Summary trees for each of the nDNA regions and the combined nDNA tree, based on data sets with ∼83 accessions.

<p>We use letters to indicate well-supported clades, and infer that these correspond to genomic groups.</p

Summary of inferred ploidy levels and genomic compositions for taxa in the current study.

<p>Ploidy levels were inferred from sequence types, flow cytometry, and cytological studies. The symbol (+) indicates that other genomic components were suggested in some analyses, but not characterized further in the current study.</p

Divergent genomes within Panicum s.s. as inferred from nDNA clades.

*<p>Asterisks indicate that the genome was found in some but not all species in a particular taxonomic section. (In contrast, genomes A and B were found in all sampled members of sections <i>Urvilleana</i> and <i>Virgata</i>, while genome F was found in all sampled members of section <i>Panicum</i>).</p>**<p>Diploid species are underlined.</p

Flow cytometry results.

<p>Predicted ploidy levels as measured by flow cytometry. Estimates based on multiple samples of the same individual are indicated with parenthetical numbers; those based on different individuals representing the same accession are indicated with hyphenated numbers.</p

Bayesian phylogram for the <i>knotted1</i> abridged dataset.

<p>Selected examples of polyploid individuals are indicated. Outgroups have been omitted for clarity.</p

Cartoon of relationships among the species of sections <i>Virgata</i> and <i>Urvilleana</i> and their close relatives.

<p>Diversification occurred at the diploid level, a hybridization event involving a seed parent with the A genome and a pollen parent with the B genome gave rise to an allotetraploid offspring. Diversification then occurred at the tetraploid level. An AB genome tetraploid crossed with another AB tetraploid to give rise to octoploids and hexaploids. Octoploid <i>P. amarum</i> is omitted for clarity.</p

Bayesian phylogram of the analysis of all accessions of sections <i>Virgata</i> and <i>Urvilleana</i>, using only the B genome of <i>knotted1</i>; topology is that presented in Supplemental Figure S1 for the <i>Virgata</i>-<i>Urvilleana</i> clade, but with sequence names replaced by colored ovals.

<p>The pink oval with the letter c indicates sequences from <i>P</i>. <i>virgatum</i> var. <i>cubense</i>. Unlabeled ovals represent sequences from tetraploids. Ovals labeled with 6x or 8x indicate hexaploid or octoploid plants, respectively, from which only one sequence type was recovered. Slender lines connect sequences from the same plant. Vertices labeled 6x or 8x indicate hexaploid or octoploid plants respectively; unlabeled vertices indicate tetraploids. Numbers above branches are Bayesian posterior probabilities.</p

Statistics and evolutionary models for separate data partitions.

<p>PIC  =  parsimony informative characters. PIC parenthetical indicates the number of parsimony informative characters within the temperate clade. MP  =  maximum parsimony; CI  =  consistency index, excluding uninformative characters; RI  =  retention index. Models are based on the Hierarchical Likelihood Ratio Test implemented in jModelTest. MP tree numbers with asterisks indicate the maximum number that was saved.</p

Bayesian phylogram based on combined cpDNA data.

<p>Support values are Bayesian posterior probability/maximum parsimony bootstrap/maximum likelihood bootstrap. Names in all caps to the right of brackets indicate sections of <i>Panicum</i> s.s. Outgroups have been omitted for clarity.</p

DNA primers and PCR parameters used for amplification and sequencing.

<p>Asterisks indicate published primer sequences that were modified for this study; underlines indicate modified nucleotide sites. Chromosomal locations of nuclear genes are based on rice.</p