2.4 Gene flow and demographic history analyses
To assess introgression patterns between all groups, we performed
different statistics including outgroup-f 3, D, F -branch
and F 4-ratio with Admixtools (Patterson et al. 2012) and the
Dsuite software (Malinsky et al. 2021). We highlighted introgression
candidates as trios with significant D values (Bon-ferroni-corrected
p-value < 0.001) and f 4-ratios > 0.05
between populations. The local ancestry of the genome haplotypes was
further inferred using Loter software (Dias-Alves et al. 2018). To infer
patterns of effective population size and population separations over
historical time, we applied SMC++ software (version 1.10.0) (Terhorst et
al. 2017). The TreeMix 1.13 software (Pickrell and Pritchard 2012) was
used to model gene flow between modern domestic goat groups. We chose
argali as an outgroup forming the root of the tree rather than domestic
goat breeds to avoid any bias.