We analyze North African whole-genome sequences and use other current and ancient data in order to characterize its internal diversity, population structure, gene flow, and population continuity

North Africa has a particular geographic location between sub-Saharan Africa, the Mediterranean Sea and the Middle East, which has shaped its own and distinct population history. Here, we present a study of individual whole genome sequences from a broad panel of current North African groups and identify more than 10 million SNPs, which, combined with published ancient genomes and other genome-wide worldwide datasets, has allowed us to characterize the variation within the region and to assess the contact with their surrounding populations. We find an endemic North African Epipalaeolithic genetic component persistent in all present populations and forming a declining gradient from Western to Eastern North Africa. This component is also observed in North African Neolithic populations and Guanches from the 7th-11th centuries, who despite being settled in the Canary Islands since 2,500 years ago coming from North Africa, mirror current North Africans' patterns of population structure and admixture. This scenario is consistent with Neolithization having shaped most of the current genetic variation in North Africa when compared to posterior back-to-North-Africa migration waves such as Arabization during the Islamic conquest during the 7th and 8th centuries. The North African genetic pool is shown as a melting pot of five main components: North African Epipalaeolithic, sub-Saharan, European and Anatolian Neolithic, Caucasus and Iran Palaeolithic and Neolithic, and Middle Eastern. A common and distinct genetic history of the region is shown, with internal different proportions of these components are mainly due to differential admixture with particular surrounding groups as well as to genetic drift due to isolation or endogamy in certain groups.