Genotyping of newly sequenced as well as previously reported modern individuals was carried out using SAMtools/bcftools (35), followed by filtering, as previously described (44). Briefly, per-individual diploid genotypes were called using SAMtools mpileup (-C50 option) and bcftools call with the consensus caller (-c option). Calls from each genome were then filtered, excluding calls with low (six reads or one-third of the average sequencing depth, whichever was higher) or high (>2 times the average depth) coverage. We further filtered variants called within 5 base pairs of each other, with a Phred posterior probability of < 30 or a strand bias or end distance bias P value of <104, or with deviations from Hardy-Weinberg equilibrium with a P value of <104 across all samples.

For population genetic analyses, those genotypes were merged with a reference panel of 2286 modern individuals from worldwide populations, genotyped at 593,610 SNPs using the Affymetrix Human Origins array (26, 27). All ancient individuals were represented by pseudo-haploid genotypes obtained by sampling a random allele at each SNP position. For the two ancient samples with higher coverage, KP1 (6.9×) and MH8 (6.8×), we also carried out diploid genotyping, as described above, to be used in the haplotype sharing analyses.

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