2.1 Sample collection, DNA extraction and sequencing
Whole-blood samples (15 ml) were collected from indigenous goats from Iraq (n=23) and Pakistan (n=25) countries. DNA was isolated from whole blood using standard phenol-chloroform extraction method. Pair-end sequence data for all individuals were generated using the Illumina Hiseq 2500. In addition, previously published genome sequence data from ancient (n=50), modern (n=163) and wild goats (n= 72) were also obtained from the Sequence Read Archive (ncbi.nlm.nih.gov). Details of the samples used in this study are described in tables (Tables S1-S3 ). High-quality reads in the present study and published data were aligned against the most recent goat reference genome (ARS1, GCF_001704415.1) using Burrows-Wheeler Aligner (BWA aln) algorithm (Li and Durbin 2010). The variant calling of sequence data were handled using GATK (McKenna et al. 2010), and the genotype likelihoods were calculated using ANGSD program (Korneliussen et al. 2014). Finally, to minimize the false-positive results, the transition sites were discarded in ancient samples.