Authenticity of the sequences was firstly evaluated on the basis of the presence of ancient DNA-specific damage patterns including increased frequency of C to T type transitions at 5′ end of the sequences due to deamination and based on short mean sequence length due to fragmentation (14, 34). PMDtools (35) was used to assess the nucleotide misincorporation patterns at the 5′ ends of the reads. All sequence data showed increased C to T frequencies at 5′ ends. The sequencing statistics of all libraries are listed in table S3. mtDNA contamination was estimated using two different methods (15, 16). In the first method (15), private or near-private alleles (less than 5% in 311 modern mtDNA sequences) with a minimum sequencing depth of 10 and with a base quality of 30 were considered. Transition-type substitutions were filtered, and the point estimate of contamination was calculated by summing the counts of consensus and alternative alleles across all sites. For the second method (16), to calculate probabilities of being authentic based on mtDNA, SAMtools “mpileup” (30) and vcftools (36) were used. Probabilities of being authentic were calculated using “contamMix” library in R.

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