Selected SNPs and linkage disequilibrium plots. Figure 1 depicts the LD (D') and the tag SNPs selected by each program. Red regions depict D' = 1.0 with strong confidence. Light blue regions are D' = 1.0 but decreased confidence. White regions are D' < 1 and state D' within the box. An X denotes that SNP was selected by the program. The gray shading in the HAPLOVIEW row represents the Gabriel blocks. The dark lines represent breaks between blocks for both HAPLOVIEW and HaploBlock Finder. For some chromosomes no blocks were identified and this is indicated by hatch marks across the SNPs.