Additional file 1: Figure S1. of Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat

Venn diagram represents the population-specific and overlapped SNPs among different populations. Figure S2. The frequency spectrum of SNPs in the A, B, and D subgenomes. Figure S3. The relative diversity of A and B subgenomes for wild emmer, durum, landrace and variety wheat. Figure S4. Nucleotide diversity (π) of the A subgenome of wild emmer, durum, the landraces, and the varieties. Figure S5. Nucleotide diversity (π) of the B subgenome of wild emmer, durum, the landraces, and the varieties. Figure S6. Nucleotide diversity (π) of the D subgenome of Ae. tauschii, the landraces, and the varieties. Figure S7. Neighbour-joining (NJ) trees of 93 accessions on the A, B and D subgenomes. Figure S8. Neighbour-joining (NJ) trees of 152 accessions on the A and B subgenomes. Figure S9. Principal component analysis of all accessions in the A, B, and D subgenomes. Figure S10. Population structure of AB and D subgenomes using ADMIXTURE. Figure S11. Absolute sequence divergence dxy value (the number of pairwise differences per site) between each pairwise accessions on A and B subgenomes. Figure S12. Principal component analysis (PCA) plots based on the first two principal components of 63 bread wheat accessions on A, B, and D subgenomes. Figure S13. ADMIXTURE analysis of 93 wheat accessions combined with the exon capture data of 26 landraces. Figure S14. Population divergence(Fst) of A, B and D subgenome. Figure S15. Nucleotide diversity (π) and population divergence (Fst) across five or four groups. Figure S16. Haplotype patterns and phylogenetic analysis of regions which length larger than 10Mb. Figure S17. Neighbour-joining phylogenetic tree of the longest haploblock on chromosome 4A. Figure S18. Divergence time of the different haplotypes of the longest haploblocks on chromosome 4A. Figure S19. Haplotype patterns of chromosome 4A in diverse populations. Figure S20. Boxplots of the sequence identity between reads of C46 mapped to chromosome 1BS and the sequence of outgroups. (DOCX 18309 kb)