Haplogroups distribution in 180 goat breeds
We differentiated the major Y-chromosomal haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B for 2223 domestic goats from 180 breeds by combining data from several sources as detailed per breed in Table S5:
  1. From the goat panel collected for the Econogene project, DNA samples of 353 male goats from 38 European or southwestern Asian breeds were analyzed by PCR amplification and dideoxy-sequencing of DDX3Y ,SRY and ZFY segments (Lenstra & Econogene Consortium, 2005) as described previously for bovine samples (Edwards et al., 2011; Nijman et al., 2008) and using the primers listed in Table S6.
  2. We used published data from five Portuguese breeds or from Moroccan goats (Pereira et al., 2009), 12 Asian breeds or national populations (Waki et al., 2015, Tabata 2018, 2019, combined with unpublished data), for eight Turkish breeds (Çinar Kul et al., 2015) and for 26 Spanish and Swiss breeds (Vidal et al., 2017).
  3. Genotypes of 85 breeds in the VarGoats dataset were derived from their position in the phylogenetic trees (Fig. S1) and/or the alleles of the diagnostic SNPs (Table S1) without any conflicting assignments.
  4. 368 DNA samples from several sources, including the AdaptMap panel (Colli et al., 2018) were genotyped by the KASP assay (Kompetitive allele specific PCR assay), at the Van Haeringen Laboratory (Wageningen, Netherlands) and differentiated Y1 vs Y2 and Y1A vs Y1B.
  5. For 31 breeds genotypes were obtained by Blast searching of the Short-Read Archive (SRA) or derived from the original WGS data. SRA data for pools of individuals were only used if this allowed an unambiguous identification of the haplogroup composition.
For samples collected by Vidal et al. (2017), a few samples analyzed by Çinar-Kul et al. (2015) and samples analyzed by KASP before genomic data became available, Y1AA and Y1AB have been both scored as Y1A haplotype. Several of these samples did not contain Y1A or belonged to breeds for which additional data were available (Table S1). However, for 17 breeds we only have the Y1A frequency. Likewise, Vidalet al. (2017) and the KASP assays did not differentiate Y2A and Y2B. Since the VarGoats and Econogene panels with a comprehensive coverage of Europe and Africa did not contain a single Y2B-carrying goat, we assigned Y2 scores in other European and African goats to Y2A.