Haplotypes of ancient DNA samples
Daly et al. (2021) assigned ancient DNA samples from southwest
Asia and southeast Europe to the domestic Y-chromosomal haplogroups on
the basis of their positions in a phylogenetic tree. Cai et
al. (2020) and Zheng et al. (2020) described eight Chinese ancient
DNA samples and one medieval sample from the northern Caucasian region.
Sample YJL2G (coverage 13.4×) clustered with the Y1AB haplogroup, but
the low coverage of the others (from 0.013 to 0.118×) resulted in an
insufficient overlap with the 552 SNPs that are variable in domestic
goats and did not display female scores or male heterozygote scores (see
above). Therefore, we relaxed the latter requirements and allowed SNPs
scoring in 1% of the females. After removal of two male samples, each
representing a unique haplotype, with a high proportion of heterozygote
scores, we excluded SNPs with male heterozygote scores only if this
occurred in a panel of 78 individuals representing different haplotypes.
This resulted in 5593 SNPs, 1018 of which were also scored in the
low-coverage aDNA samples. The combined phylogenetic signals (Table S7)
showed for sample GTM6G a high proportion of inconsistent scores,
presumably due to contamination, but allowed plausible haplogroup
assignment for samples KA1G, SMG11 and YJL2G and a tentative assignment
for GB3.