptians, especially people of the Sinai.[45]

In another 2017 study that genotyped and analyzed the same populations including Sudanese Copts and Egyptians, The ADMIXTURE analyses and the PCA displayed the genetic affinity of the Copts to the Egyptian population. Assuming few clusters, the Copts appeared admixed between Near Eastern/European populations and northeastern Sudanese and look similar in their genetic profile to the Egyptians. Assuming greater number of clusters (K≥18), the Copts formed their own separate ancestry component that was shared with Egyptians but can also be found in Arab populations. The authors commented that This behavior in the admixture analyses is consistent with shared ancestry between Copts and Egyptians and/or additional genetic drift in the Copts. The Egyptians and Copts showed low levels of genetic differentiation (FST = 0.00236), lower levels of genetic diversity and greater levels of RoH compared to other northeast African groups, including Arab and Middle Eastern groups that share ancestry with the Copts and Egyptians. A formal test (D(Ju|’hoansi,X;Egypt,Copt)), did not find significant admixture into the Egyptians from other tested groups (X), and the Copts and Egyptians displayed similar levels of European or Middle Eastern ancestry Taken together, the study suggests these results point to that the Copts and the Egyptians have a common history linked to smaller population sizes.[46]

See also

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