We carried out a maximum likelihood unsupervised clustering of 5581 ancient and present-day individuals using ADMIXTURE (v1.3.0) (23) with a cluster number (k) ranging between 2 and 20. We used the --indep-pairwise option in PLINK (v1.90) (44, 45) to prune for linkage disequilibrium by identifying SNP pairs with genotype r2 ≥ 0.2 within a 200-SNP sliding window (advancing by 25 SNPs each time) and retaining only one randomly chosen SNP (--indep-pairwise 200 25 0.2). We performed five replicates for each k with random seeds and chose the highest likelihood replicate (fig. S3). Fivefold cross-validation (CV) errors were calculated for each run.

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