3.5 KITLG-selected region was possibly introgressed from the Nubia
ibex into domestic goats
The strongest selection signal at the KITLG locus (18,116
–18,161 kb) was found to be located in the introgression segments that
have been introduced from EAFR goats into SWA population. We constructed
a haplotype map of KITLG -selected region in order to determine
relationships between all populations. Interestingly, our results show
that there are two contrasting haplotypes of this genomic region which
are variable within different Capra species, supporting their relevance
for adaptation (Figure 4c ). The haplotype that has a high
frequency in Africa, Southwest and South Asia (hereafter referred to as
the AFR-ASA) had the highest similarity with ibexes, particularly with
the Nubian ibex (Capra nubiana ), whereas the bezoar haplotype is
close to the KITLG regions in European and Chinese goat
individuals. The frequencies of this introgressed loci was higher in
EAFR (90%), IRQ (88%), WAFR (79%), IRN (77%) and PKS (72%), but
much lower in both two EUR (2%) and CHN (5%) populations
(Figure 4d ), indicating a gradual decrease from African to
Southwest and South Asia. In addition, the haplotype network of theKITLG -selected region showed two highly divergent haplogroups in
worldwide domestic goats (Figure 4e ). Of the SWA individuals,
75% < belong to AFR-ASA haplogroup. To further assess the
origin and diffusion of KITLG allele in domestic goats, an
in-depth genetic survey was carried out on ancient remains from the
Fertile Crescent region. We first detected an ancient animal havingKITLG -selected region at Bronze age of Levant (dating to
~3,500 YBP) (Figure S10 ). The results also
illustrate that one Iranian goat sample from the Medieval age
(1,641-1,473 cal AD) carried this genomic region. This finding is
consistent with the hypothesis that the gene flow from Levant goat
groups into SWA region has been occurred prior to the Medieval age.