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. E1b1b/E3b reaches its highest frequencies among North Africans, Levantine Middle Easterners, and Ethiopid East Africans. The next most common haplogroups borne by Copts are the 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 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%).
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 scientists suggest that this points to a common origin for the general population of Egypt or middle eastern and North African populations. The study says “Copts share the same main ancestral component than North African and Middle East populations (dark blue), supporting a common origin with Egypt (or other North African/Middle Eastern populations). They are known to be the most ancient population of Egypt and at k = 4 (Fig.3), they show their own component (dark green) different from the current Egyptian population which is closer to the Arabic population of Qatar.” This supports that Copts have common origin with Egypt or other North African/Middle Eastern populations. This supports that Copts originate from same ancestors as North African and Middle Eastern or Egypt. They also associate the Coptic component with Ancient Egyptian ancestry, without the later Arabian influence that is present among other Egyptians.
Hollfelder et al. (2017) analysed various populations in Sudan and observed that Egyptians and Copts showed low levels of genetic differentiation and lower levels of genetic diversity compared to northeast African groups. Copts and Egyptians displayed similar levels of European or Middle Eastern ancestry (Copts were estimated to be of 69.54% ± 2.57 European ancestry and the Egyptians of 70.65% ± 2.47 European ancestry). The authors concluded that the Copts and the Egyptians have a common history linked to smaller population sizes, and that Sudanese Copts have remained relatively isolated since their arrival to Sudan with only low levels of admixture with local northeastern Sudanese groups.
An allele frequency comparative study across 9 nine between the two main Egyptian ethnic groups, Muslims and Christians, supported the conclusion that Egyptian Muslims and Egyptian Christians genetically originate from the same ancestors. This is consistent with the Dobon 2015 study which says “Copts share the same main ancestral component than North African and Middle East populations (dark blue), supporting a common origin with Egypt (or other North African/Middle Eastern populations). They are known to be the most ancient population of Egypt and at k = 4 (Fig.3), they show their own component (dark green) different from the current Egyptian population which is closer to the Arabic population of Qatar.” This supports that Copts have common origin with Egypt or other North African/Middle Eastern populations. This supports that Copts originate from same ancestors as North African and Middle Eastern or Egypt. Copts originate from the same ancestors as Egyptians or North African/Middle Eastern populations and thus have an ancestral overlap with these populations. At the same time K = 4 to K = 5 ( Fig. 3) shows the Coptic component (Dark Green) makes up most of Copts distribution and peaks highest among Copts while the Middle Eastern/North African component(Dark blue) makes up most of Egypt and Qatar distribution at K = 4 to K = 5. K = 2 to K = 5 also shows that the Egypt distribution resembles Qatar more than it does Copts.