aDNA authentication

As a result of degrading over time, aDNA can be distinguished from modern DNA by certain characteristics: short fragments and a high frequency of C→T substitutions at the 5′ ends of sequences due to cytosine deamination. The program mapDamage2.0 (70) was used to estimate the frequency of 5′ C→T transitions.

mtDNA contamination was estimated using the method from (71).This included calling an mtDNA consensus sequence based on reads with mapping quality of at least 30 and positions with at least 5× coverage, aligning the consensus with 311 other human mtDNA sequences from (71), mapping the original mtDNA reads to the consensus sequence, and running contamMix 1.0-10 with the reads mapping to the consensus and the 312 aligned mtDNA sequences while trimming seven bases from the ends of reads with the option trimBases. For the male individuals, contamination was also estimated on the basis of chrX using the two contamination estimation methods first described in (72) and incorporated in the ANGSD software (73) in the script contamination.R.

The samples show 10% C→T substitutions at the 5′ ends on average, ranging from 6 to 17% (table S1). The mtDNA contamination point estimate for samples with >5× mtDNA coverage ranges from 0.03 to 2.02% with an average of 0.4% (table S1). The average of the two chrX contamination methods of male individuals with average chrX coverage of >0.1× is between 0.4 and 0.87% with an average of 0.7% (table S1).