2.2 Genetic diversity, population structure and phylogenetic relationship
We investigated different genomic diversity parameters including nucleotide diversity, inbreeding coefficient (F) and linkage disequilibrium (LD) decay using PLINK software (Purcell et al. 2007), with the default settings. The maximum likelihood (ML) tree was constructed for the whole-genome SNP set of all modern domestic goats. The online tool iTOL (https://itol.embl.de/) was used to display the topological structure. ADMIXTURE was performed to characterize the population structure of modern goat populations (Alexander et al. 2009). We increased the number of ancestral clusters (K ) from k = 2 to k = 6 and ran the analysis 100 times for each k . The PCA analysis was conducted using SmartPCA implemented in the EIGENSOFT package, with the “lsqproject” and “autoshrink” options (Patterson et al. 2006). In order to identify population structure among all goat populations, we performed haplotype-based approach to explore patterns of haplotype sharing using ChromoPainter and fineSTRUCTURE among all individuals (Lawson et al. 2012).