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.