Unlocking the Secrets of Ancient Grape Pips

The quest to understand the origins of some of the world's most cherished wines has taken a groundbreaking turn with a comprehensive ancient DNA (aDNA) analysis of grape seeds, or pips, unearthed from archaeological sites across France. This study, published in the prestigious journal Nature Communications on March 24, 2026, examined 49 grape pips spanning approximately 4,000 years—from the Bronze Age around 2300 BCE to the Medieval period up to 1500 CE. These tiny artifacts, often preserved in waterlogged contexts like latrines and wells, have preserved genetic material that tells a rich story of human intervention in grape evolution, domestication, and selective breeding practices that laid the foundation for modern European wines.

France, renowned as the epicenter of global winemaking, produces varieties like Pinot Noir that command premium prices and cultural reverence. Yet, until now, the biological timeline of how these grapes came to dominate French viticulture— the science and practice of grape cultivation for wine production—remained shrouded in mystery. Researchers from institutions including the University of Toulouse, INRAE (French National Research Institute for Agriculture, Food and Environment), and the University of Montpellier collaborated with international partners from the University of York in the UK and the Globe Institute at the University of Copenhagen to sequence the full genomes of these ancient pips. Their findings challenge previous assumptions and provide concrete evidence of sophisticated viticultural techniques dating back millennia.

The Methodology: Extracting DNA from Millennia-Old Seeds

Extracting viable aDNA from plant remains is no small feat, especially from desiccated or fragmented seeds. The team employed a meticulous protocol starting with mechanical crushing of the pips to access the endosperm, followed by enzymatic digestion using proteinase K to break down proteins and release DNA. Purification via phenol-chloroform extraction and silica-based columns ensured high-quality genetic material free from contaminants. The libraries were then prepared for shotgun sequencing on Illumina platforms, generating millions of short reads mapped against the Vitis vinifera reference genome (12xV2 assembly).

Post-sequencing, bioinformatic pipelines like Bowtie2 for alignment, mapDamage2 for authenticating ancient DNA damage patterns (such as cytosine deamination), and pseudo-haploidization addressed the low coverage typical of aDNA (often 0.1x to 1x depth). Population genetics tools—Principal Component Analysis (PCA), ADMIXTURE for ancestry proportions, qpAdm for admixture modeling, and f3-outgroup statistics for relatedness—unraveled the genetic histories. A novel tool, READv2, calibrated against modern grape pedigrees, detected clonal propagation by identifying identical genotypes across samples.

• Sample processing: 54 pips total (49 new + 5 prior), yielding 28 high-quality genomes.
• Geographic focus: Southern France (e.g., Marseille, Nîmes) to northern sites (Valenciennes, Troyes).
• Chronology: Bronze Age wild Vitis sylvestris; Iron Age hybrids; Roman domesticated influx; Medieval clones.

This rigorous approach minimized false positives, confirming the reliability of matches to modern cultivars like Pinot Noir.

Bronze Age Beginnings: Wild Grapes in Prehistoric France

The earliest samples, from Bronze Age sites like Nîmes (2300–2000 BCE), belong to wild grapevines (Vitis sylvestris), specifically the Western lineage Syl-W2. These showed remarkable genetic stability over centuries, with minimal admixture from domesticated forms. PCA placed them distinctly from cultivated Vitis vinifera, underscoring that wild populations thrived independently before human domestication efforts intensified.

Archaeobotanical evidence suggests these wild vines grew naturally along riverbanks, providing the genetic pool for future selection. No signs of early viticulture here—wine production likely began elsewhere in the Near East around 6000 BCE—but these pips set the stage for local adaptation.

Iron Age Domestication: Greeks Introduce Winemaking to Gaul

A pivotal shift occurred in the Iron Age (~625–500 BCE) at sites like Saint-Maximin near Marseille. Here, the first exclusively domesticated genomes appear, carrying ancestries from Caucasian Grapevine Groups (CG3, CG4, CG5, CG6). This aligns perfectly with historical records of Greek colonists founding Massalia (modern Marseille) around 600 BCE, importing viticultural knowledge and vines from the eastern Mediterranean.

Hybrids between wild sylvestris and domesticated vinifera emerged around this time, likely aiding adaptation to local climates—domesticated vines favored larger berries and higher sugar content for fermentation, while wild traits conferred disease resistance. ADMIXTURE analysis revealed up to 20-30% wild introgression in early samples, decreasing over time as selection intensified.

Roman Expansion: Global Trade Shapes Genetic Diversity

By the Roman era (0–300 CE), sites from Antibes to Limoges show a mosaic of ancestries: Iberian CG5, Western European CG6, Levantine CG1/Syl-E1, and Caucasian CG2/Syl-E2. This reflects Rome's vast trade networks, disseminating elite cultivars across the Empire. For instance, pips from Nîmes (0–100 CE) link to Balkan and Middle Eastern stocks, evidencing deliberate importation for amphorae production and elite banquets.

qpAdm modeling confirmed multi-source admixture, with Roman samples up to 50% non-local ancestry. This period marks the professionalization of viticulture, with villa estates boasting organized vineyards.

The Dawn of Clonal Propagation: Preserving Elite Varieties

One of the study's most revolutionary insights is the early adoption of vegetative propagation—cuttings rather than seeds—evident from mid-Iron Age. Identical clones span sites tens of kilometers apart and centuries, like a CG6 lineage from Lattes (500 BCE) to Medieval Aurillac (800–900 CE). READv2 detected 12 such clones, calibrated to <0.1% divergence threshold.

• Benefits: Ensures trait fidelity (e.g., flavor profiles, yield).
• Risks: Reduced diversity, vulnerability to phylloxera (as seen in 19th century).
• Timeline: Iron Age emergence, Roman dominance, Medieval persistence.

This practice, still central today (90%+ vines from cuttings), underscores ancient winemakers' sophistication.

Pinot Noir's Ancient Lineage: A Medieval Clone Lives On

The headline discovery: a pip from a 15th-century hospital toilet in Valenciennes (1400–1500 CE) is genetically identical to modern Pinot Noir. This Burgundy icon, parent to Chardonnay and Gamay, traces unbroken clonal continuity for nearly 600 years. Co-author Laurent Bouby notes the ambiguity—table grape or wine?—but genetic match is unequivocal.

Ludovic Orlando quips Joan of Arc (1412–1431) might have savored the same genetics during the Hundred Years' War. Prior 2019 studies linked Roman pips to Pinot ancestors, but this confirms stability.

Connections to Other Modern European Wines

Beyond Pinot, a Medieval Ibiza pip matches Portuguese 'Folha de Figueira'. Earlier Orléans samples (1100 CE) align with Savagnin Blanc, Pinot's parent. Overall, ancient ancestries mirror Western European clusters (CG5/CG6), comprising 70%+ of modern French repertoire (e.g., Cabernet Sauvignon traces to Iberian influx).

f3-statistics reveal close relatives: Iron Age pips as grandparents to current varieties, highlighting multi-generational selection.

Implications for Wine Heritage and Conservation

This research rewrites French wine history, confirming Iron Age origins over Neolithic diffusion myths. It validates texts like Pliny the Elder's vineyard descriptions. For industry: ~80% French vineyards clonal; study aids ampelography (vine identification) for heritage preservation amid climate change.

Stakeholders: INRAE uses data for resilient hybrids; Burgundy producers celebrate Pinot purity. Challenges: Low diversity risks diseases; solutions include wild introgression revivals. As Jazmín Ramos-Madrigal notes, "mind-blowing" 1,000-year cultivation of clones.

Academic Contributions and Future Directions

European universities drove this: Toulouse's CAGT pioneered aDNA; Montpellier's ISEM integrated archaeobotany. Cross-disciplinary teams (42 authors) exemplify higher education's role in cultural genomics.

Future: More pips, phenotyping clones, climate modeling. Potential: Reviving lost varieties, informing EU wine PDO protections. Actionable: Fund aDNA labs, train geneticists.INRAE's prior work paves way.

Photo by Dalila Moreira on Unsplash

Global Context: France's Role in European Viticulture

France's story mirrors Europe's: Georgia's 8000 BCE wines, Italy's Etruscan roots. Yet, French clonal mastery exported to New World. Today, 50M+ hectares globally; genetic insights combat warming (e.g., earlier ripening Pinot).

Outlook: aDNA guides sustainable viticulture, blending heritage with innovation.