3.1 Dataset, genetic diversity and population structure
In this study, we generated whole genomes from native goats of Iraq (n=
23) and Pakistan (n=25) countries. These data were combined with our
previously published data from modern Iranian goats and also worldwide
goat individuals (n=163). In addition, a total of 50 complete ancient
genomes from domestic goats in Anatolia, the Balkans, the eastern
Mediterranean area (Jordan and Israel, traditionally denoted as Levant),
Iran and Turkmenistan were obtained from one previous study (Daly et al.
2018, Tables S1, S2 ), resulting in a dataset of 261 domestic
goats. The ancient samples include Neolithic (~8500-5000
BC), Chalcolithic (~5100-3700 BC), Bronze Age
(~ 3300–990 BC), Iron Age (~700-330 BC)
and Medieval (~1500-901 AD) individuals. We then further
merged these data with 72 wild caprid species including different ibex
like species, bezoar and markhor goats to provide an overall
comprehensive assessment (Table S3 ). The 211 present-day
domestic samples were assigned to eight geographic subgroups, including
Europe (EUR), West-Africa (WAFR), East-Africa (EAFR), Iran (IRN), Iraq
(IRQ), Pakistan (PKS), Bangladesh (BNG) and China (CHN) (Figure
1a ).
The average nucleotide diversity (θπ) for all individuals was estimated
at 1.79e-3 and both Iranian (1.89e-3) and Iraqi (1.88e-3) groups showed
slightly higher diversity than other goat groups (Figure S1a ).
The LD was clearly higher for PKS goats than for the other populations
(Figure S1b ). The individual inbreeding coefficients (F) were
relatively high for European (~0.22) goats and lower for
both Iranian (~0.09) and Iraqi (~0.10)
goats (Figure S2 ).
A rooted ML phylogenetic tree of the whole-genome sequencing data
(Figure 1b ) shows the geographic clusters EUR-WAFR- EAFR;
IRQ-IRN; PKS-BNG and CHN. In a principal component analysis (PCA) of
modern domestic goats, PC1 shows a genetic cline from Chinese samples at
the eastern end to European goats at the western end (Figure
1c ), which is completely in agreement with the Admixture pattern
(Figures 1d and S3 ). The second PCA coordinate PC2 corresponds
to the contrast between African and northern EUR. As shown earlier by
Daly et al. (2018), ancient samples projected on the same plot are
positioned near contemporary individuals from the same region. The
results of painting algorithm from CHROMOPAINTER and fineSTRUCTURE shows
in agreement with Fig. 1, a low level of haplotype sharing of SWA (IRN
and IRQ) samples with most of the other Asian goat populations
(Figure S4 ).
A mitochondrial phylogenetic tree showed that all six previously defined
maternal haplogroups A, B, C, D, F and G are present in our dataset
(Figures S5a and S5b ). Haplogroup A is predominant in all
domestic groups. The PKS samples are with four haplogroups the most
diverse, whereas the EUR, IRQ and African individuals only harbor two
haplogroups. The analysis of Y-chromosomal haplotype diversity shows
that the haplogroup Y2A is predominant in both African and Iranian goat
individuals, and has a high frequency in Iraqi goat samples. The
haplogroup Y2B is found exclusively in Chinese domestic goats and bezoar
group (Figure S5c ). The SMC++ analysis shows that the
divergence times between all modern goat populations predated the
expected domestication time by archaeological evidence
(~11,000 years ago) (Figure S6 ).