The fixation index (FST) was used to estimate the differences in allele frequencies between the lines with high and low VE of LS (Fig. 1b). The FST was calculated using Weir and Cockerham’s pairwise estimator method [22], implemented in the VCFtools v1.16 software [23]. The FST values were estimated in 500-kb sliding windows with a step size of 250 kb. Windows with less than ten SNPs were excluded from the analysis. FST values were weighted to take differences in sample sizes between populations into account (for further details see Weir and Cockerham [22]). Relevant FST windows were those with a weighted FST value equal or above the weighted FST value in the 99.9th percentile of the distribution for all the genomes. MAF was calculated in the base population and the lines with high and low VE of LS for the relevant FST windows. Those that showed divergent changes in MAF between the rabbit lines relative to the base population were considered to be putative signatures of selection. These windows were considered as resulting from an effect of genetic drift if the MAF between the lines with high and low VE of LS at generation 11 displayed the same change relative to the base population (increase or decrease) or if one of the lines did not show any change (i.e. had a MAF equal to that in the base population).

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