Southern and eastern African populations that speak non-Bantu languages with clickconsonants are known to harbour some of the most ancient genetic lineages in humans, buttheir relationships are poorly understood. Here, we report data from 23 populations analysedat over half a million single-nucleotide polymorphisms, using a genome-wide array designedfor studying human history. The southern African Khoisan fall into two genetic groups, looselycorresponding to the northwestern and southeastern Kalahari, which we show separated withinthe last 30,000 years. We find that all individuals derive at least a few percent of their genomesfrom admixture with non-Khoisan populations that began ~1,200 years ago. In addition, theEast African Hadza and sandawe derive a fraction of their ancestry from admixture with apopulation related to the Khoisan, supporting the hypothesis of an ancient link betweensouthern and eastern Africa.
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