MOESM3 of Signatures of selection and environmental adaptation across the goat genome post-domestication

Additional file 3: Table S1. Environmental variables considered for the landscape genomic analysis. Table S2. FLK and hapFLK windows for the sub-continental groups after filtering steps. Overlapping or partially overlapping regions across the different geographical subdivisions are reported with the same letter as used for the population group (from a to m). Table S3. Selective sweeps of early adaptation. The bold values indicate overlap or partial overlap between comparisons. Table S4 Common regions between ROH and XP-EHH and/or FST analyses for the group of “fiber-producing” goat breeds and genes within these regions. Table S5. Common regions between ROH and XP-EHH and/or FST analyses for the group of “meat-producing” goat breeds and genes within these regions. Table S6. Common regions between ROH and XP-EHH and/or FST analyses for the group of “milk-producing” goat breeds and genes within these regions. Table S7. Top four regions detected for the coat color groups (Black, White and Red), indicated comparisons between the groups and genes located nearby these regions. Table S8. Results of the most significant associations involving the 57 filtered SNPs. For each SNP: SNP probe, genotype, genomic coordinate, associated environmental variable (“Env”) and scores and statistical test output values (“Gscore”, “WaldScore”, “Efron”, “AIC”, “Beta_0” and “Beta_1”) are reported. Table S9. List of genes located nearby (± 100 kb) the 57 filtered SNPs obtained by the landscape genomics analysis. Table S10. GO term biological processes. Table S11. MAF (minor allele frequency) and major allele of the 13 SNPs shared by Dry and Temperate/Continental groups. Table S12. Samβada significant results for the SNPs of the FST analyses. For each SNP probe: chromosome and position are reported, as well as Environment, G score, Wald Score, AIC, Abs_Beta1 and the Köppen group in which the SNP was detected by the FST analyses. Table S13. List of genes located nearby (± 100 kb) of the 65 SNPs selected with the FST approach and confirmed by Samβada. The * symbol indicates the SNPs with the highest value (> 0.999) also in landscape genomic analysi