Egyptian Y chromosome study shows a complicated ancestry.

Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa.

Laboratoire d’Anthropologie Biologique (CNRS FRE 2292); Musée de l’Homme MNHN, Paris, France.

The geographic location of Egypt, at the interface between North Africa, the Middle East, and southern Europe, prompted us to investigate the genetic diversity of this population and its relationship with neighboring populations. To assess the extent to which the modern Egyptian population reflects this intermediate geographic position, ten Unique Event Polymorphisms (UEPs), mapping to the nonrecombining portion of the Y chromosome, have been typed in 164 Y chromosomes from three North African populations. The analysis of these binary markers, which define 11 Y-chromosome lineages, were used to determine the haplogroup frequencies in Egyptians, Moroccan Arabs, and Moroccan Berbers and thereby define the Y-chromosome background in these regions. Pairwise comparisons with a set of 15 different populations from neighboring European, North African, and Middle Eastern populations and geographic analysis showed the absence of any significant genetic barrier in the eastern part of the Mediterranean area, suggesting that genetic variation and gene flow in this area follow the “isolation-by-distance” model. These results are in sharp contrast with the observation of a strong north-south genetic barrier in the western Mediterranean basin, defined by the Gibraltar Strait. Thus, the Y-chromosome gene pool in the modern Egyptian population reflects a mixture of European, Middle Eastern, and African characteristics, highlighting the importance of ancient and recent migration waves, followed by gene flow, in the region.


Y-Chromosome Biallelic Profiles. Allelic profiles of the 11 Y-chromosome lineages in the total sample of 164 North African samples are shown in Table 1. Of a total of 8 Y-chromosome Hgs observed, only two reached a frequency of > 10% (Hgs 21 and 9). Hg 21* is present at high frequency in Egypt (44%) and at higher frequencies in Moroccan Arabs (69%) and Moroccan Berbers (76%). This lineage shows the highest frequencies in North Africa with a decreasing frequency gradient towards the south, and it is also present at moderate frequencies in the northern Mediterranean basin. Hg 9** is the second most common lineage in the Egyptian population (35%) and is also present, although at lower frequencies, in the two NW African populations examined (Moroccan Arabs 14%; Moroccan Berbers 4%). This haplogroup shows the highest frequencies in the Fertile Crescent, and it has been suggested to be a genetic signature of migrations from the Middle East associated with Neolithic farmer expansions (Semino et al. 1996; Rosser et at. 2000; Quintana-Murci et al. 2001).

Other lineages are present at lower values in both Egyptian and NW African populations. Hg 1, which is present in Egyptians (8%) and NW Africans (Arabs 6%; Berbers 4%), indicates a limited degree of gene flow from Europe to North Africa, since it has been predominantly found in Europe, with increasing frequencies from the Middle East to northwestern Europe (Semino et al. 1996; Rosser et al. 2000). Hgs 2 and 26 are found at moderate and low frequencies, respectively, in the three populations. However, little information can be deduced from these lineages since they are present in both Europe and Asia and do not show any informative geographic variation along the Eurasian landscape. Hgs 7 and 8 are typically sub-Saharan African lineages, and they have been suggested to be genetic signatures of Khoisan and Bantu language families, respectively. They have not been recorded outside Africa (Hammer et al. 1998; Rosser et al. 2000), and their presence is unusual in North Africa (Bosch et al. 1999). In agreement with Bosch et al. (1999), Hg 7 is not observed in NW Africa and is present in two individuals from Egypt. Hg 8, which is considered to be of sub-Saharan origin, was found in one Egyptian, three Moroccan Berbers, and two Moroccan Arabs. One Egyptian individual was found with an Hg 4 Y chromosome. This lineage has not been observed in any European nor African populations, but it is present at high frequencies (-45%) in some East Asian populations, such as the Japanese and Tibetans (Karafet et al. 1999).

Classical genetic studies show a high degree of genetic heterogeneity in the modern Egyptian population, suggesting that this population is descended from a mixture of African, Asian, and Arabian stock (Mahmoud et al. 1987; Hafez et al. 1986). Genetic heterogeneity within the Egyptian gene pool is also supported by more recent studies using autosomal STR markers (Klintschar et al.

Related Results
Y-chromosome DNA haplotypes in North African populations
Population history of North Africa: Evidence from classical genetic markers

Here, we used ten Y-chromosome binary markers to define the male-specific gene pool in the Egyptian population and two NW African populations, in order to test contrasting hypotheses on the inter- and intrapopulation relationships and, in a more general context, the peopling processes of North Africa. The results of Y-chromosome haplogroup profiling in Egypt parallels previously published studies of autosomal loci, by demonstrating that Y-chromosome lineages, which are present at high frequencies in modern African (Hgs 7, 8, 21), European (Hg 1), and Middle Eastern (Hg 9) populations, are also found in the modern Egyptian population. The high incidence of Hg 21 in North African (44%-76%), and more especially among NW African, samples can be regarded as an autochthonous genetic layer of the region. This lineage may have originated somewhere in North Africa -20,000 YBP and remained in North Africa and the Middle East for 10,000 years, before it spread towards southern Europe (Hammer et al. 1998). The relatively low incidence of this lineage in Egypt, compared with the Moroccan populations, is probably due to substantial population movements from neighboring countries to Egypt, thereby effectively reducing the frequency of Hg 21 within Egypt. This is highlighted by the geographic distribution of Hg 9 in modern populations. From coalescence analysis, the polymorphism defining Hg 9 has been dated to approximately 14,800 YBP (Hammer et al. 2000). It shows its highest frequencies in the Fertile Crescent with a decreasing frequency cline towards Europe, North Africa, and India. This cline has been interpreted as the consequence of the Neolithic demic diffusion process of farmer economy from the Middle East towards Europe and South Asia (Semino et al. 1996; Rosser et al. 2000; Quintana-Murci et al. 2001). Interestingly, Hg 9 is also present at relatively high frequencies (25%) in the Ethiopian population, highlighting the extent to which Semitic peoples have left substantial traces in the Ethiopian gene pool at different times (Passarino et al. 1998). Hg 9 frequencies observed in Egypt are intermediate between those observed in the Middle East and those in NW Africa, suggesting an east-west cline of decreasing frequencies along the North African coast. It is interesting to note that within the Nile Valley, there is no evidence indicating the presence of agriculture technology before 4700 BC (Kasule 1998), a date confirmed by the oldest solid evidence of food production on the western side of the Nile delta (Hassan 1988). These agricultural food resources are considered to have been introduced from the Levant

One single individual belonging to Y-chromosome lineage Hg 4 was identified. This lineage, which has not been reported in European and African populations and shows highest frequencies in East Asia, was proposed to represent the ancestral state of the YAP lineage (Hammer et al. 1998). Lineages that are clearly derived from Hg 4 (Hgs 21 and 8) make up by far the major part of the sub-Saharan African Y-chromosome gene pool. The phylogeographic distribution of this lineage, with a high frequency in some East Asian populations (~45%), has been used to support a “back-to-Africa” migration of individuals carrying Asian Y chromosomes into the sub-Saharan African gene pool (Hammer et al. 1998). However, with the characterization of new diagnostic markers that refine further the Y-chromosome phylogeny, the exact geographic origin of Hg 4 is not clear (Underhill et al. 2001). One Egyptian individual with an Hg 4 Y chromosome is insufficient to determine the geographical origin of the Alu insertion defining this lineage and may well be due to recent gene flow. Hg 8, which is the most characteristic lineage among sub-Saharan African populations and is derived from Hg 4, has been associated with the Bantu expansions 3000-4000 years ago (Hammer et al. 1998). Here, we found Hg 8 in only one individual from Egypt and in 4%-6% of the Moroccan samples, indicating minimal gene flow from sub-Saharan Africa. We also detected low levels of another sub-Saharan Y-chromosome lineage in Egypt, Hg 7, supporting the findings by Karafet et al. (1999). Although Hg 7 is typical of Khoisan populations, it has been observed in East Africans, Gambians, and East Bantus, and its presence in Egypt is probably due, once again, to limited gene flow from East Africa, perhaps through the Nile Valley.

Our analyses suggest that migration patterns and gene flow between the southern and northern shores of the Mediterranean Sea have been very different in its western extreme (Gibraltar) compared to the eastern region (Egypt). The topology of the minimal spanning tree (Figure 1), which connects NW Africa to the Middle East and Europe through Egypt, indicates a low level of gene flow through the Gibraltar Strait. This scenario is in agreement with the spatial pattern of genetic variability described elsewhere using Y-chromosome markers, autosomal Alu-insertion polymorphisms, and autosomal STR markers (Bosch et al. 2000a, 2000b, 2001; Comas et al. 2000), where a sharp genetic discontinuity between NW Africa and the Iberian Peninsula was reported. Geographic analysis of genetic variation (Figure 2) supports a genetic barrier between SW Europe and NW Africa, the intensity of which decreases from the western to the eastern part of the North African continent. In contrast with the pattern observed in the western Mediterranean region, the MDS plot (Figure 1) indicates an intermediate genetic position of Egypt between North Africa, southern Europe, and the Middle East. In addition, the geographic analysis of genetic variation (Figure 2) provides no evidence for the existence of a genetic barrier between the southern and northern shores of the eastern part of the Mediterranean basin. The isolation-by-dislance model may well explain the genetic relationships between Egypt and the surrounding African, European, and Middle Eastern populations. This is an opposite pattern to that observed in NW Africa, where the presence of a genetic barrier is incompatible with this model. This conclusion is reinforced by Mantel-test correlations between genetic and geographic variability, since the correlation index almost doubles (0.494 –> 0.820) when populations encompassed by the first genetic barrier (defined by the Gibraltar Strait, Figure 2) are withdrawn from the analysis.

In conclusion, our analyses have identified a genetic regional continuity between the northeastern part of Africa (Egypt), the Middle East, and southern Europe. In agreement with the ethnohistorical connections between NE Africa and the Middle East, the genetic data confirm that Egypt, occupying an intermediate position along these routes, has been an important contact zone between the three continents. This is in sharp contrast with the pattern observed between NW Africa and the Iberian Peninsula where no regional continuity along the Gibraltar Strait is observed. However, the previous observation of a continuum of gene flow in another African strait, the Bab-el-Mandeb Strait (Quintana-Murci et al. 1999) highlights the need to consider each geographic feature independently, rather than to extrapolate general conclusions on their influence on gene flow. Moreover, given the absence of recombination for most of the Y chromosome, which behaves effectively as a single genetic locus, the direct inference of population processes from Y-chromosome variation is not without risks. Different factors, such as different effective population sizes, differences in male vs. female cultural and social habits and selection, could affect Y-chromosome variation and distribution in human populations. Future studies integrating data from multiple independent loci (mtDNA, autosomal markers) may reveal additional information on the population structure and the peopling processes of North Africa.

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