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.