Additional file 1: of Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

Table S1. Description and accession numbers for canine genomes processed in this study. Indications for whether or not a sample was used in the ADMIXTURE analysis, selection scans (FST, XP-CLR, or VST) are provided. Table S2. Coordinates and annotations of outlier FST loci identified through the empirical approach, including intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S3. Parameters incorporated into demographic model for neutral evolution in village dog and wolf populations. Table S4. Coordinates and annotations of outlier FST loci identified through the simulation informed (non-empirical) approach, including genes as well as intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S5. Coordinates and annotations of outlier XP-CLR candidate domestication regions identified through simulation approach, including intersecting genes as well as intersecting Axelsson, Cagan and Blass, and Freedman loci [5, 8, 29]. Table S6. Predicted SNP effects (per variant effect predictor [42]) for sites in XP-CLR candidate domestication regions. Table S7. Coordinates of VST copy number outliers on autosomes and chromosome X. Table S8. Gene enrichment results for XP-CLR candidate domestication regions following p value adjustment (BLAST2GO). Table S9. Gene enrichment for XP-CLR candidate domestication regions following p value adjustment (EMBL-EBI). Table S10. Gene enrichment results for VST copy number outliers following p value adjustment. Table S11. Coordinates of VST copy number outliers on chromosome unknown (chrUn). Table S12. ddPCR results from 30 village, 3 New Guinea singing, and 5 breed dog samples of AMY2B segmental duplications. Table S13. ddPCR results from 48 breed dog samples of AMY2B segmental duplications. (XLSX 328Â kb)