Figure 6

Phylogenetic relationships between dandelions used in the study. The ITS sequences of Taraxacum kok-saghyz (TKS), other Taraxacum species of interest, US dandelions, and outgroup specimens from Southeastern US were aligned using MAFFT^62,63, trimmed with SeaView-Gblocks⁶⁵ to remove the uninformative characters, and used for thorough-bootstrap RAxML⁶⁶ analysis (100 runs with 10,000 repeats, rapid hill-climbing mode, GTR substitutions, multiple outgroup), over 451 distinct alignment patterns. The Gblocks regions alignment was 660 bp long. Proportion of gaps and completely undetermined characters in this alignment: 3.39%. The resultant tree was built using FigTree, and the branches are colored as per the bootstrap support (indicated on the color legend). Arrows indicate positions of sequences pulled from NCBI (T. ceratophorum: consensus of three ITS sequences deposited; T. erythrospermum: consensus of 12 ITS sequences; T. officinale: consensus of 49 sequences; Supplementary Table S2), of the historical T. officinale specimen (TofficinaleW413345: WTU 413345; picture published with permission of the Burke Museum, University of Washington) and the historical specimens of TKS (TKSherbKent: KE 650; TKSherbMontana: MONT 51683), or other species³⁴ (for TKS, Ceratoidea). No ITS sequences for T. brevicorniculatum were found at NCBI. The sample origin (population names) or Taraxacum species names are indicated. Dotted grey box delimits the out-group for RAxML (non-Taraxacum species by ITS BLAST of sequences); orange box indicates the TKS. Sample ESKUSA E55/12 was used for de novo sequencing and development of the gSSRs used in this study. Pictures of exemplary specimens show TKS, T. brevicorniculatum (BRE), and T. officinalis (OFF; the dashed lines are indicating which specimens are shown). Samples of TKS, T. officinale, and T. brevicorniculatum marked with S were grown for another study²⁶.