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. 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. A study published in 1993 was performed on ancient mummies of the 12th Dynasty, which identified multiple lines of descent.
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.
2017 DNA study.
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.
The study was able to measure the mitochondrial DNA of 90 individuals, and it showed that the mitochondrial DNA composition of Egyptian mummies has shown a high level of affinity with the DNA of the populations of the Near East. A shared drift and mixture analysis of the DNA of these ancient Egyptian mummies shows that the connection is strongest with ancient populations from the Levant, the Near East and Anatolia, and to a lesser extent modern populations from the Near East and the Levant. In particular the study finds "that ancient Egyptians are most closely related to Neolithic and Bronze Age samples in the Levant, as well as to Neolithic Anatolian and European populations". However, the study showed that comparative data from a contemporary population under Roman rule in Asia Minor, did not reveal a closer relationship to the ancient Egyptians from the same period. furthermore, "Genetic continuity between ancient and modern Egyptians cannot be ruled out despite this sub-Saharan African influx, while continuity with modern Ethiopians is not supported".
Genome-wide data could only be successfully extracted from three of these individuals. Of these three, the Y-chromosome haplogroups of two individuals could be assigned to the Middle-Eastern haplogroup J, and one to haplogroup E1b1b1 common in North Africa. 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, who "range from 14 to 21%."( When using East African admixed population as reference) 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.
The data suggest a high level of genetic interaction with the Near East since ancient times, probably going back to Prehistoric Egypt: "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"
Professor Stephen Quirke, an Egyptologist at University College London, expressed caution about the researchers’ broader claims, saying that “There has been this very strong attempt throughout the history of Egyptology to disassociate ancient Egyptians from the modern population.” He added that he was “particularly suspicious of any statement that may have the unintended consequences of asserting – yet again from a northern European or North American perspective – that there’s a discontinuity there [between ancient and modern Egyptians]".
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.
2020 DNA analysis by Zahi Hawass' researchers, Egypt.
Analysis of the mitochondrial and Y-chromosomal haplogroups of several mummies of 18th Dynasty Including Tutankhamun was 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. The proposed sibling relationship between Tutankhamun’s parents, Akhenaten and the mummy known as the "younger lady" (KV35YL) is further supported. Population genetics point to a common origin at ca. 14.000–28.000 years before present.
Genetic analysis indicated the following haplogroups:
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.
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.
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
Other studies have shown that modern Egyptians have genetic affinities primarily with populations of North Africa, the Middle East and the Horn of Africa, and to a lesser extent European populations.
Some genetic studies done on modern Egyptians suggest a more distant relationship to Sub Saharan Africans and a closer link to other North Africans. In addition, some studies suggest lesser ties with populations in the Middle East, as well as some groups in southern Europe. 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. 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 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.
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.
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. It is related to the Coptic ancestral component (see Copts), having diverged from these and other West Eurasian-affiliated components prior to the Holocene.
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.
A recent genetic study published in the "European Journal of Human Genetics" in Nature (2019) showed that Northern Africans are closely related to Europeans and West Asians as well as to Southwest Asians. Northern Africans can clearly be distinguished from West Africans and other African populations dwelling south of the Sahara.
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. E1b1b reaches its highest frequencies among native populations such as Amazighs and Somalis. The next most common haplogroups borne by Copts are R1b (15%), most common in Europe, and the widespread African haplogroup B (15%).
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.
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. 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.