Fig. 3: SVs contributed to high-altitude adaptation and domestication of yaks.

a F_ST and Φ_ST between SV haplotypes in wild yaks and other bovine species (wisent, bison, European taurine). There is a significant linear relationship between the F_ST and Φ_ST (Pearson’s r = 0.98, p < 2.2e-16). b GO and KEGG enrichment analysis of the candidate genes of the identified SVs. c, d The two SV-haplotypes of EPAS1 (facultative adaptation) and MB (obligate adaptation) genes are determined by the presence or absence of 254 bp and 155 bp in the intron, respectively. Hap-0: SV haplotypes in non-QTP cattle, guar, bison, wisent and outgroup buffalo. Hap-1: SV haplotype in wild yaks. A retrotransposons LINE1 that overlaps with SV of EPAS1 is indicated with brown bar. VISTA plot of conserved shows sequence similarity of non-coding elements (CNEs) around and in the SVs of EPAS1 and MB (indicated by triangles) to the BosMut3.0 reference. e, f Luciferase signals and expression of two SV-haplotypes of EPAS1 and MB. Values are shown as means ± SD from three biological replicates; Exact p-values are shown; two-sided Student’s t-test. g, h Frequencies of SV-haplotypes of EPAS1 and MB in domestic yak, wild yak and cattle from graph genomes. i Frequency distribution of SVs haplotypes (dots) in wild and domestic yaks. j–l SV-haplotypes (Hap-0, mainly in wild yaks; Hap-1, mainly in domestic yaks) of SV-DISC1, VWC2 and SNX3 and corresponding luciferase signals. Values are shown as means ± SD from three biological replicates; Exact p-values are shown; two-sided Student’s t-test. Source data are provided as a Source Data file.