THE GENETIC STRUCTURE OF THE COPTS AND MUSLIMS OF EGYPT 2: THE GENETIC STRUCTURE OF THE MUSLIMS OF EGYPT SHOWN FOR THE FIRST TIME
In Part 1, we discussed the opposing claims on the matter of the ethnicity of the Copts and Muslims of Egypt, we showed that they were based mainly on political, historical and anthropometric considerations, and we said that only recently have genetics really entered as a tool to decide the debate. Here, in this part, we review an important study that gave us the genetic structure of Muslim Egyptians based on their single nucleotide polymorphisms (SNPs) – a study that formed a good basis for further studies. The study was published in 2012 in PLOS Genetics, and authored by Henn et al, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. The authors introduced their study by telling us that, prior to their study, little is known about the genetic make-up of Mediterranean North Africa, a huge area inhabited by over 160 million people. They, hence, set themselves up to analyse the genetic structure of seven North African populations, spanning from Egypt to Morocco: Egyptian, Libyan, Tunisian, Algerian, North Moroccan, South Moroccan and Sahrawi (from Western Sahara). The study was designed for more than just determining the genetic structure of these populations: it analysed also the genetic influence of migrants from neighbouring countries in the genomes of these populations. The authors, therefore, included in their study nine populations from Africa, Asia and Europe for comparison: 6 populations from sub-Saharan Africa (4 populations from western Africans [from Nigeria: Yoruba, Hausa, Bulala and Fulani], and 2 populations from eastern Africa [from Kenya: Luhya and Maasai], 2 populations from Europe (Spanish Basque and Italian Tuscans), and one population from Asia (Near East [Qatari]). This was done to test three proposed migrations into North Africa from neighbouring regions:
- A migration (what is called “back-to-Africa gene flow”) from Eurasia in the Palaeolithic Era – an era also called Old Stone Age, and lies in prehistory, from about 2.6 million years ago to around 10,000 BC (exactly 10,300 BC).
- An Arabic migration across the whole of North Africa 1,400 years ago (i.e., since the Arab invasion of the area in the seventh century).
- A trans-Saharan transport of slaves from sub-Saharan Africa.
The authors analysed ~730,000 single nucleotide polymorphisms (SNPs) from across the human genome of the seven North African populations. And, by using ADMIXTURE, a computational unsupervised clustering algorithm for estimation of ancestry,  they analysed the common autosomal SNP loci of the 16 populations [based on approximately 300 K autosomal SNP loci in common]. They were able to describe the effect of the hypothesised migrations from the Near East, Europe and Sub-Saharan Africa into North Africa; and so they identified:
- A gradient of likely autochthonous (indigenous, native) ancestry that decreases from west to east across northern Africa: high in the Sahrawi population and less in the Egyptian population) . The indigenous North African ancestry (which the authors call “Maghrebi ancestry”) is more frequent in populations with historical Berber ethnicity. And they concluded that this ancestry was likely derived from “back-to-Africa” gene flow more than 12,000 years ago.
- A gradient of Near Eastern Arabic ancestry that decreases from east to west: high in the Egyptian population and less in the Sahrawi population. The study showed a substantial shared ancestry with the Near East.
- Significant signatures of sub-Saharan African ancestry in the seven Northern African populations that vary substantially among them. These sub-Saharan ancestries appear to be recent introduction into North African populations; and they vary in time, source and destination, possibly reflecting the patterns of the trans-Saharan slave trade:
- There is genetic evidence of western African migration into southern Morocco that began about 1,200 years ago.
- In Egypt, the evidence points to a migration of individuals with Nilotic ancestry into Egypt that occurred about 750 years ago (which corresponds to the beginning of the Bahri Mamelukes).
The following figure [A] shows, i. a map with the locations of the 7 North African populations and the 9 neighbouring populations in sub-Saharan Africa, Europe and the Near East; ii. the population structure analysis of the 7 North African populations (with the Qatari also shown), and the two distinct, opposite gradients of ancestry [as shown at k=8]: the indigenous Maghrebi ancestry decreasing in proportion from west to east (indicated by the light blue colour) and the Arab ancestry from the Near East (Qatar) decreasing in proportion from east to west (indicated by the green colour). The other colours in the population structure analysis match those colours of the populations in the open circles in the map.
Figure B shows the population structure analysis (at k=2, 4, 6 and 8) of the 16 populations:
The genetic structure of the Egyptian Muslims with their ancestry composition is represented below (k=6) is shown below in a magnified form (each bar represents an individual in the sample population):
We see that the Muslim Egyptians have indigenous Maghrebi component, which resulted from an ancient “back-to-Africa” gene flow a long time ago (shown here in light blue colour), a stronger Arab (Qatari) component in a larger proportion that resulted from gene flow since the Arab invasion of Egypt in the 7th century (shown here in green colour), a significant genetic signature from east Africa (Maasai and Luhya from Kenya) that was introduced in the late 13th century, as result of the slave trade that started heavily in the late 13th century (shown in orange and red).
This is the first time that genome-wide SNP genotyping array data for Egyptians has been analysed to study the genetic make-up of Egyptians and identify their ancestry components. The Copts were not included in the Henn et al’s study but at least we have now the genetic structure of the Egyptian Muslims, and, as we can see in the next article, others analysed the genetic structure of some Copts and, using the data for the Egyptian Muslims obtained from Hen et al, were able to compare the genetic composition of the Copts v. Egyptian Muslims, with very interesting result.
We shall study that in the next part.
 Henn BM , Botigué LR , Gravel S , Wang W , Brisbin A , et al. Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genet. 8(1): e1002397 (2012).
 The study included 152 individuals representing the seven different North African populations. After quality control filtering, 125 individuals remained, with 19 from Egypt, 17 from Libya, 18 from Tunisia, 19 from Algeria, 18 from North Morocco, 16 from South Morocco and 18 from Western Sahara.
 Apart from the Spanish population, the genome-wide SNP genotyping array data were available from previous studied. The authors had to analyse that of the Spanish population (Basque Country) together with the seven North African populations as no prior study analysed its genetic structure.
 The Palaeolithic Era (Old Stone Age) was followed by the Neolithic Era (New Stone Age), which began around 10,000 BC and ended in Egypt in 3,000 BC, when the Egyptians discovered writing, and history began. Both the Palaeolithic and Neolithic periods are part of Pre-history, and both comprise the Stone Age. In the Palaeolithic period that lasted for over 1 ½ million, the Earth was inhabited by many human species, who were nomadic hunter-gatherers; in the Neolithic period, only Homo sapiens sapiens remained, who were largely settled and survived on growing crops and animals that they were able to domesticate.
 It estimates of ancestry in unrelated individuals. For more on ADMIXTURE, read: Alexander et al (2009), Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19: 1655.
 That is in the Upper Palaeolithic Era (the Upper part of the Palaeolithic Era is the period extending from 126,000 to 11,700 years ago).
 The authors successfully analysed nine ancestral clusters (k=2 through 10) of the 16 populations.