The genetic history of the demographics of Egypt reflects Egypt's geographical location at the crossroads of several major biocultural areas: Northeast Africa, Northwest Africa, Southwest Asia, the Sahara, Sub-Saharan Africa, the Middle East, and the Mediterranean.
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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. One successful 1993 study was performed on ancient mummies of the 12th Dynasty, by Dr. Svante Pääbo and Dr. Anna Di Rienzo, which identified multiple lines of descent, some of which originated in Sub-Saharan Africa.
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 some also to northern Haratin populations.
DNA studies on modern Egyptians
Genetic analysis of modern Egyptians reveals that they have paternal lineages common to indigenous other Afro-Asiatic-speaking populations in Northeast and Northwest Africa (Maghreb and Horn of Africa), and to Middle Eastern peoples to a lesser extent—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 and its 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 Asia, North and Northeast Africa, and to a lesser extent Middle Eastern and 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 recent 2007 study had concluded that M1 has West Asia origins not a Sub Saharan African 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
On 13 January 2012, an exhaustive genetic study of North Africa's human populations was published. The researchers analyzed around 800,000 genetic markers, distributed throughout the entire genome in 125 North African individuals belonging to seven representative populations in the whole region (Saharawi, South Moroccans, North Moroccans, Algerians, Tunisians Berbers, Libyans and Egyptians) and the information obtained was compared with the information from the neighbouring populations. The results of this study show that there is a native genetic component ("Maghrebi") which defines North Africans. The study identified mainly two distinct, opposite gradients of ancestry: an east-to-west increase of this native North African ancestry and an east-to-west decrease in likely Middle Eastern Arab ancestry.
The study also reveals that the genetic composition of North Africa's human populations is very complex and is the result of five distinct ancestries : a local component (Maghrebi) dating back thirteen thousand years and the varied genetic influence of neighbouring populations on North African groups during successive migrations (European, Middle Eastern, eastern and western Sub-Saharan Africa). According to the authors, the people inhabiting North Africa today are not descendants of either the earliest occupants of this region fifty thousand years ago, or descendants of the most recent Neolithic populations. The data shows that the ancestors of today's North Africans were a group of populations which already lived in the region around thirteen thousand years ago. Furthermore, this local North African genetic component is very different from the one found in the populations in the south of the Sahara, which shows that the ancestors of today's North Africans were members of a subgroup of humanity who left Africa to conquer the rest of the world and who subsequently returned to the north of the continent to settle in the region. As well as this local component, North African populations were also observed to share genetic markers with all the neighbouring regions, as a result of more recent migrations, although these appear in different proportions. There is an influence from the Middle East, which becomes less marked as the distance from the Arabian Peninsula increases, similar proportions of European influence in all North African populations, and, in some populations (South Moroccans, Saharawi...), there are even individuals who present a large proportion of recent influence from the South of the Sahara in their genome.
Admixture analysis
Recent genetic analysis of North African populations have found that, despite the complex admixture genetic background, there is an autochthonous genomic component which is likely derived from "back-to-Africa" gene flow older than 12,000 years ago (ya) (i.e., prior to the Neolithic migrations). This local population substratum seems to represent a genetic discontinuity with the earliest modern human settlers of North Africa (those with the Aterian industry) given the estimated ancestry is younger than 40,000 years ago. North Morocco, Libya and Egypt carry high proportions of European and Middle Eastern ancestral components, whereas Tunisian Berbers and Saharawi are those populations with highest autochthonous North African component.
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 Afro-Asiatic-speaking populations (Beja, Ethiopians, Sudanese Arabs), as well as many Nubians. E1b1b/E3b reaches its highest frequencies among Berbers and Somalis. 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%).
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 Afro-Asiatic-speaking populations, including Berbers and Ethiopic peoples. Of the N derivatives borne by Copts, U6 is most frequent (28%), followed by the haplogroup T (17%).
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, Afro-Asiatic-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 Afro-Asiatic-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 Arabian influence that is present among other Egyptians.