Additional file 1: Table S1. Statistics for the window selection analysis. Table S2. Groups of breeds that were compared in this study. Table S3. Estimates of effective population size (Ne) over time (from 13 to 142 generations ago). Table S4. Single-SNP-based FST distances between pairs of rabbit populations. Table S5. Window-based FST distances between pairs of rabbit populations. Table S6. The most relevant results obtained from the PCAdapt analysis that overlap with those of the FST analyses. Table S8. Pearson’s correlations for genome windows FST values obtained from Method 1 and Method 2 (P-value < 2E−16). The reported values are the means of the correlations of the SNPs across all the chromosomes and all the genome windows. Table S9. Statistics on the single-breed window-based FST analyses (Method 1 and Method 2). Table S10. Statistics on the identified genome regions from the single-breed window-based FST analyses. Table S14. List of relevant genes identified with the FST single-marker-based analysis in the single-breed approach based on the two methods also applied in the window-based analyses (Method 1 and Method 2). FST values of the markers at the extreme lower end of the distributions (99.95th percentile) and mapped to genes of interest are presented. Table S17. Genome regions including candidate genes and the total number of genes included in the genome windows identified with the window-based single-breed FST analysis. This table is complementary to Table 3. Table S18. Statistics for the window-based FST analyses in the approach based on groups of breeds. Table S20. List of relevant genes identified with the FST single-marker-based analysis in the approach based on groups of breeds. FST values of the markers at the extreme lower end of the distributions (99.95th percentile) and mapped to genes of interest are presented. Table S26. Gene enrichment analysis. Gene sets (99.0th percentile) related to the group-based FST analyses were tested for over-represented biological features.