Human populations show subtle allele-frequency differences that lead to geographical structure, and available methods thus allow individuals to be clustered according to genetic information into groups that correspond to geographical regions. In an early worldwide survey of this kind, division into five clusters unsurprisingly identified (1) Africans, (2) a widespread group including Europeans, Middle Easterners, and South Asians, (3) East Asians, (4) Oceanians, and (5) Native Americans. However, division into six groups led to a more surprising finding: the sixth group consisted of a single population, the Kalash.1 The Kalash are an isolated South Asian population of Indo-European speakers residing in the Hindu Kush mountain valleys in northwest Pakistan, near the Afghan frontier. With a reported census size of 5,000 individuals, they represent a religious minority with unique and rich cultural traditions. DNA samples from the Kalash have been distributed as part of the cell-line panel from the Foundation Jean Dausset’s Human Genome Diversity Project and Centre d’Etude du Polymorphisme Humain (HGDP-CEPH) for over a decade and have formed part of several genetic analyses.2 Analyses of uni-parental (Y chromosome and mitochondrial) DNA markers characterized the Kalash as a small population that had undergone a population bottleneck during their recent migration to their present-day abode.3,4 This was confirmed by the study of genome-wide autosomal SNPs, which highlighted a strong pattern of genetic drift in this population.5 A recent exploration of admixture at fine scales suggested that a major admixture event between the Kalash and present-day western Eurasians occurred between 990 and 210 BCE and related this to Alexander’s invasion of the Indian sub-continent in 327–326 BCE,6 although no evidence of such admixture was detected by an analysis of Y chromosome and autosomal short tandem repeat (STR) variation in the Kalash.7,8