Population genetics analyses were restricted with known present-day genetic variation to minimize false positives. Two different present-day reference panels including (i) the Human Origins genotype data set (41, 42) and (ii) the 1000 Genomes whole-genome sequence data (43) were used to call the SNPs of ancient individuals sequenced in this study and in published individuals (table S5).

Human Origins data set. A curated version of the Human Origins data set consisting of 594,924 autosomal SNP genotype calls for 2730 present-day individuals was obtained from (41). Using SAMtools (version 1.3) “mpileup” (30), SNPs of the ancient individuals overlapping with this data set were discovered. Genotypes of the ancient samples for positions of C/T or G/A type substitutions were encoded as missing data. For overlapping SNPs, genotypes of ancient individuals were merged with reference data set, and a full data set was haploidized by randomly picking one allele per position using a custom script. This data set consisting of 2730 present-day individuals together with a total of 364 ancient samples (table S5) was used for ADMIXTURE and PCA.

1000 Genomes project data set. For statistical analysis, we used an SNP data set ascertained in African Yoruba population as in (26). For this, a data set of 1,979,918 transversions with minor allele frequencies of greater than 10% in African Yoruba individuals from 1000 Genomes Project phase 3 (43) was obtained from (26). SNPs of the ancient individuals overlapping with those were discovered using SAMtools (version 1.3) “mpileup” (30) and merged with this data set using PLINK (44). A full data set was haploidized, as described above.

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