The Kalash Are an Ancient Genetic Isolate
PSMC analysis applied to the high-coverage Kalash, three African genomes (YRI, LWK, and MKK), and six non-African genomes showed that the Kalash, like other non-Africans, experienced a severe bottleneck 50,000–70,000 years ago. The Kalash recovered slightly after the bottleneck but never achieved an effective population size above 20,000, as observed in the GIH (the other South Asian genome) and other non-African genomes, except the MXL (Figure 2A). The Kalash have maintained a low effective size below 10,000 for more than 20,000 years before the present. This pattern of unusually small effective population size in the Kalash is also supported by the estimate from the decay of LD, which was significantly lower (p = < 2 × 10−14) than that of neighboring populations from Pakistan (Figure 2B), although the estimated absolute sizes differed between the two approaches.
To examine the time of divergence between the Kalash and other genomes, we used multiple sequentially Markovian coalescent (MSMC) analysis on phased high-coverage genomes. The estimates based on pairs of genomes showed that the Kalash split first from Africans (LWK, MKK, and YRI) and then from East Asians (CHB and JPT). The split from Europeans (CEU and TSI) and South Asians (GIH) appears to have happened around the same time (Figure 2C), approximately 8,000 years ago. Examination based on LD decay in genotyping data also showed that the Kalash were the first population to split from the Central and South Asian cluster around 11,800 (95% CI = 10,600–12,600) years ago (Figure 2D). This estimate was obtained by UPGMA (unweighted pair group method with arithmetic mean) phylogenetic analysis comparing the structure of the tree in the Kalash and other South and Central Asian populations. This split time remained constant even after the addition of the YRI population. We also estimated these split times by using different subsets of non-African populations. The resulting UPGMA trees were not strongly affected by different subsets of European or South Asian populations (Figure S5), and the split times between the Kalash and other populations ranged from 9,600 to 12,600 years ago.