We used multiple measures to authenticate the generated aDNA data. (i) To control for potential laboratory contamination, blank extractions and library preparations were included and analyzed for each sample batch (data file S3). (ii) Levels of DNA deamination damage in the mapped reads were estimated using mapDamage (v2.0) (39) and compared to the expected values in ancient skeletal element. (iii) We measured human mitochondrial DNA contamination using schmutzi (40). (iv) The genetic sex was inferred for each individual by calculating the ratio of the X and Y chromosome coverage (normalized by the autosomal average coverage). We next used ANGSD (v0.910) (41), which compares mismatch rates between polymorphic sites on the X chromosome to estimate nuclear contamination in males.

To avoid bias associated with including related individuals into analyzed populations, we calculated the pairwise allele mismatch rates of all newly reported individuals following a method described elsewhere (fig. S1) (42).

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