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.

Ancient DNA

Contamination from handling and intrusion from microbes create obstacles to the recovery of ancient DNA.[1] 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.[2][3][4][5] A study published in 1993 was performed on ancient mummies of the 12th Dynasty, which identified multiple lines of descent.[6]

In 2013, Khairat et al. conducted the first genetic study utilizing next-generation sequencing to ascertain the ancestral lineage of an Ancient Egyptian individual. The researchers extracted DNA from the heads of five Egyptian mummies that were housed at the institution. All the specimens were dated to between 806 BCE and 124 CE, a timeframe corresponding with the Late Dynastic and Ptolemaic periods. The researchers observed that one of the mummified individuals likely belonged to the mtDNA haplogroup I2, a maternal clade that is believed to have originated in Western Asia.[7]

A study published in 2017 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. Modern Egyptians generally shared this maternal haplogroup pattern, but also carried more Sub-Saharan African clades. However, analysis of the mummies' mtDNA haplogroups found that they shared greater mitochondrial affinities with modern populations from the Near East and the Levant compared to modern Egyptians. Additionally, three of the ancient Egyptian individuals were analysed for Y-DNA, two were assigned to the Middle-Eastern haplogroup J and one to haplogroup E1b1b1 common in North Africa. 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.[8]

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.[9]

DNA studies on modern Egyptians

Genetic analysis of modern Egyptians reveals that they have paternal lineages common to other indigenous Afroasiatic-speaking populations in Maghreb and Horn of Africa, and to Middle Eastern peoples, these lineages would have spread during the Neolithic and were maintained by the predynastic period.[10][11]

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.[12]

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", which in the study refers specifically to Egypt and Libya[13][14]

Other studies have shown that modern Egyptians have genetic affinities primarily with populations of Asia, North and Horn of Africa,[15][16][11][10] and to a lesser extent Middle Eastern and European populations.[17]

Some genetic studies done on modern Egyptians suggest a more distant relationship to Sub Saharan Africans.[18] and a closer link to other North Africans.[11] In addition, some studies suggest lesser ties with populations in the Middle East, as well as some groups in southern Europe.[10] A 2004 mtDNA study of upper Egyptians from Gurna found a genetic ancestral heritage to modern Northeast Africans, 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.[16][19] Though there has been much debate of the origins of haplogroup M1 a recent 2007 study had concluded that M1 has West Asia origins not a Sub Saharan African origin[20] Origin 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 in Berbers and has a low frequency outside North Africa. 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.[4]

Y-DNA haplogroups

A study using the Y-chromosome of modern Egyptian males found similar results, namely that North East African haplogroups are predominant in the South but the predominant haplogroups in the North are characteristic of North African and West Eurasian populations.[21]

Population Nb A/B E1b1a E1b1b1 (M35) E1b1b1a (M78) E1b1b1b (M81) E1b1b1c (M123) F K G I J1 J2 R1a R1b Other Study
Egyptians 360 1.3% 2.4% 3.2% 21.8% 11.8% 6.7% 1% 0.2% 5.6% 0.5% 20.8% 6.7% 2.1% 5.9% 10% Bekada et al. (2013)[22]
Egyptians1472.7%2.7%018.4%8.2%9.5%07.5%9.5%019.7%12.2%3.4%4.1%2.1%Luis et al. (2004)[13]
Egyptians from El-Hayez Oasis (Western Desert)3505.70%5.7%28.6%28.6%0000031.4%0000Kujanová et al. (2009)[23]
Egyptians from Siwa Oasis (Western Desert)9328.0%6.5%2.2%6.5%1.1%2.2%003.2%07.5%6.5%028.0%8.3%Dugoujon et al. (2009)[24]
Northern Egyptians442.3%04.5%27.3%11.4%9.1%6.8%2.3%009.1%9.1%2.3%9.9%6.8%Arredi et al. (2004)
Southern Egyptians290.0%0017.2%6.9%6.9%17.2%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 360 21.8% 0.8% 7% 0.8% 7% 1.6% 2.4% Bekada et al. (2013)[22]
Southern Egyptians7950.6%44.3%1.3%3.8%1.3%Cruciani et al. (2007)[25]
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)

Autosomal DNA

Genomic analysis has found that Berber and other Maghreb communities are defined by a shared ancestral component. This Maghrebi element peaks among Tunisian Berbers.[26] It is related to the Coptic ancestral component (see Copts), having diverged from these and other West Eurasian-affiliated components prior to the Holocene.[27][28]

North Moroccans as well as Libyans and Egyptians carry higher proportions of European and Middle Eastern ancestral components, respectively, whereas Tunisian Berbers and Saharawi are those populations with the highest autochthonous North African component.[29]

Copts

According to Y-DNA analysis by Hassan et al. (2008), around 45% of Copts in Sudan carry the haplogroup J. The remainder mainly belong to the E1b1b clade (21%). Both paternal lineages are common among other local Afroasiatic-speaking populations (Beja, Ethiopians, Sudanese Arabs), as well as many Nubians.[30] E1b1b/E3b reaches its highest frequencies among Berbers and Somalis.[31] The next most common haplogroups borne by Copts are the Western European-linked R1b clade (15%), as well as the archaic African B lineage (15%).[30]

Maternally, Hassan (2009) found that Copts in Sudan exclusively carry various descendants of the macrohaplogroup N. This mtDNA clade is likewise closely associated with local Afroasiatic-speaking populations, including Berbers and Ethiopid peoples. Of the N derivatives borne by Copts, U6 is most frequent (28%), followed by the haplogroup T (17%).[32]

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 Northeast 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%). The scientists suggest that this points to a common origin for the general population of Egypt.[27] They also associate the Coptic component with Ancient Egyptian ancestry, without the later Arabian influence that is present among other Egyptians.[33]

See also

References

  1. ↑ Encyclopedia of the Archaeology of Ancient Egypt By Kathryn A. Bard, Steven Blake Shubert pp 278-279
  2. ↑ Keita SO, Boyce AJ (June 2009). "Genetics, Egypt, and History: Interpreting Geographical Patterns of Y Chromosome Variation". History in Africa. 32 (1): 221–246. doi:10.1353/hia.2005.0013.
  3. ↑ Shomarka Keita (2005), S. O. Y. (2005). "Y-Chromosome Variation in Egypt". African Archaeological Review. 22 (2): 61–75. doi:10.1007/s10437-005-4189-4.
  4. 1 2 Keita SO (2005). "History in the interpretation of the pattern of p49a,f TaqI RFLP Y-chromosome variation in Egypt: a consideration of multiple lines of evidence". American Journal of Human Biology. 17 (5): 559–67. doi:10.1002/ajhb.20428. PMID 16136533.
  5. ↑ Shomarka Keita: What genetics can tell us
  6. ↑ Paabo S, Di Rienzo A (1993). "A molecular approach to the study of Egyptian history.". In Davies V, Walker R. Biological Anthropology and the Study of Ancient Egypt. London: British Museum Press. pp. 86–90.
  7. ↑ Khairat R, Ball M, Chang CC, Bianucci R, Nerlich AG, Trautmann M, Ismail S, Shanab GM, Karim AM, Gad YZ, Pusch CM (August 2013). "First insights into the metagenome of Egyptian mummies using next-generation sequencing". Journal of Applied Genetics. 54 (3): 309–25. doi:10.1007/s13353-013-0145-1. PMID 23553074.
  8. ↑ Schuenemann VJ, Peltzer A, Welte B, van Pelt WP, Molak M, Wang CC, Furtwängler A, Urban C, Reiter E, Nieselt K, Teßmann B, Francken M, Harvati K, Haak W, Schiffels S, Krause J (May 2017). "Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods". Nature Communications. 8: 15694. doi:10.1038/ncomms15694. PMID 28556824.
  9. ↑ Borgognini Tarli SM, Paoli G (1982). "Survey on paleoserological studies". Homo. 33: 69–89.
  10. 1 2 3 Manni F, Leonardi P, Barakat A, Rouba H, Heyer E, Klintschar M, McElreavey K, Quintana-Murci L (October 2002). "Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa". Human Biology. 74 (5): 645–58. doi:10.1353/hub.2002.0054. PMID 12495079.
  11. 1 2 3 Arredi B, Poloni ES, Paracchini S, Zerjal T, Fathallah DM, Makrelouf M, Pascali VL, Novelletto A, Tyler-Smith C (August 2004). "A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa". American Journal of Human Genetics. 75 (2): 338–45. doi:10.1086/423147. PMC 1216069. PMID 15202071.
  12. ↑ Krings M, Salem AE, Bauer K, Geisert H, Malek AK, Chaix L, Simon C, Welsby D, Di Rienzo A, Utermann G, Sajantila A, Pääbo S, Stoneking M (April 1999). "mtDNA analysis of Nile River Valley populations: A genetic corridor or a barrier to migration?" (PDF). American Journal of Human Genetics. 64 (4): 1166–76. doi:10.1086/302314. PMC 1377841. PMID 10090902.
  13. 1 2 Luis JR, Rowold DJ, Regueiro M, Caeiro B, Cinnioğlu C, Roseman C, Underhill PA, Cavalli-Sforza LL, Herrera RJ (March 2004). "The Levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations". American Journal of Human Genetics. 74 (3): 532–44. doi:10.1086/382286. PMC 1182266. PMID 14973781.
  14. ↑ Underhill (2002), Bellwood and Renfrew, ed., Inference of Neolithic Population Histories using Y-chromosome Haplotypes, Cambridge: McDonald Institute for Archaeological Research, ISBN 978-1-902937-20-5.
  15. ↑ Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, Pennarun E, Parik J, Geberhiwot T, Usanga E, Villems R, et al. (November 2004). "Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears". American Journal of Human Genetics. 75 (5): 752–70. doi:10.1086/425161. PMC 1182106. PMID 15457403.
  16. 1 2 Stevanovitch A, Gilles A, Bouzaid E, Kefi R, Paris F, Gayraud RP, Spadoni JL, El-Chenawi F, Béraud-Colomb E, et al. (January 2004). "Mitochondrial DNA sequence diversity in a sedentary population from Egypt". Annals of Human Genetics. 68 (Pt 1): 23–39. doi:10.1046/j.1529-8817.2003.00057.x. PMID 14748828.
  17. ↑ Luca Cavalli-Sforza L, Menozzi P, Piazza A (1996-08-05). The History and Geography of Human Genes. Princeton University Press. ISBN 978-0-691-02905-4.
  18. ↑ Cavalli-Sforza, L.L., P. Menozzi, and A. Piazza. 1994, The History and Geography of Human Genes. Princeton:Princeton University Press,
  19. ↑ Kivisild T, et al. (November 2004). "Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears". American Journal of Human Genetics. 75 (5): 752–70. doi:10.1086/425161. PMC 1182106. PMID 15457403.
  20. ↑ González AM, Larruga JM, Abu-Amero KK, Shi Y, Pestano J, Cabrera VM (July 2007). "Mitochondrial lineage M1 traces an early human backflow to Africa". BMC Genomics. 8: 223. doi:10.1186/1471-2164-8-223. PMC 1945034. PMID 17620140.
  21. ↑ Lucotte G, Mercier G (May 2003). "Brief communication: Y-chromosome haplotypes in Egypt". American Journal of Physical Anthropology. 121 (1): 63–6. doi:10.1002/ajpa.10190. PMID 12687584.
  22. 1 2 Bekada A, Fregel R, Cabrera VM, Larruga JM, Pestano J, Benhamamouch S, González AM (2013-02-19). "Introducing the Algerian mitochondrial DNA and Y-chromosome profiles into the North African landscape". PLOS One. 8 (2): e56775. doi:10.1371/journal.pone.0056775. PMC 3576335. PMID 23431392.
  23. ↑ Kujanová M, Pereira L, Fernandes V, Pereira JB, Cerný V (October 2009). "Near eastern neolithic genetic input in a small oasis of the Egyptian Western Desert". American Journal of Physical Anthropology. 140 (2): 336–46. doi:10.1002/ajpa.21078. PMID 19425100.
  24. ↑ Dugoujon J.M., Coudray C., Torroni A., Cruciani F., Scozzari F., Moral P., Louali N., Kossmann M. The Berber and the Berbers: Genetic and linguistic diversities
  25. ↑ Cruciani F, La Fratta R, Trombetta B, Santolamazza P, Sellitto D, Colomb EB, Dugoujon JM, Crivellaro F, Benincasa T, Pascone R, Moral P, Watson E, Melegh B, Barbujani G, Fuselli S, Vona G, Zagradisnik B, Assum G, Brdicka R, Kozlov AI, Efremov GD, Coppa A, Novelletto A, Scozzari R (June 2007). "Tracing past human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12". Molecular Biology and Evolution. 24 (6): 1300–11. doi:10.1093/molbev/msm049. PMID 17351267.
  26. ↑ Henn BM, Botigué LR, Gravel S, Wang W, Brisbin A, Byrnes JK, Fadhlaoui-Zid K, Zalloua PA, Moreno-Estrada A, Bertranpetit J, Bustamante CD, Comas D (January 2012). "Genomic ancestry of North Africans supports back-to-Africa migrations". PLoS Genetics. 8 (1): e1002397. doi:10.1371/journal.pgen.1002397. PMC 3257290. PMID 22253600.
  27. 1 2 Dobon B, Hassan HY, Laayouni H, Luisi P, Ricaño-Ponce I, Zhernakova A, Wijmenga C, Tahir H, Comas D, Netea MG, Bertranpetit J (May 2015). "The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape" (PDF). Scientific Reports. 5: 9996. doi:10.1038/srep09996. PMC 4446898. PMID 26017457.
  28. ↑ Hodgson JA, Mulligan CJ, Al-Meeri A, Raaum RL (June 2014). "Early back-to-Africa migration into the Horn of Africa". PLoS Genetics. 10 (6): e1004393. doi:10.1371/journal.pgen.1004393. PMC 4055572. PMID 24921250. ; "Supplementary Text S1: Affinities of the Ethio-Somali ancestry component". doi:10.1371/journal.pgen.1004393.s017. Retrieved 21 April 2016.
  29. ↑ Sánchez-Quinto F, Botigué LR, Civit S, Arenas C, Avila-Arcos MC, Bustamante CD, Comas D, Lalueza-Fox C (2012). "North African populations carry the signature of admixture with Neandertals". PLOS One. 7 (10): e47765. doi:10.1371/journal.pone.0047765. PMC 3474783. PMID 23082212.
  30. 1 2 Hassan HY, Underhill PA, Cavalli-Sforza LL, Ibrahim ME (November 2008). "Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history" (PDF). American Journal of Physical Anthropology. 137 (3): 316–23. doi:10.1002/ajpa.20876. PMID 18618658.
  31. ↑ Trombetta B, D'Atanasio E, Massaia A, Ippoliti M, Coppa A, Candilio F, Coia V, Russo G, Dugoujon JM, Moral P, Akar N, Sellitto D, Valesini G, Novelletto A, Scozzari R, Cruciani F (June 2015). "Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent" (PDF). Genome Biology and Evolution. 7 (7): 1940–50. doi:10.1093/gbe/evv118. PMID 26108492. ; Supplementary Table 7 Archived 2016-12-26 at the Wayback Machine.
  32. ↑ Mohamed, Hisham Yousif Hassan. "Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan" (PDF). University of Khartoum. Retrieved 13 October 2016.
  33. ↑ Dobon B, Hassan HY, Laayouni H, Luisi P, Ricaño-Ponce I, Zhernakova A, Wijmenga C, Tahir H, Comas D, Netea MG, Bertranpetit J (May 2015). "The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape" (PDF). Scientific Reports. 5: 9996. doi:10.1038/srep09996. PMC 4446898. PMID 26017457. The North African/Middle Eastern genetic component is identified especially in Copts. The Coptic population present in Sudan is an example of a recent migration from Egypt over the past two centuries. They are close to Egyptians in the PCA, but remain a differentiated cluster, showing their own component at k = 4 (Fig. 3). Copts lack the influence found in Egyptians from Qatar, an Arabic population. It may suggest that Copts have a genetic composition that could resemble the ancestral Egyptian population, without the present strong Arab influence.
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