3.2 High genetic affinity between modern goat populations in
Southwest Asia and East-Africa
To determine genome-wide introgression between present-day domestic
groups, D and F -branch (f b) statistics were calculated
with Dsuite software (V3, Malinsky et al. 2021). The results show strong
signals of introgression between IRQ-IRN (f b = 0.61, Z=35.21),
EAFR-IRQ (f b = 0.419, Z = 14.32) and EAFR -IRN (f b =
0.374, Z =11.98) populations (Figure 2a ). Additional
cross-drainage introgression was also detected between some trios such
as between common ancestor of African and both IRQ (f b=0.58,
Z=12.32) and IRN (f b=0.51, Z=9.58) populations, while we did not
find evidence of gene flow between WAFR goats and SWA populations. These
values are higher than the EAFR-IRQ and EAFR-IRN values and may suggest
that the latter values reflect introgression of the common ancestor of
EAFR and WAFR in the Levant region. The f b results also
highlighted excessive allele sharing between CHN/BNG, PKS/IRN and
EUR/WAFR populations (Figure 2a ). The results were further
supported by TreeMix analysis which reveals signals of genomic
introgressions from EAFR goats into IRQ (m = 1) and IRN (m = 2),
explaining 99.7% and 99.9% variance, respectively (Figure 2b
and Figure S7 ).
Quantifying gene flow of EAFR goats into both IRQ and IRN populations by
using the Loter program (Dias-Alves et al. 2018) shows that the
proportion of introgression was not uniform among present-day goats in
different parts of SWA region. The frequency of gene flow gradually
decreased with the increase of distance from EAFR
(Figures 2c and 2d ). The average frequency
was highest (~65%) and lowest (~36%)
in samples located in IRQ and south parts of IRN, respectively. Using
the f d statistic (Malinsky et al. 2021) we further localize
genomic regions with significant probability of introgression from EAFR
goats into both IRQ and IRN populations (Figures S8a and S8b ).
The length of the introgressed regions varies from several hundreds to
more than 200,000 base pairs. Selecting the top 1% of these regions, we
obtained 2456 (2218 genes) and 974 (966 genes) autosomal regions as
high-confidence introgressed segments for IRQ and IRN goat groups,
respectively (Tables S4 and S5 ).