Linkage disequilibria (LD) and haplotype clustering in the region surrounding the MHC of Alpine ibex.

<p>(A) LD heatmap (r²) of chromosome 23 for the Alpine ibex population Cape au Moine. The color gradient scale represents the range of r² values. Red is used for the highest estimates of linkage disequilibrium. The chromosomal position of SNP16397 (diagnostic for <i>Caib-DRB</i>*2) is indicated by a blue asterisk. The red circle shows a SNP of a low minor allele frequency (0.06) that may explain the low LD. (B) NeigborNet networks were constructed from SNP haplotypes in three regions of chromosome 23. <i>Caib-DRB</i>*1 and <i>Caib-DRB</i>*2 haplotypes are colored in green and red, respectively. Networks are shown separately for three chromosomal sections of similar length comprising 7, 21 and 3 SNPs, respectively.