Genomic Ancestry of North Africans Supports Back-to-Africa Migrations

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.

Genetic variation in Tunisia in the context of human diversity worldwide

“…The analysis of 73 populations including eight populations from the study by Henn et al (2012), used the 102 SNPs common to that study and the present report. Supporting Information Table S2 identifies these 102 SNPs.…”

“…A recent study by Henn et al (2012) made available genotypes for 145 individuals from seven populations in North Africa (Western Sahara, northern and southern Morocco, Algeria, Tunisia, Libya, and Egypt) along with a sample of Spanish Basque. Supporting Information Table S1B lists the populations and the number of individuals in each group from the Henn et al (2012) study.…”

“…Supporting Information Table S1B lists the populations and the number of individuals in each group from the Henn et al (2012) study.…”

“…More specifically, numerous studies targeting particular genes, especially those suspected to be of clinical interest, have accumulated in the scientific literature on particular North African populations, but as yet few studies of North African populations incorporating large sets of DNA polymorphisms exist. One of two recent exceptions is the report by Henn et al (2012) which does sample a large number of autosomal SNPs from seven locations in North Africa with about 18 individuals from each site; however, the study has a limited number of comparative population samples from nearby geographical regions. Their work supports the presence of indigenous genomic variation extending back 12 to 40 thousand years ago with ancient gene flow in different periods from south of the Sahara, Southwest Asia, and Europe.…”

“…Our study examines these eight North African groups for a set of 399 autosomal SNPs also studied in 57 other populations. Some combined analyses included the 7 North African groups and a Spanish Basque group studied by Henn et al (2012) for the subset of 102 SNPs that are shared in common. The results support the view that this part of North Africa is a genetically unique region of the world worthy of more studies of autosomal genetic markers.…”