We selected 3102 published ancient human genomes from Eurasia (Table S1) from Paleolithic to Middle Age, whom DNA sequencing data generated with whole genome shotgun or hybridization capture technics, from the merge dataset v42.4 available at -ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data. We retained non-related individuals with more than 10,000 SNPs hit on the 1240k panel. We also added ancient individuals from two recent publications about Middle East37 and Mongolian Steppe38.
To verify possible projection limitation of our method, we also perform a PCA with LASER v276. We generated a reference space using 1915 Eurasian present-day individuals (including the Central Asian individuals), after filtering for a minimum allele frequency of 0.05. Then we downloaded the bam files for 635 relevant ancient individuals13,17,18 and projected independently every ancient individual into the reference space with 10 replicates. We obtained similar plots, with nearly perfect correlation between the first 3 PCs for the ancient individuals generated by smartpca and LASER (Supplementary fig. S2) indicating no significant limitation in our first PCA.
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