Additional file 1:

Origins of individual accessions. A detailed assessment of the origin of each species/accession based on ETS features (phylogeny, shared polymorphisms), cpDNA haplotype, ploidy and genome size is given. The file also includes some ecogeographic, morphological and floristic information and a table containing source information for all accessions including the outgroup.

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Additional file 2:

Patterns of ETS recombination. Cloned sequences of nine interclade hybrid accessions (H. olympicum, H. mixtum, H. prenanthoides 1187, H. caesium, H. pilosum 1226/2, H. villosum 1305, H. gymnocephalum 1215, H. heterogynum, H. plumulosum) and H. kittanae, the non-hybrid accession with the highest number of intra-individual polymorphisms, are shown. Cloned sequences are compared with intra-individual polymorphisms and dominant character states revealed by direct sequencing. All cloned accessions with recombinant sequences are included. Patterns of gene conversion and the distribution of accession-specific polymorphisms across the cloned sequences can be traced. Color coding of diagnostic character states as in Figure 5.

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Additional file 3:

Summary of intra-individual polymorphisms. All intra-individual polymorphisms are listed according to their position in the alignment along with the accessions in which they occur, discriminating additive, unique, and shared variation. Among the shared polymorphisms, homoplasious and informative ones are identified according to specified criteria.

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Additional file 4:

Alignment of Hieracium ETS sequences. A FASTA file is given comprising two sequences for each accession (i) one with all polymorphic sites included (lower case letters indicate weak [i.e., second peak small] or indel polymorphisms): the sequence name is composed of the abbreviated species name and the number of the accession/plant, and (ii) one resolved for the major sequence in case of skewed ratios: same label, but preceded by an 'M'. Additionally, cloned sequences are given for the respective accessions: same label, but preceded by the clone number. The positions in the alignment correspond to Table 1, Figure 4, and Additional files 2 and 3.

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Additional file 5:

Species/accessions, their origin, cytotype, ETS and cpDNA features. This table summarizes the information about individual accessions.

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Additional file 6:

ETS phylogeny with ribotypes present only in hybrids. The file contains the phylogenetic analyses on which Figure 5 is based. One out of 1402 equally parsimonious trees is shown (1752 steps, ri = 0.952, ci = 0.982; 182 variable characters of which 95 were parsimony informative) with bootstrap support indicated above the branches. The strict consensus tree topology corresponds to the branches with support values. Bootstrap values for ML and posterior probabilities for Bayesian analyses are given below the branches. Diploid Hieracium species are indicated in boldface. All lineages comprise diploids (the 'unknown Western 1' ribotype also occurs in low amounts in diploid H. lucidum which was not cloned). The Wx, Wy, and Ex lineages are represented by all non-recombinant clones of these ribotypes. Identical clones of the same accession were included only once (see also Additional file 2: Patterns of ETS recombination). The four hybrid accessions still maintained in Figure 2 were excluded, and also H. lachenalii and H. sparsum because of inferred chloroplast capture. Figure 5 uses the basic structure of this tree on which all inferred reticulation events were mapped.

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