Scientists Reconstruct Genetic Makeup of One of Oldest Known Neanderthal Communities

Inside Stajnia Cave, a limestone shelter perched 359 meters above sea level in Poland's Kraków-Częstochowa Upland, excavators working between 2007 and 2010 recovered nine human teeth from sediment layers dating to the Middle Palaeolithic [1]. Sixteen years later, those teeth have become the basis for the oldest multi-individual genetic reconstruction of a Neanderthal group in Central-Eastern Europe — a cluster of at least seven people who shared the cave roughly 100,000 years ago [2].

The study, published in Current Biology on April 20, 2026, by a team led by Andrea Picin and Sahra Talamo of the University of Bologna, alongside Wioletta Nowaczewska of the University of Wrocław, Adam Nadachowski of the Polish Academy of Sciences, and Mateja Hajdinjak of the Max Planck Institute for Evolutionary Anthropology, represents what Picin calls "an extraordinary result because, for the first time, we are able to observe a small group of at least seven Neanderthals from Central-Eastern Europe who lived around 100,000 years ago" [1][3].

The Site and the Specimens

Of the nine teeth recovered from Stajnia Cave, five had previously been identified as Neanderthal on morphological grounds [4]. The new study subjected all nine to mitochondrial DNA (mtDNA) extraction and sequencing, ultimately confirming at least seven — and possibly eight — distinct individuals [2]. Molecular branch-shortening estimates place all samples within Marine Isotope Stage 5 (MIS 5), a warm interglacial period, with point estimates ranging from approximately 119,700 to 92,498 years ago [1][3].

This dating matters. Most Neanderthal genetic data come from specimens younger than 70,000 years old, concentrated in Western Europe and Siberia. The Stajnia assemblage pushes the timeline back by tens of thousands of years and shifts the geographic focus to a region that has long been treated as peripheral to Neanderthal population dynamics [2][3].

Kinship Within the Group

Three of the teeth — two belonging to juveniles and one to an adult — carried identical mitochondrial DNA sequences [1]. Because mtDNA is inherited exclusively through the maternal line, this finding indicates the three individuals shared a recent common maternal ancestor and were likely close biological relatives. "This suggests that these individuals might be closely related to each other," said Hajdinjak [2].

The study is limited to mitochondrial genomes rather than full nuclear genomes, which constrains the precision of kinship analysis. MtDNA can confirm shared maternal lineage but cannot distinguish, for example, between a mother and her children versus maternal cousins. The researchers acknowledge this limitation and describe the group as a "small community" rather than a defined family unit [3].

How This Compares to Previous Neanderthal Genetic Studies

The Stajnia findings build on a growing but still small corpus of multi-individual Neanderthal genetic datasets. The most significant prior study came in 2022, when Laurits Skov, Benjamin Peter, and colleagues published nuclear genome data from 13 Neanderthals recovered from two sites in the Altai Mountains of southern Siberia — Chagyrskaya Cave and Okladnikov Cave [5]. That study, published in Nature, identified a father-daughter pair and a pair of second-degree relatives among the Chagyrskaya individuals, establishing that at least some of them lived at the same time [5][6].

Source: Max Planck Institute / Nature / Science compilations

Data as of Apr 22, 2026CSV

The Chagyrskaya study also estimated that the local Neanderthal community comprised roughly 20 individuals, with 60 to 100 percent of the females being migrants from other communities — a pattern that suggested female-mediated gene flow between small, dispersed bands [5]. Mitochondrial DNA diversity at the site was much higher than Y-chromosome diversity, consistent with a social system where females routinely left their natal groups [6].

By comparison, the Stajnia group is both older and geographically distinct. While the Chagyrskaya Neanderthals date to approximately 54,000 years ago, the Stajnia individuals lived nearly twice as long ago [1][5]. And while Siberia lies at the eastern margin of the Neanderthal range, southern Poland sits near its center, along what appears to have been a major migration corridor north of the Carpathian Mountains [3].

Small Groups in a Big Landscape

Source: Nature (2022), Spikins et al., various ethnographic sources

Data as of Apr 22, 2026CSV

The estimated community sizes for Neanderthals — roughly 20 individuals at Chagyrskaya, at least seven identified at Stajnia — are strikingly small compared to band sizes documented in modern human hunter-gatherer societies, which typically range from 25 to 35 individuals, with broader social networks extending to around 150 (the so-called Dunbar number) [5][7].

These small group sizes have direct implications for genetic health. The high-quality genome of the Altai Neanderthal, a female from Denisova Cave, revealed long runs of homozygosity — stretches of DNA where both copies of each gene are identical — indicating her parents were related at the level of half-siblings [8]. At Chagyrskaya, roughly 13 percent of one individual's genome was homozygous, consistent with a population of no more than 60 individuals [8][9].

Population geneticists have estimated that this level of inbreeding left Neanderthals with at least 40 percent lower fitness than modern humans on average, because small populations are less efficient at purging harmful mutations through natural selection [9][10]. A 2019 study in PLOS ONE modeled whether inbreeding alone could have driven Neanderthals to extinction and concluded that inbreeding by itself was insufficient — but when combined with low birth rates (fewer than 25 percent of females reproducing in a given year, comparable to rates in modern hunter-gatherers) and random demographic fluctuations, extinction became probable across all population sizes within 10,000 years [10].

The Stajnia data, being restricted to mitochondrial genomes, cannot directly measure inbreeding levels. But the presence of closely related individuals within a small group at a single site is consistent with the broader pattern of Neanderthal communities that were small, isolated, and genetically constrained [2][3].

A Lineage That Spanned a Continent

One of the study's most significant findings concerns the geographic distribution of the Stajnia Neanderthals' maternal lineage. Their mtDNA falls within the same phylogenetic branch as that of Neanderthals found in the Iberian Peninsula, southeastern France, and the northern Caucasus [1][2]. This suggests the lineage was widespread across western Eurasia before being replaced by the mitochondrial lineages characteristic of later Neanderthal populations [3].

The researchers draw a specific comparison to "Thorin," a Neanderthal fossil discovered in Mandrin Cave in France, which carries a mitochondrial genome similar to that of the Stajnia Neanderthals [1]. Thorin has so far been assigned a chronology of around 50,000 years ago, which would make the survival of this lineage anomalously long. The Stajnia team urges caution: "When radiocarbon values approach the limit of calibration, it is essential not to assign more precision than the data can actually support," said Talamo [1][3].

The Technical Challenge of 100,000-Year-Old DNA

Extracting usable genetic material from specimens this old is a formidable technical achievement. DNA degrades over time through chemical processes, chiefly depurination (the loss of purine bases from the DNA backbone) and deamination (the conversion of cytosine to uracil, which reads as thymine during sequencing) [11][12]. These processes leave characteristic damage patterns — an overrepresentation of C-to-T substitutions clustered at the ends of DNA fragments — that serve both as a challenge and, paradoxically, as an authentication tool: damage patterns consistent with ancient DNA help distinguish genuine ancient sequences from modern contamination [12].

Contamination is the field's perennial adversary. Human DNA is among the most common contaminants in paleogenomic laboratories, and because Neanderthals are closely related to modern humans, distinguishing the two requires identifying diagnostic positions where Neanderthal and modern human sequences differ [11][13]. Mitochondrial contamination can be assessed by counting how many DNA fragments at these positions support the modern human base rather than the Neanderthal base [13]. However, mitochondrial contamination levels can diverge from nuclear contamination levels, a complication that applies less to the Stajnia study since only mitochondrial genomes were recovered [13].

Methods developed over the past decade — including computational tools that jointly estimate contamination, sequencing error, and demographic parameters — have substantially improved reliability [13]. Still, the Stajnia study's reliance on mitochondrial DNA alone means the dataset carries less information than a nuclear genome would, and the findings should be interpreted within those bounds.

How Much of the Neanderthal Genome Do We Have?

The first draft of the Neanderthal nuclear genome was published in 2010 by Svante Pääbo's team at the Max Planck Institute, based on DNA from the Vindija Cave in Croatia [14]. By 2013, the team had produced a high-quality genome from the Altai Neanderthal, sequenced to a depth comparable to modern medical-grade human genomes [8]. Additional high-quality genomes from Vindija (2017) and Chagyrskaya (2020) followed [14][15].

Source: OpenAlex

Data as of Jan 1, 2026CSV

Today, researchers have sequenced nuclear or mitochondrial genomes from over two dozen Neanderthal specimens, and the field has produced more than 7,300 academic papers on Neanderthal genomics since 2011 [14]. Comparisons show that 99.7 percent of Neanderthal and modern human nucleotide sequences are identical [14]. The remaining 0.3 percent includes regions linked to skull structure, skin morphology, energy metabolism, and — most intriguingly — cognition [14][15].

The speech-related gene FOXP2, for instance, carries mutations in Neanderthals identical to those in modern humans, suggesting that the genetic foundations for language capacity were shared [14]. Neanderthal-derived genetic variants in living humans have been shown to affect neurogenesis (the production of new neurons), myelination (the insulation of nerve fibers), and skull shape [15]. However, selection against introgressed Neanderthal variants has been strongest precisely in genes related to cognitive function, suggesting that most Neanderthal cognitive-related variants were disadvantageous in the Homo sapiens context and were progressively eliminated [16].

Between 12 and 20 percent of the total Neanderthal genome survives, fragmented across the genomes of living non-African humans, each of whom carries roughly 1 to 3 percent Neanderthal ancestry [14][16]. Regions of the genome involved in immune function — particularly the human leukocyte antigen (HLA) system — retain some of the highest levels of Neanderthal introgression, suggesting that Neanderthal immune variants provided adaptive advantages that were positively selected [16].

Interbreeding: Neanderthals, Denisovans, and Modern Humans

The Stajnia study does not report evidence of interbreeding with modern humans or Denisovans, which is consistent with the early date of the specimens: at approximately 100,000 years ago, the Stajnia Neanderthals predate the main documented period of Neanderthal–modern human gene flow, which occurred roughly 50,500 to 43,500 years ago [17][18].

The broader genetic record, however, documents extensive interbreeding among archaic and modern human groups. The most striking example is "Denny" (Denisova 11), a female discovered in Denisova Cave, Siberia, whose genome showed she was a first-generation hybrid — her mother was a Neanderthal and her father a Denisovan [19]. As much as 17 percent of the Denisovan genome from Denisova Cave represents DNA from the local Neanderthal population, and Denny's Denisovan father himself carried Neanderthal ancestry introduced hundreds of generations before his lifetime [19][20].

Given the rarity of archaic hominin specimens, the discovery of a first-generation hybrid suggested such mixing was not rare. "When they did [meet], they must have mated frequently — much more so than we previously thought," researchers noted [19].

What Ancient DNA Cannot Tell Us

The Stajnia study reconstructs a community through mitochondrial genomes — a powerful but limited lens. Several researchers have argued that popular science coverage systematically overstates what ancient DNA can reveal about behavior, culture, and intelligence.

The core problem is what geneticists call the genotype-phenotype gap: limited understanding of how the expression of a genome shapes physical and cognitive traits is the main obstacle to linking genetic and morphological evidence [21]. A shared FOXP2 variant, for example, does not prove that Neanderthals spoke language in the way modern humans do — the gene is necessary but not sufficient for complex speech, which also depends on vocal anatomy, neural circuitry, and social learning [14][21].

More broadly, genetic data lack intrinsic geographical and cultural context [21][22]. A 2013 review in Current Anthropology documented systematic misunderstandings between paleogenomicists, archaeologists, and paleoanthropologists, noting that "molecular biologists often try to fit results to pre-existing hypotheses, sometimes chosen randomly by authors unfamiliar with current research in other fields" [22]. Genetic results with limited phylogenetic resolving power frequently did not allow favoring one hypothesis over another [22].

The Stajnia researchers themselves are cautious in their claims, framing their results in terms of maternal lineages and demographic connectivity rather than speculating about the culture, behavior, or cognitive abilities of the individuals they studied [1][3]. This restraint stands in contrast to some popular coverage of the study, which has used language like "reconstructing a community" in ways that imply more social and behavioral detail than mitochondrial genomes can provide.

Ethics, Ownership, and Deep-Time Remains

The ethical frameworks governing human remains — particularly laws like the Native American Graves Protection and Repatriation Act (NAGPRA) in the United States and the 2007 United Nations Declaration on the Rights of Indigenous Peoples — were designed to protect the cultural and spiritual rights of descendant communities [23][24]. These frameworks presuppose an identifiable connection between remains and a living group.

Neanderthal remains present a fundamentally different case. Homo neanderthalensis went extinct approximately 40,000 years ago and predates any living group's direct ancestry in the regions where specimens are found [23]. While all non-African modern humans carry some Neanderthal DNA, no living population can claim direct cultural or lineal descent from a specific Neanderthal community [16][23].

This creates a legal gray area. As a 2020 review in the Journal of Human Evolution noted, legal gaps and inadequate definitions of what constitutes a fossil have meant that a "finders keepers" approach is often applied to the ownership and control of hominin remains [23]. The entire genus Homo is considered human anthropologically but not always legally, leaving Neanderthal specimens without clear protections in many jurisdictions [23].

In practice, Neanderthal remains are typically governed by national antiquities laws. The Stajnia specimens fall under Polish heritage law and are curated by the Institute of Systematics and Evolution of Animals of the Polish Academy of Sciences [1][3]. No Indigenous consultation process applies in this case — a contrast to the contentious debates over specimens like Kennewick Man in the United States, where cultural affiliation claims complicated research for decades.

Some ethicists have argued that the absence of descendant communities does not eliminate ethical obligations. The destructive nature of ancient DNA extraction — which consumes irreplaceable material — raises questions about how specimens should be allocated between competing research groups and how data should be shared [25]. Minimum reporting standards and open data policies have become increasingly important as the field grows, particularly given paleogenomics' reliance on destructive sampling that cannot be repeated once material is consumed [25].

What Comes Next

The Stajnia results establish that Central-Eastern Europe was not a backwater in Neanderthal population dynamics but a crossroads where genetically diverse groups moved and interacted [3]. The shared maternal lineage linking Poland to Iberia, France, and the Caucasus points to continent-wide connectivity among Neanderthal populations during MIS 5, a pattern that later fragmented as populations contracted and genetic lineages turned over [1][2].

Whether nuclear DNA can eventually be extracted from the Stajnia teeth remains an open question. Mitochondrial DNA, present in hundreds of copies per cell, is far easier to recover than nuclear DNA, which exists in only two copies [11]. But advances in extraction and sequencing methods continue to push the boundaries of what is possible — the field has moved from fragments to full genomes in barely 15 years.

For now, eight teeth from a limestone cave in southern Poland have added a new chapter to the genetic history of a species that vanished tens of thousands of years ago — and whose legacy persists, scattered across billions of living human genomes.