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

In this context, we have analyzed DNA samples from the modern Egyptian population to distinguish between two possible demographic scenarios: (1) the genetics of modern Egyptians may reflect their intermediate geographic location between northern Africa, the Middle East, and southern Europe, sharing genetic components from each of these regions, or (2) different cultural, geographic, and/or demographic factors may have acted as barriers to gene flow between the southeastern and northeastern shores of the Mediterranean Sea, leading to a genetic fracture between these regions. In order to distinguish between these two scenarios and to identify the different population layers constituting the current population of Egypt, Y-chromosome variation was defined and, for comparative purposes, two NW African populations (Arabs and Berbers from Morocco) were also studied. These data were compared with an extended database of populations located around the Mediterranean Sea from North Africa, the Middle East, and Europe.

Materials and Methods

Sample. Genetic analyses were performed on a sample of 164 Y chromosomes from three North African populations. The northeast (NE) African population consisted of 63 unrelated individuals living in Cairo (Egypt). The NW African sample consisted of 50 Moroccan Berbers and 51 Moroccan Arabs. The Egyptian samples were collected as dried blood stains and DNA was extracted by standard procedures. For Moroccan samples, whole blood was obtained and DNA was extracted by means of a standard phenol/chloroform protocol. Appropriate informed consent was obtained from all participants in this study. Y-Chromosome Biallelic Polymorphism Typing. To define Y-chromosome lineages, 10 UEPs (Unique Event Polymorphisms), defining 11 Y-chromosome haplogroups (Hgs), were analyzed. The markers used were SRY-2627 (Veitia et al. 1997), SRY-1532 (Knok et al. 1996), SRY-8299 (Whitfield et al. 1995), 9287 (Mathias et al. 1994), Tat (Zerjal et al. 1997), YAP (Hammer and Horai 1995), sY81 (Seielstad et al. 1994), LLY22g (E. Righetti and C. Tyler-Smith, unpublished), M9 (Underhill et al. 1997), and 12f2 (Casanova et al. 1985). The marker typing was carried out as described in Rosser et al. (2000). The deep-rooting markers SRY1532, M9, 9287, YAP, and 12f2 were typed in all samples, and, in some cases, the remaining markers were typed hierarchically; e.g., SRY8299 and sY81 only on YAP chromosomes, LLY22g and Tat only on those M9G and 92R7C chromosomes, and SRY2627 only on those 92R7T and SRY 15 32A chromosomes. The Y-chromosome haplogroup nomenclature follows that of Rosser et al. (2000).

Measures of Genetic Diversity. Two genetic diversity estimators were computed by means of the Arlequin vs. 2.0 software (Schneider et al. 2000). Intrapopulation diversity was measured through the gene diversity index (Nei 1987). Interpopulation diversity was calculated through conventional F-statistics (Wright 1965) and genetic relationships among populations were visualized in a Multidimensional Scaling plot.