Hierarchical clustered heatmaps of preselected genetic loci for 12 chicken genomes. Every block in the heatmap indicates estimated CN values of 1 kb non-overlapping windows in the preselected region. These heatmaps are generated from hierarchical cluster analysis using Pearson’s correlation coefficient of the CN values. The colors for each bar denote different copy number (CN). (A) DX and SK which are predicted to be doubled within dermal hyperpigmentation loci are clustered together. (B) Upstream and downstream of the SOCS2 locus reveal higher CN values in DX, TB and WC especially LX. (C) WL shows specific expansion in the POPDC3 locus and is split into a separate clade.