Supplemental Figures and Tables (Captions)
Figure S1. (a) Nucleotide diversity of domestic populations. (b) The decay of linkage disequilibrium (LD) over different genomic distances measured as the squared correlation coefficient for each domestic population.
Figure S2. Inbreeding coefficient (F) for different domesticated goat populations in this study.
Figure S3. ADMIXTURE model-based clustering analysis for each individual assuming different number of ancestral population (K  = 2 to 6).
Figure S4. The heat map of ChromoPainter’s coancestry matrix. Each row corresponds to the recipient genomes and columns represent the donor individuals. Iran-Iraq goat individuals (red box) have higher haplotype sharing with African samples, compared with other Asian goat groups (black box).
Figure S5. Mitochondrial genome and Y-chromosome haplotype analysis. (a) Maximum Likelihood phylogeny of the mitochondrial genomes from global domestic goat populations. (b) The pie chart shows the proportions of mitochondrial haplogroups in different goat populations. Haplogroup A is the predominant variant in all modern populations, but not in the bezoar. (c) Piechart plot representing the proportion of Y chromosome haplogroups in worldwide goat populations.
Figure S6. Inference of population size from whole-genome sequences. Effective population size histories are inferred from autosomes by using SMC++ software with a generation time of g=2 and a mutation rate per generation of μg= 4.32×10-9.
Figure S7. Admixture graph constructed with Treemix depicting the relationship between EFAR goats and samples from IRQ and IRN. The scale bar shows 10 times the average standard error (s.e.) of the entries in the sample covariance matrix. (a) ML tree with no migrations explaining 99.72% of the variance. (b) ML tree with one migration event from EAFR to IRQ explaining 99.7% of the variance. (c) ML tree with adding a migration event from EAFR to samples from IRN explaining 99.9% of the variance.
Figure S8. Genome-wild introgressions from East-African goats into Iraqi (a) and Iranian (b) goat populations. The East-African goats serving as proxy of the ancient Levant population that presumably has been the source of introgression.
Figure S9. D statistics using different ancient Iranian goats as the test population (X). A positive D value indicated the test population has a closer relationship with EAFR/ancient Levant goat group.
Figure S10. Genotyping information at the KITLG loci for the ancient goats. The presence of heterozygosity and homozygosity is colored in intermediate green and green, respectively. The absence of the derived allele is depicted in gray. Non-genotyped positions or individuals are indicated in white.
Table S1. Summary of breed information and geographic groups of modern domestic goat samples in this study.
Table S2. List of the published ancient samples from different archeological periods used in this study.
Table S3. Published wild Capra species samples used in this study.
Table S4. Introgressed segments from East-Africa gotas into Iraqi goat population.
Table S5. Introgressed segments from East-Africa samples into Iranian goat population.
Table S6. Summary of candidate selective sweeps.