Researchers from the University of Copenhagen have uncovered a dramatic chapter in European prehistory through ancient DNA analysis of skeletons from a megalithic tomb near Paris. The study, published in Nature Ecology & Evolution, reveals a complete population turnover around 3000 BC, where a local Neolithic farming community vanished, leaving the area to newcomers from southern France and the Iberian Peninsula. This finding sheds new light on the enigmatic Neolithic decline that swept across northwestern Europe, marking the end of an era defined by monumental stone constructions.
The discovery challenges previous assumptions about continuity in western European populations during this turbulent period. Unlike the steppe migrations seen further north, this replacement appears to be an internal shift within Neolithic farmer groups, driven by a confluence of factors including infectious diseases and environmental pressures. The work highlights the power of ancient DNA (aDNA) techniques to reconstruct not just genetic histories but also social structures and demographic crises long erased from the archaeological record.Read the full study here.
The Allée Sépulcrale de Bury: A Window into Prehistory
The Bury site, located about 50 kilometers north of Paris in the Paris Basin, is one of France's largest Neolithic burial complexes. Excavated in 2013, this allée sépulcrale—a long, covered passage tomb typical of megalithic architecture—housed remains of over 300 individuals across two distinct phases separated by a centuries-long hiatus. Phase 1 dates to the late fourth millennium BC (roughly 3200–3100 BC), just before the Neolithic decline, while Phase 2 resumes in the early to mid-third millennium BC (around 2900–2470 BC).
Archaeological evidence shows stark differences in burial practices. Early burials featured extended body positions in collective chambers, reflecting communal rituals. Later ones adopted flexed positions, suggesting cultural shifts. The gap in activity aligns perfectly with the broader Neolithic decline, a period of population contraction evident from reduced settlement density and forest regrowth across the region.
This tomb's reuse after abandonment provides a rare snapshot of continuity and change, allowing scientists to compare genomes directly from the same location before and after the crisis.
Genetic Discontinuity: No Family Ties Across the Divide
By sequencing 132 ancient genomes from teeth sampled at the site, the Copenhagen team achieved remarkable coverage (median 0.126x), enabling detailed kinship and ancestry modeling. Principal component analysis (PCA) clearly separated the phases: Phase 1 individuals clustered with northern French and German Neolithic farmers, showing genetic diversity including elevated Western Hunter-Gatherer (WHG) ancestry. Phase 2 genomes, however, were strikingly homogeneous, deriving over 80% ancestry from Middle Neolithic Iberian sources.
Identity-by-descent (IBD) sharing and pedigree reconstruction confirmed the rupture. Phase 1 burials included three large multi-generational families practicing female exogamy, indicating close-knit communities. Phase 2 featured smaller patrilineal groups dominated by Y-haplogroup I2a1a1, with far fewer close relatives—many unrelated individuals suggest selective burial practices. Simulations using msprime ruled out genetic continuity, estimating effective population sizes plummeted in Phase 1, consistent with catastrophe.
This discontinuity implies near-total local extinction, followed by repopulation by southern migrants exploiting the vacuum.
Migration from the South: Iberian Neolithic Farmers Move North
Admixture modeling pinpointed Phase 2 origins: a northward flux of Iberian-like Neolithic ancestry around 2900 BC, preceding the later Bell Beaker expansions. Maps of western European aDNA illustrate this: while Phase 1 reflects local Paris Basin mixtures, Phase 2 mirrors southern profiles, with strontium isotopes confirming post-arrival stability and limited mobility.
This internal replacement contrasts with Scandinavia's steppe influx, suggesting regional variations in the Neolithic decline's aftermath. The migrants likely brought new cultural elements, contributing to the site's reuse and the persistence of farmer ancestry in western Europe.University of Copenhagen press release details the migration patterns.
Disease Signatures: Plague and Pathogens in the Genome
Pathogen screening via KrakenUniq identified Yersinia pestis (plague) in four individuals—three from Phase 1, basal to known Neolithic strains (e.g., RV2039). Other detections included Borrelia recurrentis (relapsing fever), Yersinia enterocolitica, and Human alphaherpesvirus 1. Prevalence was low (4% Phase 1), lacking outbreak-scale clustering, but combined with juvenile mortality skew points to elevated disease burden.
Martin Sikora, senior author from Copenhagen, notes: 'Plague was present, but not the sole cause—the total disease load, alongside environmental stress, likely tipped the balance.' This aligns with plague's role in other Neolithic declines, like Sweden's Falköping site.
Social Reorganization: From Clans to Lineages
Kinship analyses via NgsRelate and PRIMUS revealed Phase 1's communal ethos: extended pedigrees spanning siblings, parents, and grandchildren, with male-biased burials (71%). Phase 2 shifted to patrilocal structures, fewer kin links, and continued male dominance (73%). These changes mirror broader transitions from egalitarian megalith builders to hierarchical Bronze Age societies.
Frederik Seersholm explains: 'Not only the population changed, but society itself—at least in funerary practices.' This reorganization may reflect migrants' traditions or adaptations to sparse post-collapse conditions.
Environmental Echoes: Forests Reclaim the Land
Pollen data from nearby cores show forest regrowth during the hiatus, indicating abandoned fields and dwindled human impact. This palynological evidence corroborates the genetic collapse, painting a picture of depopulated landscapes ripe for recolonization.
The Neolithic Decline: A Europe-Wide Cataclysm
The Bury findings anchor the Neolithic decline (~3500–2500 BC) in concrete data: population crashes, halted monuments, and turnovers. Previously documented in pollen proxies and site abandonments, causes likely multifactorial—climate cooling (4.2 ka event), soil exhaustion, intergroup conflict, and pathogens. In the Paris Basin, it ended megalithic traditions, paving for Bronze Age innovations.
Laure Salanova (CNRS) states: 'The demographic pattern indicates crisis, creating space for southern expansion.'
Ancient DNA Methods: Pushing the Boundaries
Conducted in Copenhagen's clean labs, the study employed cementum sampling for optimal preservation, dual library prep (with/without USER), and low-coverage calling via tools like schmutzi. Kinship via IBDseq and simulations validated discontinuity. Pathogen phylogenies used EPA-ng. This integrates genomics, isotopes, dating, and palynology, exemplifying interdisciplinary aDNA.
University of Copenhagen's GeoGenetics Leadership
The Globe Institute's Lundbeck Foundation GeoGenetics Centre, directed by Eske Willerslev, spearheaded this with collaborators from CNRS, Gothenburg, and beyond. Their expertise in large-scale aDNA (e.g., 100 Denmark genomes) positions U Copenhagen as Europe's hub for prehistoric genomics. Kristian Kristiansen (Gothenburg) praises the 'wide disciplinary forces' unlocking transitions.
For European higher ed, this underscores Denmark's investment in life sciences, fostering global impacts. Explore research positions at AcademicJobs.com/research-jobs.
Photo by Tomás Robertson on Unsplash
Implications and Future Horizons
Bury redefines the Neolithic decline as regionally variable, with western Europe's farmer continuity masking turnovers. It links demography to cultural endpoints like megaliths, informing models of resilience and migration. Future work: expand sampling, model disease dynamics, integrate climate proxies.
This advances paleogenomics, revealing how crises shape ancestry—echoing modern migrations. As Seersholm notes, 'The end of monuments coincides with their builders' disappearance.'