Fig. 2

Linkage disequilibrium. Gaussian kernel smoothed pairwise linkage disequilibrium (LD), r², by SNP pair distance (bp) for chromosomes 1 and 6. Pairwise LD was calculated for all pairs of SNPs on each chromosome using Plinkv1.9, and a Gaussian kernel smoother (σ = 500) fit to model the relationship between SNP distance and pairwise LD on each chromosome. Most chromosomes resembled chromosome 1 (top) in that LD quickly decayed to a baseline of ~ 0.1 r². Several chromosomes such as chromosome 6 (bottom), however, were subject to large linkage blocks as a result of linkage drag around conversion loci on these chromosomes. Similar plots for the other chromosomes can be found in Additional file 2: Figure S2