Fig. 3: Tracing the basal lineages for wheat domestication.

a NJ tree of WE and DT accessions constructed with AHG-based distances for the A&B subgenomes. The six basal lineages are noted by colored areas, and branches of DT accessions are collapsed. The percentage of AHGs in domesticated wheat gene pools that were found in each WE accession (contribution) and the genomic proportion of each WE accession that contributed AHGs to domesticated wheat gene pools (coverage) is shown. 6 basal lineages, consisted of 12 accessions, are highlighted. b Cumulative contribution of 6 WE founder lineages and other WE accessions to the domesticated wheat genetic pools is shown for individual chromosomes. c Mosaic graphs of AHGs for 5 WE and 5 DT accessions across chromosome 1 A. d Chloroplast SNP based NJ-tree provides cytoplasmic evidence for the origin of wheat. The tree is rooted by assigning Ae. speltoides (SS) accessions as an outgroup. Main clades are separated by gray dash lines. Clades containing T. polonicum (Polish wheat, tetraploid) and T. petropavlovskyi (Xinjiang wheat, hexaploid) were labeled, consistent with reported genomic introgression among the two populations28. Source data are provided as a Source Data file.