Fig. 4: Origin of introgressed fragments in Indonesian cattle.
a The mean ratio of SNPs shared with two outgroups, Javan banteng and gaur, in inferred introgressed regions of each admixed cattle population, based on Hmmix. b Pairwise identity by state matrix (mibs) calculated from overlapping archaic regions (probability > 0.9) between two individuals using a 10 Kb window size. Insert: neighbor-joining tree of the genetic distance (1-mibs) in pairwise overlapping archaic regions. c Inference of admixture time using AdmixtureHMM with one pulse model. Numbers shown are average generation times across 100 bootstraps. d Genome-wide heterozygosity in two admixed populations, Aceh (n = 24) and Madura (n = 17), when stratified by the three possible ancestry states: homozygous for zebu ancestry (“Zebu” on x-axis), homozygous for banteng ancestry (“Banteng”), heterozygous for zebu/banteng ancestry (“Mixed ancestry”) and finally across the whole genome (“All”). Results for all admixed populations and East Asian zebu are in Supplementary Fig. 14. Boxplots indicate median (centre line), the 25th and 75th percentiles (box), and the highest and lowest values within the upper and lower quartiles ± 1.5* interquartile range, respectively (whiskers). e PCA analysis on genome segments of banteng ancestry origin and zebu ancestry origin respectively, as inferred by LOTER. To remove any distant relatedness among samples, we removed one of each pair of individuals with K1 > 0.2 identified by ngsRelate for (b, d) (Supplementary Fig. 31).
