PRESENT-DAY EGYPTIANS ARE GENETICALLY DIFFERENT FROM THE ANCIENT EGYPTIANS – AN IMPORTANT RESEARCH REVEALS

One of the researches obtaining a sample from a jaw bone of one of the Egyptian mummies

In 2017 an important study was published in Nature Communications under the title ‘Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods’.[1] Outside Egypt, it received much attention (see, e.g. CNN: DNA discovery reveals genetic history and Independent: Ancient Egyptians more closely related to Europeans than modern Egyptians, scientists claim); inside Egypt, it has been wilfully ignored or suppressed. The main findings of the study, which changed inaccurate perceptions, are:

1. The Ancient Egyptians mummies from which DNA was extracted and analysed, and who lived in Abusir el-Meleq (see below), in Middle Egypt in the period (1388 BC, New Kingdom – 426 AD, Roman Age) show similar mitochondrial DNA profiles, pointing to genetic continuity during that long period and no mix with foreigners, Libyans, Kushites, Assyrians, Persians, Greeks and Romans, who occupied Egypt following the fall of the New Kingdom in c. 1000 BC. As Dr Wolfgang Haak (one of the research contributors) has explained: “The genetics of the Abusir el-Meleq community did not undergo any major shifts during the 1300-year timespan … studied, suggesting that the population remained genetically relatively unaffected by foreign conquest and rule.”[2]

2. The ancient Egyptians were genetically distinct from the modern Egyptians. The genome of the mummified individuals contains almost no sub-Saharan DNA that dominates the genetic profile of modern Egyptians. Possible reasons for the high sub-Saharan ancestry in modern Egyptians include:
   1. Increased mobility down the Nile and increased long-distance commerce between sub-Saharan Africa and Egypt.
   2. The trans-Saharan slave trade is known to have moved between 6 and 7 million sub-Saharan slaves to Northern Africa, including Egypt, over a span of some 1250 years, reaching its high point in the nineteenth century.

3. The ancient Egyptians whose mummies were studied were closer towards Near Eastern and European samples. “Our analyses,” wrote the researchers “reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians.” And they added: “We find that ancient Egyptians are most closely related to Neolithic [started 1000 BC by the invention of agriculture and fixed human settlements] and Bronze Age [in the Near East, this historical age that knew bronze and writing extended from 3300 to1200 BC] samples in the Levant, as well as to Neolithic Anatolian and European populations.” “When comparing this pattern with modern Egyptians, we find that the ancient Egyptians are more closely related to all modern and ancient European populations that we tested, likely due to the additional African component in the modern population.”

The study was led by Verena J. Schuenemann, a professor from The Institute for Archaeological Sciences, University of Tübingen, Germany, and fifteen other prominent scientists contributed to it: from other German institutions and non-German institutions (Cambridge University, UK; University of Adelaide, Australia; and the Polish Academy of Sciences, Poland). For the first time the researchers were able to obtain uncontaminated full genome sequences of Ancient Egyptians. This they did by carefully sampling bones and teeth in the mummies. Previous attempts to do that were thwarted by contamination of the samples and degradation of materials obtained from soft tissues such as muscles, and such studies were, therefore, unreliable.

The mummies were taken from an archaeological site on the River Nile, Abusir el-Meleq (أبو صير الملق),[3] in Middle Egypt, which was inhabited from 3250 BC to 700 AD, until it was destroyed after the Arab Conquest. It was an important religious and trading centre in ancient Egypt where Osiris, the god of the dead, was worshipped, and where many Egyptians from across Egypt loved to be buried. From the mummies, which represented the complete spectrum of society, the scientists, using high-throughput DNA sequencing methods, obtained:[4]

1. Ninety complete Mitochondrial DNA (mtDNA) genomes from 90 individuals who lived during that lengthy period (1388 BC – 426 AD). The mtDNA is passed through the female line.
2. Three genome-wide SNA data from three male individuals who lived between 1300 BC (in the late New Kingdom) and 30 BC (around the beginning of the Roman Period). This nuclear data is significant because, at its most simple, it is inherited from all ancestors, while mtDNA stems from the maternal line only. As Professor Schuenemann says: “Nuclear DNA represents the full human genome and therefore contains much more information as mtDNA that covers only a small part of the human genome and represents only the maternal ancestry.”[5]

The samples were grouped into three time periods:

1. Pre-Ptolemaic Period (New Kingdom [1520 – 1075 BC],[6] Third Intermediate Period [1075 – 715 BC] and Late Period [715 – 332 BC]).
2. Ptolemaic Period (332–30 BC).
3. Roman Period (30 BC – 640 AD).

Why did they do this? The researchers wanted – through reliable extraction and analysis of DNA from ancient Egyptian mummies, and then comparing it with DNA sets from modern peoples in and out of Egypt – to study Egypt’s population history (how the inhabitants of Egypt changed genetically overtime by mixing with other peoples who came to Egypt through immigration or conquests or slavery and trade). As Professor Krause says: “One of the questions that motivated us for our study is trying to find out when Egypt was conquered by the Greeks or Alexander the Great or by the Nubians or by the Romans, and did that actually have an impact on the population?”[7]  Dr Alexander Peltzer, another contributor, adds: “In particular, we were interested in looking at changes and continuities in the genetic makeup of the ancient inhabitants of Abusir el-Meleq. Specifically, the team wanted to see if ancient populations were affected, at the genetic level, by foreign conquest and domination during the time period.”[8] These matters were previously assessed using literary and archaeological sources, or by analysing the DNA of modern Egyptians (which show genetic diversity), but these are not entirely reliable and could be misleading. Their method greatly contributes towards a more accurate and refined understanding of Egypt’s population history.

RESULTS

The various analyses that were undertaken in the research, and their results, on the ninety mtDNA genomes (A) and the genome=wide DNA from the three ancient Egyptians (B & C) are detailed below.

A. ANALYSIS OF 90 ANCIENT EGYPTIAN MITOCHONDRIAL GENOMES

The 90 mitochondrial genomes were grouped into three temporal categories based on their radioactive dates:

44 from Pre-Ptolemaic Periods

27 from the Ptolemaic Period

19 from the Roman Period

The scientists tested for genetic differentiation and homogeneity by comparing haplopeptide composition, calculating Fst-statistics and applying a test for population continuity on the mitochondrial genome data from the three ancient populations and two modern-day populations from Egypt and Ethiopia. The frequencies of the mitochondrial DNA haplogroup are shown in 1.

Figure 1: Mitochondrial DNA haplogroup frequencies of three ancient and two modern-day populations

The test showed that:

• The three ancient Egyptian groups possess similar halopeptide profiles.
• Modern Egyptians share this profile but in addition show a marked increase of African mtDNA lineages L0-L4 up to 20%.
• No continuity with modern Ethiopians (who carry > 60% African L lineage).

The authors state that despite the sub-Saharan influx into the blood of modern Egyptians, the formal test that they applied cannot rule out genetic continuity between ancient Egyptians and modern Egyptians. It is important to note here that by saying “they cannot rule out genetic continuity between ancient Egyptians and modern Egyptians” it does not mean that there is continuity – it just means that this particular test cannot rule it out. The other tests will clarify this.

The scientists then performed a principal component analysis (PCA) (based on haplogroup frequencies and Multidimensional Scaling [MDS] of pairwise genetic distances) in order to further test genetic affinities and shared ancestry with modern-day African and West Eurasian populations. 2 and Fig. 3 show that.

Figure 2: Principal Component Analysis based on haplogroup frequencies: sub-Saharan Africa (green), North Africa, including modern Egyptians [EGY, EGY P, EGYKU] (light green), Near East (orange), Europe (yellow), ancient [including ancient Egyptians: PPP = Pre-Ptolemaic Period group, PP = Ptolemaic Period group, RP = Roman Period group] (blue). 

Figure 3: MDS of HVR-I sequence data: colour scheme as above (note that ancient groups were pooled)

The PCA test showed that:

• All the 3 ancient Egyptian groups cluster together, supporting genetic continuity across their 1300 year transect.
• These three ancient Egyptian groups have high affinities with modern populations from the Near East and the Levant compared to modern Egyptians.

B. PRINCIPAL COMPONENT ANALYSIS AND GENETIC CLUSTERING OF GENOME-WIDE DNA FROM THREE ANCIENT EGYPTIANS

Two analyses were made on this:

PCA analysis. The SNP data of the three ancient Egyptian individuals were merged with 2367 modern individuals and 294 ancient genomes, and a PCA analysis was performed on the joint data set. The result is shown on 4.

Figure 4: Principal Component Analysis-based genome-wide SNP data of three ancient Egyptians, 2,367 modern individuals and 294 previously published ancient genomes

This showed that:

• The ancient Egyptian samples fell distinct from modern Egyptians, and closer towards Near Eastern and European samples.
• In contrast, modern Egyptians shifted towards sub-Saharan African population.

ADMIXTURE analysis. Next, the scientist performed model-based clustering using ADMIXTURE. The result is shown in 5.

Figure 5: Subset of the full ADMIXTURE analysis

The ADMIXTURE analysis further supported the PCA analysis’ results. It revealed that:

• The three ancient Egyptians differed from modern Egyptians by a relatively larger Near Eastern genetic component, in particular a component found in Neolithic Levantine ancient individuals.
• In contrast, a substantially larger sub-Saharan African component, found primarily in West African Yoruba (an ethnic group that mostly live in Nigeria), is seen in modern Egyptians compared to ancient samples.

C. SHARED DRIFT AND MIXTURE ANALYSIS OF THE THREE ANCIENT EGYPTIANS WITH OTHER MODERN AND ANCIENT POPULATIONS

The scientists then used a special statistical test (outgroup f3- statistics) for the ancient and modern Egyptians to measure shared genetic drift with other ancient and modern populations, using Mbuti (an indigenous pygmy group that lives in the Congo) as outgroup. The results are shown in 6, a & b.

Figure 6: (a) Outgroup f3-statistics measuring shared drift of the three ancient Egyptian samples and other modern and ancient populations, (b) The data shown in a, compared with the same estimates for modern Egyptians, ordered by shared drift with modern Egyptians, (c) Admixture f₃-statistics, testing whether modern Egyptians are mixed from ancient Egyptians and some other source. The most negative Z-scores indicate the most likely source populations.

This showed 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.
• When comparing this pattern with modern Egyptians, it is found that the ancient Egyptians are more closely related to all modern and ancient European populations that the scientists tested (Fig, 6b). This, the scientists say, is likely due to the additional African component in the modern Egyptians observed above.

The scientists then determined whether modern Egyptians could be modelled as a mixture of ancient Egyptians and other populations. For this, they computed f3-statistics. The result is shown in 6c, and it points towards sub-Saharan African populations as the missing component, confirming the result of the ADMIXTURE analysis.

Next, the scientists estimated the fractions of sub-Saharan African ancestry in ancient and modern Egyptians. For this, they used two methods (qpdm and the f4-ratio test). They came with the following result: modern Egyptians inherit 8% more ancestry from African ancestors than the three ancient Egyptians do, which is also consistent with the ADMIXTURE results above (absolute estimates in the three ancient Egyptians ranged from 6 to 15%, and in the modern Egyptians from 14 to 21%).[9]

Lastly, the scientists estimated the time of a putative pulse-like admixture event. For this, they used ADLER. They estimated that the admixture occurred 24 generations ago (700 years ago). This confirms the finding by Henn et al (2012).[10] This result of course does not by itself rule out the possibility of much older and continuous gene flow from African sources, as the authors point. But the substantially lower African component in the _~ 2000 year old ancient samples (from the Roman Period) suggest that the African gene flow in modern Egyptians occurred predominantly within the last 2000 years.

The paper is aware that their findings cannot be extended to all Egypt: “… all our genetic data were obtained from a single site in Middle Egypt and may not be representative for all of ancient Egypt.” On the possibility that ancient Egyptians might have had a similar sub-Saharan component like that of modern Egyptians, the paper says: “It is possible that populations in the south of Egypt were more closely related to those of Nubia and had a higher sub-Saharan genetic component, in which case the argument for an influx of sub-Saharan ancestries after the Roman Period might only be partially valid and have to be nuanced. Throughout Pharaonic history there was intense interaction between Egypt and Nubia, ranging from trade to conquest and colonialism, and there is compelling evidence for ethnic complexity within households with Egyptian men marrying Nubian women and vice versa. Clearly, more genetic studies on ancient human remains from southern Egypt and Sudan are needed before apodictic statements can be made.”

But Professor Johannes Krause, one of the contributors to the study, wants to stress the importance of the study: “This is not just the DNA of one person. It’s the DNA of the parents, grandparents, grandparents’ parents, grand-grand-grandparents’ parents and so forth. So, if we don’t find sub-Saharan African ancestry in those people, that is pretty representative, at least for Middle Egypt.”[11]

It is indeed an important study even if it does not please the Arabs of Egypt. We can safely take the conclusions of the study as true for Middle Egypt. On the situation of Lower Egypt and Upper Egypt, we just don’t know. But that should not be used to criticise the study or deny its conclusions; or, more importantly, continue to assert, without evidence, that present inhabitants of Egypt are not genetically distinct from the ancient Egyptians.

Even though the paper was clear about its limitation, one Egyptologist, Professor Stephen Quirke of UCH in London was quick to criticise it:

There has been this very strong attempt throughout the history of Egyptology to disassociate ancient Egyptians from the modern population. I’m 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. When we are discussing it, we have to be much more sensitive to how these kinds of statements are read outside where we are at the moment. We are not yet anywhere near being able to make very drastic conclusions about the tens of millions of people living in Egypt.[12]

Of course, the paper did not make any drastic conclusions, but it added very important scientific evidence to Egypt’s population history. Quirke obviously has made his conclusions from literary and archaeological evidence (not from the genetic evidence), which are defective. He adds:

While there have been a number of influxes of people from outside Egypt, he suggested that the impact could sometimes be over-stated. For example, …, many thousands of soldiers had taken part in the Arab Invasion of Egypt in the 7th century, but they were still vastly outnumbered by the resident population of about six million.”

I must say that Quirke is being economic with the truth, and ignoring the waves after waves of immigration and settlement in Egypt following the Arab Conquest on Egypt in 640 AD – probably millions of Muslims from diverse directions of the old world came to Egypt in the last fourteen centuries and made Egypt their home. They were not just Arabs but Turks, Persians, Kurds, Berbers, Nubians, Syrians, Caucasians, etc. They intermingled, to a greater or lesser degree, with those Muslims they had found already in the country. On top of that, Quirke ignores the millions of slaves who were brought to Egypt, as a consequence of wars with non-Muslims or bought in salve markets, and who added to the modern Egyptians’ blood.

The result is not surprising. It actually supports to a large extent the literary and archaeological evidence. It debunks the weak theory that the modern Egyptians are genetically identical to the ancient Egyptians, and that most of the Muslims of Egypt are the sons of the Copts, the direct descendants of the ancient Egyptians, who converted to Islam. We acknowledge that this study on its own cannot completely debunk this theory. More needs to be done.

When the researchers use DNA from “modern Egyptians” as they compare it with that from the mummies of ancient Egypt, we must understand by it the DNA of the Muslims of Egypt mainly, as they form the overwhelming majority of Egypt, and not that of the Copts. The Copts need to be studied separately, and homogeneity and continuity with the ancient Egyptians must be done. Actually, any DNA obtained from the Copts and added to the DNA set of the “modern Egyptians”, in our opinion, decrease the strength of the findings of the research that are listed above. Without any Coptic DNA included in the set, the results would have been even more dramatic, and shown the lack of homogeneity and continuity between the ancient Egyptians and the “modern Egyptians”.

The study of the genetics of Copts as a separate and distinct group in Egypt that almost all scientists are in agreement that they are the direct descendants of the ancient Egyptians and the purest representation of them has not been forthcoming. One suspects that political correctness plays part in avoiding taking the Copts as a group distinct ethnically and historically from the majority in Egypt which define itself as Arab. Restrictions imposed on scientists by the Egyptian government are also a factor. But if the scientists really want to study population history of Egypt using genetic evidence, there is no way they cannot do that without the help of the Coptic genome studied properly and comprehensively. They can compare the Coptic genome with the ancient Egyptian genome and genome taken from the Muslims of Egypt.

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[1] Nat Commun 8, 15694 (2017).

[2] The First Genome Data from Ancient Egyptian Mummies. Study finds that ancient Egyptians were most closely related to ancient populations from the Near East in the website of Max Planck Institute for the Science of the Human Body (May 30, 2017).

[3] This village lies in the west bank of the Nile in Banu Swaif Governorate, near the eastern edge of the Fauyum Basin. Adjacent to it, to the west, is an extensive ancient Egyptian necropolis which was used from the pre-dynastic to the early Byzantine period. It must be differentiated from Abusir (ابو صير‎) which is located in Badrashin Markaz in the Giza Governorate, and possesses an old necropolis from the Old Kingdom.

[4] The scientists extracted DNA from 151 mummified individuals, obtaining 166 samples from them, but only 90 individuals’ samples were included in the later analysis, as the rest did not pass quality control.

[5] Victoria Wollaston, Rare mummy DNA revealed clues about the relatives of ancient Egyptians. Researchers recovered ancient DNA from Egyptian mummies dating from approximately 1400 BCE to 400 CE, in WIRED (30 May 2017).

[6] After the New Kingdom, which is marked by the death of death of Pharaoh Ramesses XI in 1075 BC and the end of the 20^th Dynasty, Egypt was ruled by foreigners. All the following dynasties from the 21^st to the 31^st were really foreign dynasties.

[7] Bianca Nogrady: Who were the ancient Egyptians? Mummy DNA reveals surprising clues in ABC Science (30 May 2017).

[8] Victoria Wollaston, Rare mummy DNA revealed clues about the relatives of ancient Egyptians.

[9] Depending on method and choice of reference populations.

[10] Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet. 8, e1002397 (2012).

[11] Thomas Page , DNA discovery reveals genetic history of ancient Egyptians in CNN (June 23, 2017).

[12] Ian Johnston, Ancient Egyptians more closely related to Europeans than modern Egyptians, scientists claim in Independent (30 May 2017).