FIGURE 2.

Overview of the iterative procedure to define haplotype blocks with haplovalidate. After identifying candidate SNPs and calculating the window size (step 0), the haplotype reconstruction starts with stringent parameters (step 1). The allele frequency trajectory correlation of SNPs from different blocks on the same chromosome (focal block correlation) is compared to the correlation of SNPs from blocks located on different chromosomes and tested for significant differences (step 2, 3). If focal block correlations are higher than the background correlations, this indicates that a too stringent correlation cut‐off was used; and haplotype reconstruction is repeated using less stringent parameter (back to step 1). If focal block correlations are similar to background correlations, the least significant haplotype reconstruction is used and regions with overlapping blocks are filtered for the most dominant block (step 4) [Colour figure can be viewed at wileyonlinelibrary.com]