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).