Supplemental Tables (see separate file)
Table S1. Diagnostic SNPs used in this and previous studies. Mutations are relative to the goat reference sequence, which has haplotype Y1AB. Haplotype assignments are consistent with their position on the phylogenetic trees.
Table S2. Selection of Y-chromosomal scaffolds in the ARS1 assembly with the lowest frequency of heterozygote SNP scores in male goats. Scaffolds used as source of SNPs are printed in bold.
Table S3. Individual codes (see Figs. 1 and 3) and SRA accession numbers of WGS data used retrieved from the Sequence Read Archive and used for phylogenetic analysis. Other SRA accession codes are in Table S5.
Table S4. Y-chromosomal haplotypes in domestic goats (A) and bezoars (B) used for Figs. 1b and 2. See Fig. 1 for the individual codes. Horizontal lines separate animals with the same haplotype. Haplotypes for the Neighbor-joining tree in Fig. 1b are based on allele-sharing distances. For the Median-Joining Network in Figure 2 trees, transboundary goats outside their countries have been omitted and ≤18 goats per breed were considered. Eight haplotypes for Fig. 1b were fused to other haplotypes by the default settings of the program Popart used for the construction of the Median-Joining Network.
Table S5. Haplogroup distributions in breeds or populations, in ancient DNA and in the bezoar. Kasp, (Kompetitive allele-specific PCR assay); ddSeq, dideoxy sequencing. Codes starting with ERX or SRX indicate Short Reads Archive accessions.
Table S6. Primers for amplification and dideoxy sequencing ofDDX3Y , SRY and ZFY fragments and genomic coordinates of sequence covered by the sequence reads excluding the most upstream and most downstream primer sequences.
Table S7. Identification of haplogroups for ancient DNA samples. Minor allele frequencies are based on a panel of 354 male goats with call rates >5%.