MOESM2 of Signatures of selection and environmental adaptation across the goat genome post-domestication

Additional file 2: Figure S1. MDS plot of the breeds, grouped by production purpose: milk, meat and fiber groups. Group colors: milk = green, meat = red, fiber = blue; MDS and box plots of the first two components pre-filtering (upper) and MDS plots after filtering. Figure S2. Manhattan plot of the FLK results for the sub-continental group after filtering steps. Sub-geographical group names are given on top of each plot. Chromosomes are alternately red and black. Figure S3. Manhattan plot of the hapFLK results for the sub-continental group after filtering steps. Sub-geographical group names are given on top of each plot. Chromosomes are alternately red and black. Figure S4. Genomic distribution of FLK and hapFLK signals across population groups. For each chromosome and each sub-continental group, the chromosomal position detected with at least one of the two approaches is indicated. Figure S5. Signatures of selection on chromosome 5 for the North western Africa, South eastern Africa and South western Africa groups. North western Africa (NWA): red; South eastern Europe (SEE): green; South western Europe (SWE): blue. The table (bottom-right) reports the genes within the region in which a signature was detected. Figure S6. Signatures of selection on chromosome 6 for the Central Asia, East Africa and South east Europe groups. Central Asia (CA): red; East Africa (EA): green; South east Europe (SEE): blue. The table (upper-right) reports the genes within the region in which a signature was detected. Figure S7. Signatures of selection on chromosome 13 for the Alpines and Central Asia groups. Alpines (Alps): red; Central Asia (CA): blue. The table (right) reports the genes within the region in which a signature was detected. Figure S8. Signatures of selection on chromosome 1 for the Alpines and South Western Europe groups. Alpines (Alps); red; South Western Europe (SWE): blue. The table (bottom-right) reports the genes within the region in which a signature was detected. Figure S9. FLK signals on chromosome 6 around the casein gene cluster. The cluster of unannotated genes between YTHDC1 and SULT1B1 consists of genes coding for glucuronosyltransferase enzymes. Alps; red; East Arica (EA): blue. The table (right) reports the genes within the casein cluster region. Figure S10. Signatures of selection on chromosome 6 for the Egypt, South Eastern Europe and South Western Europe groups. Egypt (Egypt): red; South Eastern Europe (SEE): green; South Western Europe (SWE): blue. The table (bottom-right) reports the genes within the region in which a signature was detected. Figure S11. Signatures of selection on chromosome 12 for the Central Asia and South Western Europe groups. Central Asia (CA); red; South Western Europe (SWE): blue. The table (right) reports the genes within the region in which a signature was detected. Figure S12. ROH, FST and XP-EHH results for the group of “meat-producing” goat breeds. Types of analysis are indicated with different plot colors, within the most external squared-based circle, where each color represent a chromosome (chromosome number outside the squares): green (external) = ROH; blue (middle) = Fst; violet (internal): XP-EHH. For the three analyses, the regions above the threshold are marked in red. Figure S13. ROH, FST and XP-EHH results for the group of “milk-producing” goat breeds. Types of analysis are indicated with different plot colors, within the most external squared-based circle, where each color represent a chromosome (chromosome number outside the squares): green (external) = ROH; blue (middle) = Fst; violet (internal): XP-EHH. For the three analyses, the regions above the threshold are marked in red. Figure S14. CDA for the region on chromosome 25 detected for the group of “fiber-producing” goat breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S15. CDA for the region on chromosome 25 detected for the group of “meat-producing” goat breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S16. CDA for the region on chromosome 25 detected for the group of “milk-producing” goat breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S17. MDS plot of breeds considered for the panel of coat colors. Breed codes and subdivisions based on the coat color pattern are indicated in the right part of the plot. Figure S18. CDA for the region on chromosome 18 near the MC1R gene detected for the group of coat color breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S19. CDA for the region on chromosome 13 near the ASIP gene detected for the group of coat color breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S20. CDA for the region on chromosome 5 near the ADAMTS20 gene detected for the group of coat color breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S21. MDS plot of the filtered dataset considering components 1 and 2. Animals are color-coded based on the Köppen classification of groups: Tropical (green), Dry (red), Temperate (orange), Continental (blue). Figure S22. FST plot of the comparison of the Dry group vs. the other groups. The threshold line in red represents the 0.995 of the percentile distribution (FST = 0.398). Figure S23. FST plot of the comparison of the Temperate group vs. the other groups. The threshold line in red represents the 0.995 of the percentile distribution (FST = 0.320). Figure S24. FST plot of the comparison of the Continental group vs. the other groups. The threshold line in red represents the 0.995 of the percentile distribution (FST = 0.507)