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.