Recent Historical Migrations Have Shaped the Gene Pool of Arabs and Berbers in North Africa

Abstract

North Africa is characterized by its diverse cultural and linguistic groups and its genetic heterogeneity. Genomic data has shown an amalgam of components mixed since pre-Holocean times. Though no differences have been found in uniparental and classical markers between Berbers and Arabs, the two main ethnic groups in the region, the scanty genomic data available have highlighted the singularity of Berbers. We characterize the genetic heterogeneity of North African groups, focusing on the putative differences of Berbers and Arabs, and estimate migration dates. We analyze genome-wide autosomal data in five Berber and six Arab groups, and compare them to Middle Easterns, sub-Saharans, and Europeans. Haplotype-based methods show a lack of correlation between geographical and genetic populations, and a high degree of genetic heterogeneity, without strong differences between Berbers and Arabs. Berbers enclose genetically diverse groups, from isolated endogamous groups with high autochthonous component frequencies, large homozygosity runs and low effective population sizes, to admixed groups with high frequencies of sub-Saharan and Middle Eastern components. Admixture time estimates show a complex pattern of recent historical migrations, with a peak around the 7th century C.E. coincident with the Arabization of the region; sub-Saharan migrations since the 1st century B.C. in agreement with Roman slave trade; and a strong migration in the 17th century C.E., coincident with a huge impact of the trans-Atlantic and trans-Saharan trade of sub-Saharan slaves in the Modern Era. The genetic complexity found should be taken into account when selecting reference groups in population genetics and biomedical studies.

Keywords: Berbers; North Africa; admixture; genome wide SNPs; haplotype; population genetics.

Fig. 1.

Population Structure in North Africa. Principal component analysis (PCA) and sample location. Berber-speaking samples are highlighted in the map and PCA legend.

Fig. 2.

ADMIXTURE plots with North African and surrounding populations. ADMIXTURE plots from k = 2 to k = 5 of the high density dataset are shown.

Fig. 3.

Haplotype sharing and FineStructure cluster distribution in North Africa. The right horizontal barplots in each geographic location show individual proportions of inferred haplotype sharing with Yoruba, Tunisian Berbers from Chenini, Syrians, and Basques, estimated using a mixture model that incorporates ChromoPainter results (colors according to the bottom right legend in the figure). Within each geographic location, left vertical barplots show the proportion of individuals from each population assigned to each of 13 North African fineSTRUCTURE genetic clusters (colors match the fineSTRUCTURE simplified dendrogram represented at the top of the figure).

Fig. 4.

Runs of homozygosity (ROH) in North Africa. Barplot showing the ROH estimated for each genetic cluster starting at 1.5 MB.

Fig. 5.

Globetrotter estimations in North Africa. (A) The three density plots on the top of the figure show the admixture times estimated for each cluster for each of 100 bootstrap re-samples: top, older event when two admixture events are estimated; middle, recent event when two admixture events are estimated, and; bottom, only one admixture event estimated. (B) The barplot at the bottom of the figure shows the proportion of the four components (Middle Eastern, North African, sub-Saharan, and European) inferred in each cluster, considering the minor source (up) and major source (down) and the estimated times of admixture.