We used the VarLD software [24] to evaluate the magnitude of the differences in LD patterns (Fig. 1c) between two populations. We analysed the pairwise comparison of the three populations: base population with the line with high VE of LS (Base-High), base population with the line with low VE of LS (Base-Low), and between the lines with high and low VE of LS (High–Low). Sliding windows of 50 SNPs with a step size of one SNP were used to calculate the correlation matrix of each population per chromosome. The program computed the r2 metric for each pair of SNPs to determine the strength of LD in each window. The difference between the eigenvalues of the correlation matrices of both populations determined the VarLD score, which was standardized by the mean and the standard deviation of all the scores along each chromosome. A genomic window was relevant when its standardized VarLD scores were equal or above the standardized VarLD score in the 99.9th percentile distribution for all the genomes. The relevant windows identified in both the Base-High and Base-Low comparisons were considered as putative signatures of selection and the relevant windows identified only in the High–Low comparison were considered as resulting from the effect of gene drift.

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