Even more differentiation was observed when we fit analysis of variance models including location, gender, and their interaction. Since exploratory analyses indicated that the Anza and Dchiera samples are indistinguishable either for gene expression or genotypes, these were combined into a single location, Agadir, in all subsequent analyses. In the three-way comparison, 8,459 probes (38%) were significant at the 1% FDR threshold for location (Supplementary Table 2 online). Boutroch differs from both Ighrem and Agadir at over seven thousand probes each, with a high degree of overlap (Fig. 3a; Table 1). Ighrem and Agadir are much more similar to one another, in part because there is considerably more diversity within the Ighrem sample that reduces the significance of the location contrast. We also noted that women are much more differentiated among locations than men (Table 1). These results confirm our previous report2 of substantial differentiation between Bedouin nomads, urban Anza, and another remote Amazigh village, Sebt Nabor.
