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Table S1 Segregating sites and different haplotypes observed at the mtDNA control region (411 bp) of 145 European wild boar and 47 pig samples sequenced in this study. Haplotype frequencies observed in wild boar sampling areas and pig breeds are shown. The following abbreviations are used for wild boar sampling areas: IAre (Arezzo, Italy), IFor (Forlì, Italy), ISie (Siena, Italy), ISal (Salerno, Italy), IFlo (Florence, Italy), IMrp (Maremma Regional Park, Italy), ISrp (San Rossore Regional Park, Italy), ICpr (Castel Porziano Presidential Reserve, Italy), ISar (Sardinia, Italy), IGor (Gorizia, Italy), SCot (El Coto, Spain), FHam (Haute Marne, France), ADif (Austria, different areas), PDif (Poland, different areas), HDif (Hungary, different areas). The following abbreviations are used for domestic pig breeds: Pig 1 (Cinta Senese), Pig 2 (Sarda), Pig 3 (Calabrese), Pig 4 (Casertana) and Pig 5 (Nera Siciliana).

Table S2 List of the 804 Sus scrofa mitochondrial control region sequences downloaded from GenBank or obtained by the authors which were used in the study.

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