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Northwest African populations occupy a strategic geographical area that has always been a zone of influence for diverse human groups from different regions. This article focuses on the analysis of the genetic contribution of sub-Saharan African populations by means of four short tandem repeat (STR) systems (HUMTPOX, HUMVWA31/A, HUMTH01, and HUMF13B), which have proven informative in establishing genetic relationships between human populations. Genetic trees and multivariate analyses of European and Near Eastern populations show that the Moroccan population shares a common genetic substrate with all of them. However, the latter defines a specific lineage. Evolutionary factors inherent in the population’s geographical isolation in early times, together with genetic flow from sub-Saharan populations (mainly as reflected by HUMF13B and HUMTPOX), appear to be particularly relevant in understanding the peculiarities of the genetic character of the present-day population.