Fig 3. Evolutionary relationships between accessions based on the A_T-genome.

Most accessions are located according to expectation from previous studies and in agreement between the A_T- and D_T-genome based trees. Consensus bootstrap neighbor-joining trees were constructed (by PHYLIP) based on distance matrices representing SNPs between each pair of accessions. The root representing the point of connection to the diploid relatives. Individuals from AD₁ are colored blue, AD₂ colored green, and other tetraploid species colored red. Branch numbers indicate percent bootstrap support for that split. The A_T- and D_T-genome trees largely agreed in regard to the topology of the AD₂ clade, with the exception of the positioning of a sub-clade containing the 3 cultivars: Deltapine-340, Giza-7, and Phytogen-76. The AD₁ clade was similarly constructed in the A_T- and D_T-genome phylogenies, although the cultivars are so closely related to one another that their precise arrangements varied between trees.