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.