A gradient of shared IBD segments is observed from southern to northern Europe (based on WEA; Fig. 2 and SI Appendix, Table S3). This sharing is highest in the Iberian Peninsula for both North Africa and Sub-Saharan African IBD segments. Interestingly, the Basques are an exception to this pattern because they show similar levels of sharing to other European populations, but inhabit the Iberian Peninsula. Additionally, IBD sharing between North Africa and Europe is nearly an order of magnitude higher than that between Sub-Saharan Africa and Europe, of which a total of 30% of its IBD segments are also shared between North Africa and Europe. Interestingly, these segments represent only 2% of the bulk of IBD segments shared between North Africa and Europe, a proportion similar to that found in previous studies based only on Sub-Saharan populations (9). Considering that only 2% of the segments shared between North Africa and Europe have a Sub-Saharan origin, it is not likely that the gradients observed in Fig. 2B is driven primarily by theSub-Saharan segments. Finally, high correlation (0.83) exists among the values of WEA between Sub-Saharan Africa and Europe, and North Africa and Europe. Overall, these results support the hypothesis that Sub-Saharan gene flow detected in Europe entered with North African gene flow. We regressed the North African–European IBD metric (WEA) on the sine of latitude to evaluate the strength of this gradient and find a significant relationship across southern-to-northern Europe, P = 7.4 × 10−8 (Fig. 2D).
At k = 4, the ancestry assignment differentiated between non-Jewish European populations (from now on referred to as “European”), European Jews, Sub-Saharan Africans, and a group formed by Near Eastern and North African populations. At k = 5,6 components mainly assigned to North African populations and Tunisian Berbers, respectively, clearly appear. European populations sharing this North African ancestral component are almost exclusively in southern Europe (Fig. 1 and SI Appendix, Fig. S3). Southern European populations have a high proportion (5–35%) of joint Near Eastern | North African ancestry assigned at k = 4. However, identification of distinct Near Eastern and North African ancestries in k ≥ 5 differentiates southeastern from southwestern Europe. Southwestern European populations average between 4% and 20% of their genomes assigned to a North African ancestral cluster (SI Appendix, Fig. S3), whereas this value does not exceed 2% in southeastern European populations. Contrary to past observations, Sub-Saharan ancestry is detected at <1% in Europe, with the exception of the Canary Islands. In summary, when North African populations are included as a source, allele frequency-based clustering indicates better assignment to North African than to Sub-Saharan ancestry, and estimates of African ancestry in European populations increase relative to previous studies. European ancestry is also detected in North African populations. At k = 6 it ranges between 4% and 16% in the rest of North Africa, with notable intrapopulation variation (35) and is absent in most Maghrebi (western North African) individuals from Tunisia and Western Sahara.