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Appendix S1. Species samples, taxonomic groups, origin and GenBank accession numbers of the investigated oak material. Botanic Garden Institution codes: HILL, Sir Harold Hillier's Botanical Garden and Arboretum, Romsey, UK; BR, National Botanic Garden of Belgium, Meise, Belgium; PAL, Botanic Garden of the University of Palermo, Italy; TUSC, Botanic Garden of the University of Tuscia, Viterbo, Italy; VAL, Botanic Garden of the University of Valencia, Spain.

Appendix S2. Main characteristics of the variation detected with the joined plastid markers and the nuclear 5.8S + ITS2 region in 104 oak individuals partitioned into subgeneric groups as defined by Denk & Grimm (2009, 2010). S, polymorphic sites; k, average number of nucleotide differences between sequences (Tajima, 1983); Pi (nucleotide diversity) = average number of nucleotide differences per site between two sequences (Nei, 1987); H, number of haplotypes; Hd, haplotype diversity; p, uncorrected p distance.

Appendix S3. Single and multi-region BLASTClust outputs, reporting haplotype ID, number of grouped sequences and species samples.

Appendix S4. Maximum likelihood tree obtained with GARLI with the dataset comprising only the ITS2 sequences. Posterior probabilities (PPs) and maximum likelihood bootstrap support (MLBS) obtained with GARLI are reported above the branches (if higher than 50%). Box: accessions attributed to Groups Ilex, Cerris and Quercus.

Appendix S5. Maximum likelihood tree obtained with GARLI with the total dataset comprising ITS2 and plastid sequences (trnH-psbA + matK). Posterior probabilities (PPs), decay values and maximum likelihood bootstrap support (MLBS) obtained with GARLI are reported above the branches (if higher than 50% for PP and MLBS).

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