LDA seed classification (Threshold p ≥ 0.9).

This study presents an extensive analysis of 1,768 well-preserved waterlogged archaeological grape pips covering approximately 7000 years of history. These samples originate from 25 Italian archaeological sites spanning from the Early Neolithic (6th millemmium BC) to the Medieval period (8th-14th centuries AD). Employing geometric morphometrics and linear discriminant analyses, we compared these archaeological grape pips with modern reference collections to differentiate between wild and domestic grape types. Additionally, we analysed phenotypic changes in grape pip length and shape over the studied period to the present day to highlight traits associated with domestication syndrome. During the Early Neolithic, no evidence of morphologically domesticated grapes was observed. Data from Early Bronze Age sites (ca. 2050–1850 BC) display the same trend observed for the Early Neolithic period. The Middle Bronze Age sites (ca. 1600–1300 BC) continue to exhibit a predominance of wild grape pips. However, a notable transition occurs at the end of the Late Bronze Age (ca. 1300–1100 BC), with the majority of grape pips classified as domestic, indicating the definitive establishment of cultivation practices and selection of domestic grape by these communities. In the Iron Age, grape pips from Etruscan sites dating to the 4th century BC are predominantly domestic, suggesting an advanced viticulture for this period. During the Roman period (1st-6th centuries AD), some sites exhibited a high presence of domestic grape pips and intermediate forms between wild and domestic morphotypes, suggesting introgression between local wild and domestic grape allowing the formation of new varieties. Finally, the Medieval period (8th-14th centuries AD) sites demonstrate a widespread prevalence of domestic grape pips across archaeological sites, indicating a reduction of intermediate forms between wild and domestic morphotypes and displaying morphometric characteristics entirely similar to modern domestic grape references. Overall, our study provides valuable insights into the evolution of grapevine cultivation in Italy, highlighting the gradual transition from wild to domesticated types over millennia.