Phylogeny of Y-chromosomal haplogroups
A phylogenetic tree of the wild and domestic goats (Fig. 1A) shows an intermingling of bezoars and the domestic goat. From the other wild goat species, the markhor is the closest relative of the bezoar and the domestic goat.
We found 107 different haplotypes in our panel of 352 domestic goats and 27 bezoars with markhor as outgroup. A phylogenetic tree (Fig. 1B) shows haplogroups that correspond to the haplotypes Y1B, Y2A (Lenstra & Econogene Consortium, 2005) and Y2B (Waki et al., 2015) whereas the Y1A haplotypes are split in haplogroups Y1AA and Y1AB. This is confirmed in a dataset of mainly Asian and Moroccan goats (Fig. S1). All domestic haplotypes differ from the Iranian or Anatolian bezoar haplotypes, which also differ from each other. The bezoar haplotypes are associated with the domestic Y1AA or Y2B clusters (CaY1AA and CaY2B, respectively), are linked to the Y1 or Y2 roots (CaY1 and CaY2) or are outside the domestic cluster (Y0).
Fig. S2 shows subtrees containing all 352 domestic goats. This figure also indicates goats with the previously proposed local haplotypes (Vidal et al., 2017; this study, Table S2): Y1AB2 (this study), Y1B2 and Y1C. Y1B2 is represented by Swiss, French and Dutch goats. Our goat panel does not contain goats with the Y2C diagnostic allele (Çinar Kul et al., 2015).
The phylogenetic relationships of domestic and bezoar haplotypes are confirmed by a Median-Joining Network (MJN, Fig. 2). Both the NJ tree and the MJN network allow a few interesting observations to be made: (i) a close relationship of Y1B sequences from Switzerland and Korean Native goats, suggesting a recent crossbreeding; (ii) likewise, a close relationship of Y1AA sequences from Central as well as South Asia, from South-African Boer goats and from other Y1AA goats in southern and eastern Africa and iii) a clear divergence of the Malagasy Y2A haplotypes from the African continental haplotypes.