Neanderthals in Belgium: what Meuse Valley DNA reveals about their diversity

Some regions weigh far more heavily in the history of a science than their size on the map would suggest. The Meuse Valley, between Namur and Liège, is one of them. Over a handful of kilometres, its limestone cliffs riddled with caves have yielded some of the most important fossils in European palaeoanthropologyPalaeoanthropologyThe science that studies human evolution from the fossil remains of hominins (bones, teeth, footprints) and their context, to reconstruct our biological origins.→. It was here, at Spy, that in 1886 two skeletons first anchored the NeanderthalsNeanderthalsA fossil humanity of Eurasia, robust and cold-adapted, extinct around 40,000 years before present.→ in a clear stratigraphyStratigraphyThe study of the superimposed layers (strata) of an archaeological site; each layer corresponds to a phase of occupation and yields a relative chronology.→. It was here, at Scladina, that a child's tooth yielded in 2006 one of the oldest human DNADNAThe molecule carrying genetic information, used to reconstruct kinship between species.→ sequences ever read. And it was here again, at Goyet, that a bone fragment provided in 2026 the world's fifth very high quality Neanderthal genome. In June 2026, an international team gathered the ancient DNAAncient DNAGenetic material preserved in old remains, often degraded, sequenced with cutting-edge techniques.→ of 27 of these vanished humans to ask a simple and formidable question: were the last Neanderthals of north-western Europe, genetically speaking, already doomed?¹

Spy, 1886: Belgium at the cradle of Neanderthal

The story begins with a fertile misunderstanding. When the archaeologist Marcel De Puydt and the geologist Max Lohest excavated the small cave of Spy, near Namur, in June 1886, they were not looking for fossil humans. Yet in the deepest layers of the fill they uncovered two adult skeletons mingled with stone tools and the bones of extinct animals, mammoth and woolly rhinoceros foremost among them. The anatomist Julien Fraipont was called in to study them. His verdict changed everything.²

Until then, the fossil found in Germany's Neander Valley in 1856 had remained contested: many scholars saw in it a diseased or deformed modern individual, not the representative of a different humanity. At Spy, for the first time, bones of Neanderthal type appeared in an indisputable archaeological context, sealed beneath metres of sediment, accompanied by a stone industry and a PleistocenePleistoceneThe geological epoch of the great ice ages (c. 2.6 Ma–11,700 BP), spanning most of human prehistory.→ fauna. Fraipont and Lohest showed that these robust skulls, with their sloping foreheads and heavy brow ridges, closely resembled the German fossil. The pathological-individual argument collapsed: there had indeed once existed humans whose bodies and skulls differed from ours. Spy thus tipped the scientific community towards the idea of human evolution, and Belgium entered the history of the discipline through the front door.²

Scladina, the child who gave up its genetic code

A century later, the same valley struck again. In Scladina cave, at Sclayn, the patient excavations carried out since the 1970s unearthed the remains of a Neanderthal child who died between the ages of ten and twelve. Its jaw and teeth, buried in an ancient sediment, were to become a mine of information of an entirely new kind. For it was no longer only the shape of the bones that would speak, but the molecules they contained.³

In 2006, Catherine Hänni's team in Lyon managed to extract 123 base pairs of mitochondrial DNA from a molar. At the time, it was the oldest Neanderthal DNA sequence ever obtained, estimated at around 100,000 years old. And the surprise was considerable: the Scladina sequence diverged clearly from the other, more recent Neanderthals then known. The researchers drew a conclusion that still resonates today: before 42,000 years ago, Neanderthals were genetically more diverse than had been thought, and this diversity later shrank, perhaps under the effect of demographic bottlenecks. In 2019, a Max Planck study from Leipzig, led by Stéphane Peyrégne, returned to the child's jaw and teeth, this time to extract nuclear DNA. It linked Scladina to the old German femur from Hohlenstein-Stadel and suggested that all late Neanderthals descend, at least in part, from these very early European populations. Neanderthal palaeogeneticsPalaeogeneticsThe study of ancient DNA extracted from remains (bones, teeth, sediments, walls) to reconstruct the past of populations.→, born partly in this Meuse Valley cave, had just gained an unprecedented depth of field.³

2026: twenty-seven Neanderthals on the table

It is in this lineage that the study published in 2026 in the journal Nature takes its place, carried out by a Max Planck team in partnership with the Royal Belgian Institute of Natural Sciences. Its ambition: to reason no longer about one or two isolated individuals, but about a genuine population. The researchers gathered the DNA of 27 late Neanderthals from ten sites, mostly caves of the Meuse Basin in Belgium, supplemented by a few French sites. Never before had such a regional sample been assembled for this crucial period, that of the very last Neanderthals of north-western Europe, around 45,000 to 40,000 years ago.¹

The stakes went far beyond regional curiosity. Until this study, only four very high quality Neanderthal genomes were available, and three of them came from Siberia, that is, from the extreme eastern margin of the species' range. In other words, much of what we thought we knew about Neanderthal genetics rested on peripheral, perhaps atypical, populations. Documenting the European heart of the species, where it lived longest and most densely, became essential to check whether conclusions drawn from Siberia held for the whole. The Meuse Valley, with its unique concentration of sites and long tradition of excavation, offered the ideal ground.¹

Goyet Q56-1: a genome read twenty-two times over

At the heart of the study lies an exceptional specimen. Most of the bones analysed contained only a minute quantity of usable DNA, eroded by time and by the temperate, humid climateClimateThe long-term average atmospheric conditions of a region; its variations (glaciations, aridifications) shaped migrations, agriculture and the collapse of prehistoric societies.→ of our regions, poorly suited to molecular preservation. But one fragment from the Goyet caves, catalogued Q56-1, stands out as a miracle of preservation.¹

In this fragment, 37 percent of the sequences matched human DNA, a remarkable figure for a fossil of this age. The researchers were able to read its genome an average of 22.4 times over, a coverage that makes it the fifth very high quality Neanderthal genome ever obtained, and the first of this quality for Western Europe. The Goyet individual lived about 45,000 years ago; the analyses indicate it was a woman. Such a degree of resolution allows far more than identifying a lineage: it makes it possible to measure inbreedingInbreedingReproduction between related individuals; it leaves long identical stretches in the genome and reduces genetic diversity.→, to spot the long stretches of DNA inherited from an ancestor common to both parents, to estimate population sizes and to compare the burden of harmful mutations from one generation to the next. That is the whole point of a high quality genome: it turns a mere presence into a genuine demographic narrative.¹

No genetic poverty among the last Belgian Neanderthals

The study's main result runs counter to a narrative that had become dominant. One expected to find, in these twilight Neanderthals, the signatures of a collapse: heavy inbreeding, diversity in free fall, accumulation of harmful mutations. The Meuse genomes say the opposite.¹

Many of these individuals are not closely related to one another, which argues for relatively large and well-connected groups rather than a handful of families turned in on themselves. Unlike other Neanderthal populations studied, this one shows little sign of marked inbreeding. Above all, by comparing early and late Neanderthals, the researchers detect no significant increase in the burden of harmful mutations over time, nor any erosion of genetic diversity. In plain terms, nothing in these genomes supports the idea of a growing "genetic poverty" that would have condemned the species from within. The authors also note a telling detail: some of these individuals carry the imprint of an older Neanderthal lineage, predating the split of the late Neanderthals, a sign of a population history richer and more layered than a straight line towards extinction.¹

Another result deserves emphasis. Even though these Neanderthals coexisted in Europe with the first Homo sapiensHomo sapiensThe present-day human species, which emerged in AfricaAfricaThe cradle of humankind: the continent where the first hominins appeared, then Homo sapiens around 300,000 years ago, before the expansion to the rest of the world.→ around 300,000 years ago, the only surviving human lineage after the extinction of Neanderthals and Denisovans.→, their genomes carry no trace of recent interbreedingInterbreedingGenetic mixing between human populations or species; between Neanderthals and Homo sapiens it left 1 to 2% of Neanderthal DNA in non-Africans.→ with them. The genetic exchanges between the two humanities, real enough, had taken place earlier and elsewhere, notably in the Near EastNear EastA region of western Asia (Levant, Mesopotamia, Anatolia, Iran), cradle of the Neolithic revolution, agriculture, the first cities and writing.→. In the Meuse Valley, at the very end of their history, these Neanderthals remained genetically themselves.¹

Thorin and the Siberians: Neanderthal's other face

It would nonetheless be misleading to conclude that Neanderthals everywhere formed large, genetically healthy populations. Other studies, equally recent, paint a radically different picture, and it is from their confrontation that the whole interest of the debate arises.⁴

In 2024, a team led by Ludovic Slimak published in Cell Genomics the genome of "Thorin," a Neanderthal from Grotte MandrinGrotte MandrinPrehistoric site at Malataverne (Drome, France) whose layer E, around 54,000 years ago, yielded the oldest possible traces of bow and arrow in Europe.→, in the Rhône Valley, who lived between 42,000 and 50,000 years ago. The genetic portrait is striking: Thorin's lineage appears to have remained isolated from other groups for nearly 50,000 years, without the slightest genetic exchange with geographically neighbouring Neanderthals. It seems to have split from the main branch about 105,000 years ago. And the genome bears the clear marks of recent inbreeding, with high levels of homozygosityHomozygosityState of an individual whose two chromosomes carry the same version of a gene; long homozygous segments reveal related parents.→. Earlier still, the Siberian genomes, notably that from Denisova cave, had revealed tiny communities in which unions between close relatives were frequent. On one side, then, isolated, small and inbred groups; on the other, at the same period but in the Meuse Valley, a diverse and connected population. Both images are true at once.⁴

Inbreeding, isolation and extinction: a reopened file

How can these contradictory results be reconciled? The firmest lesson is no doubt that there was no single Neanderthal way of life, but a mosaic of local situations. Neanderthal did not vanish everywhere for the same reasons or at the same pace.¹

The long-attractive hypothesis of an extinction through genetic impoverishment, with populations too small, too inbred, too burdened with harmful mutations to survive, finds support in Thorin and the Siberians, but collides head-on with the Meuse genomes. If, at the very end of their history and in the heart of their range, some Neanderthals remained genetically healthy and well connected, then "genetic failure" cannot be the universal cause of their disappearance. The authors of the 2026 study are cautious: their results do not rule out that a vulnerability linked to population size or structure played a role locally, nor that a decline affected unstudied regions. But they clearly shift the centre of gravity of the debate. The answer probably lies elsewhere, or rather in a combination of factors: abrupt climate change, habitat fragmentation, competition with Homo sapiens arriving in numbers, regional demographic dynamics. Neanderthal's extinction looks less and less like a fate written into the genes, and more and more like a contingent history, made of local contexts.¹

Belgium, a laboratory of Neanderthal genetics

At the end of this journey, one thread stands out: the consistency with which the Meuse Valley has, for nearly a century and a half, fed the great questions of palaeoanthropology. From Spy in 1886 to Goyet in 2026, by way of the Scladina child, these Belgian caves have never ceased to supply the raw material of scientific revolutions.⁵

The comparison with our own species lights up the whole picture. Neanderthals, taken as a whole, showed lower genetic diversity than Homo sapiens, consistent with modest total numbers spread over an immense territory. But "lower on average" does not mean "everywhere impoverished": the Meuse study shows that within this whole, certain populations retained real genetic vitality. Where Sapiens, after leaving Africa, experienced a spectacular demographic expansion that mixed and amplified its diversity, Neanderthal remained a species of low densities, living in scattered groups, sometimes isolated and inbred, sometimes connected and diverse depending on region and period. It is perhaps this very heterogeneity that constitutes the deepest teaching of recent palaeogenetics.⁵

Shadows remain in the picture. The bones of our regions, exposed to a humid climate, preserve DNA poorly, and the Goyet fragment will long remain a happy exception. Each new high quality genome is wrested from the laboratories at great cost. But the direction is clear: by moving from a handful of genomes to samples of whole populations, palaeogenetics is leaving the individual portrait for demography, and our vanished cousins are ceasing to be silhouettes and becoming societies once more. In this slow work of resurrection, the Meuse caves, from Spy to Goyet, will long continue to have their say.⁶