3.4 Local adaptation by selective sweeps
The adaptation of indigenous livestock species in the SWA region to hot and dry desert ecosystems (Middleton 1986, Vaghefi et al. 2019) may have effect on the hair and skin traits, which directly related to heat loss ability (Deng and Xu 2018, Berihulay et al. 2019). For example, most of the SWA indigenous sheep breeds have coarse wool coats, whereas the majority of local goat breeds in the cold climate of northern Asia are cashmere-producing (Du et al. 2011). In order to gain insight into the adaptation to desert climate, we compared the native goats from SWA with Northeastern-Asia by calculating pairwise genetic differentiation (F ST) and differences in nucleotide diversity (π ln-ratio Northeastern Asia/SWA). After merging consecutive windows with high values, we found 46 windows with the top 1% values in bothF ST and ln-ratio, spanning 72 candidate genes (Figure 4a and Table S6 ). The top F SToutlier window contains introgressed signals related to KITLGgene on chromosome 5 (18,075–18,160 kb) which is associated with hair follicle traits (Guenther et al. 2014). Low π and Tajima’s D values and high composite likelihood ratio (CLR) scores suggest strong positive selection at this locus in SWA goats (Figure 4b ). Previous studies showed that KITLG is an important modulator of skin pigmentation in animals, which plays a vital role in follicular survival and the development of the melanocyte lineage in adult skin (Yang et al. 2018). Melanin pigments have a direct role in the protection against UV-radiation and thermoregulation, which can pleiotropically influence a variety of behavioral and physiological traits in mammals (Sulem et al. 2007, Yang et al. 2018, Deng and Xu 2018). We did not find any non-synonymous mutations within the coding region, suggesting a role of regulatory mutations.