Fig. 4: Phylogenomic analysis of nuclear genomes and dating.

a Best maximum-likelihood Brachypodium phylogenomic tree based on 745,854 syntenically aligned nuclear SNVs. Most branches show strong support (Supplementary Fig. 6). Divergence times for key branches are indicated based on the tree in Supplementary Fig. 7. B. stacei (red), B. distachyon (blue), B. hybridum D plastotypes (S subgenome, brown; D subgenome, green), B. hybridum-S plastotype (S subgenome, yellow; D subgenome, purple). b, c Bayesian genomic structure analysis based on 5443 SNVs. Percentages of membership of genomes and subgenomes to the inferred genomic groups: b B. stacei and S subgenomes (k = 2), c B. distachyon and D subgenomes (k = 3). d Cross-bracing analysis to determine the dates of formation for the recent and ancient B. hybridum clades. The numbers on the diagonals represent the estimated divergence times of the D and S subgenomes from the diploid progenitor B. distachyon and B. stacei genomic lineages.