Abstract
North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.
Highlights
The census size of Mediterranean North Africa exceeds 160 million people [1], but relatively little is known about the genetic makeup of these populations and the demographic history of migration between North Africa and neighboring regions
We extend a principal component analysis-based (PCA) method of local ancestry assignment [20] in order to allow for three possible ancestral populations
In order to test whether subSaharan African ancestry was an ancient or recent migration signature, we considered the length of sub-Saharan haplotypes
Summary
The census size of Mediterranean North Africa exceeds 160 million people [1], but relatively little is known about the genetic makeup of these populations and the demographic history of migration between North Africa and neighboring regions. Mediterranean North Africans are often grouped with Near Eastern populations because populations in both regions speak primarily Afro-Asiatic languages, like Arabic, and phenotypic attributes, like lighter skin pigmentation, differentiate many North Africans from sub-Saharan Africans. We clarify the population structure of North Africa and explicitly interrogate the history of gene flow into North Africa from the Near East, Europe and sub-Saharan Africa. Largely from uniparentally inherited markers, have not resolved the location origin of North African populations or the timing of human dispersal(s) into North Africa. Analyses based on the frequencies of a small number of autosomal genetic polymorphisms and uniparental markers have shown that the genetic landscape follow an east-west pattern with little to no difference between Berber- and Arab-speaking populations [6,7]. Do current North Africans retain genetic continuity with the first modern human occupants of northern Africa from more than 50,000 years ago (ya) or was Author Summary
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