Mitochondrial consensus sequence per sample was called using SAMtools “mpileup” (30) and vcftools (36). Haplogroups were determined using Haplofind (37), and final assignment of haplogroups was performed on the basis of visual inspection of each consensus against PhyloTree mtDNA tree (build 17) (38). Variable site calls were prepared using MITOMASTER (39). Mitochondrial DNA genomes of a number of individuals published here were discussed in detail elsewhere (11).

Similarly, Y chromosome sequences were filtered out from BAM files aligned to the human reference genome 19 (hs37d5) using SAMtools version 0.1.19 (30). The Y chromosome haplogroups were assigned using haplogroup identifying SNPs included in minimal PhyloTreeY (version 30-Nov-2014) (40) and ISOGG Y-DNA haplogroup tree 2017 version 12.29 (International Society of Genetic Genealogy). Only SNPs of base and mapping qualities of 30 were used. Whenever possible, the haplogroup assignment was restricted to derived transversions to avoid misclassification resulting from damage. All uniparental markers are listed in table S3.

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