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

Human Biology, Oct 2002 by Manni, Franz, Leonardi, Pascal, Barakat, Abdelhamid, Rouba, Hassan, Et al

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.