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.