New DNA study of Neanderthals bolsters suspicions of human-driven extinction

The human mind is a tool for coping with reality, which can be unbearably confusing. Millions of years of evolution have produced a brain capable of generating a useful sense of order for survival out of the overwhelming complexity of the world. Identity is a fundamental part of that simulation, and it is often built in opposition. We know too much about ourselves, and we struggle to simplify ourselves enough to define who we are, but we believe we know what we are not. We are not the barbarians, with their repulsive faces and customs, and since we began discovering human species that were not entirely like us, we have not been Neanderthals: brutish, technologically backward, and doomed to extinction.

But the human mind is paradoxical and has also created a method for glimpsing a little more of the reality concealed by that simulation: science, which seeks to adhere to data and strips away the comfort the brain creates when it convinces us that our intuitions and prejudices are truth. On Wednesday, the journal Nature published the work of a group of scientists who have transformed our understanding of Neanderthals — and continue to do so.

Before Nobel laureate Svante Pääbo and other contributors to the study published this Wednesday made it possible to recover and sequence DNA from fossils tens of thousands of years old, we thought Neanderthals had vanished without a trace. Today, we know that interbreeding between species occurred many times and that a small percentage of the genomes of those other humans lives on in each of us.

An international team of scientists led by the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, analyzed DNA from 27 Neanderthals recovered at 10 sites between Belgium and France to reconstruct their genetic relationships. The findings remind us that, like modern humans, not all Neanderthals lived identical lives.

Around 50,000 years ago, just a few millennia before their disappearance, and contrary to what earlier findings had suggested, not all Neanderthals were doomed by the effects of inbreeding and isolation. Many lived in large, well-connected groups, challenging the idea that genetic decline led to the species’ collapse.

The large number of new genomes is one of the study’s main contributions. Only partial sequences exist for a few dozen Neanderthals, and until now, only four high-quality sequences were known — those that provide a level of information comparable to that obtained from modern genomes and that allow researchers to reconstruct an individual’s family history.

Three of those four sequences came from the Denisova and Chagyrskaya caves in the Altai Mountains in Siberia. There, on the edge of the territory once inhabited by the species, individuals dating from between 60,000 and 120,000 years ago showed a history of intense inbreeding among close relatives, including half-siblings.

“This was not unusual in this case,” says Alba Bossoms-Mesa, a researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and the study’s lead author, “because they were geographically isolated.”

“Our results show that the picture emerging from one region cannot simply be applied to all Neanderthals,” says Benjamin M. Peter, a co-author of the study and group leader at the Max Planck Institute for Evolutionary Anthropology. “Late Neanderthals of northwestern Europe appear to have been part of an interconnected regional population rather than small isolated groups with frequent mating between close relatives.”

The paper published on Wednesday presents a fifth high-quality genome — one that allows researchers to study both maternal and paternal chromosomes and reconstruct the individual’s family history. This Neanderthal, who lived 45,000 years ago, was found in the Goyet cave in Belgium and did not show the kind of DNA evidence of incestuous relationships seen in the Siberian individuals.

Interestingly, at the Belgian site, no close relatives were identified among the other individuals analyzed — not even between a newborn child and the adult females found alongside it. The bones and DNA of these Neanderthals tell a darker story. Many of the remains bear marks of defleshing and breakage to access the marrow. Previous research on Goyet has interpreted these remains as one of the clearest examples of Neanderthal cannibalism documented in Europe.

“We know the Goyet Neanderthals were not local. And they are precisely the ones who were cannibalized,” Bossoms-Mesa says. What is most striking is that the DNA shows that these cannibalized individuals belonged to the same broad genetic group as other Neanderthals in the region, meaning they were not members of a completely different population. Were they victims of conflict between Neanderthal groups, episodes of ritual cannibalism, or simply a drastic response to hunger? The answer is still unknown.

Carles Lalueza-Fox, an ancient DNA expert at the Institute of Evolutionary Biology (CSIC-UPF) in Barcelona who did not take part in the study, says these results suggest a different idea about the process of Neanderthal extinction. “Modern humans already existed then, but they do not show the demographic decline signals seen in other Neanderthals or in endangered animal populations,” he says. “Those species have populations of very few individuals for hundreds or thousands of years and go extinct through an accumulation of the genetic effects of low diversity, but this Goyet individual does not show those effects; they were not undergoing demographic decline.”

“But there are species that go extinct suddenly — humans are capable of extinguishing species in a few decades — and they do not have time to accumulate those demographic-decline signals,” he adds. This could suggest that humans were responsible for a faster extinction. “In any case, it was at least a heterogeneous process,” the researcher says.

The large number of genomes also confirms a puzzling finding about interbreeding with Neanderthals. As Bossoms-Mesa explains, several ancient Homo sapiens genomes show evidence of very recent Neanderthal ancestors. ““If we look at a Neanderthal, however, we have never found one with a great-great-grandparent who was human,” she says. Researchers have significantly expanded the number of individuals analyzed and still have not detected this recent gene flow in the opposite direction.

The researcher offers several possible explanations. Maybe encounters between the two species occurred in regions not yet studied. Social or cultural factors could also be at play. “Imagine that modern humans were willing to raise and incorporate into the community a baby who was half Neanderthal and half human, but Neanderthals were not,” she suggests.

Beyond its biological conclusions, the study also represents a technical breakthrough. Many of the samples analyzed would have been unusable just a few years ago. The team developed new tools to recover genetic information from highly degraded remains. Thanks to these methods, it was possible to reconstruct family relationships, identify individuals represented by multiple bone fragments, and even revise previous archaeological interpretations.

Bossoms-Mesa says these advances allow many questions about the relationships of those Neanderthals to be answered using an unprecedented amount of data. “The goal is not just to sequence isolated individuals but to reconstruct entire populations and understand how they interacted during the last millennia of their existence,” she says.

The wealth of information will help researchers continue to reconstruct Neanderthal life without reducing them to clichés, despite the difficulty of doing so for individuals who lived more than 40,000 years ago.

Lalueza-Fox notes that one common stereotype these new findings help refine is the idea that Neanderthals were lovers of cold climates. Sequences from 40 mitochondrial genomes — which are inherited solely through the maternal line and make it possible to trace female lineages over time — have been used to date periods of expansion and contraction in Neanderthal populations

“Although we have the idea that they were well adapted to cold, they actually expanded when the climate was warmer, and I think if we had older data, we would see even more of that expansion during warm peaks,” he says. Neanderthals were able to survive in cold environments, but their greatest periods of population growth may have occurred during milder phases.

These new techniques will help reconstruct with greater accuracy the evolutionary history of Neanderthals, who may have had flourishing and declining societies, which were at times violent and at times peaceful. And they, too, likely viewed the groups of their own species with whom they interacted—from Croatia to the Meuse basin—as “barbarians,” against whom they defined their own identities.

The new techniques will help reconstruct the evolutionary history of Neanderthals with greater fidelity—these other humans, who may have had flourishing and declining societies, both violent and peaceful. And they, too, likely saw other groups they encountered — from Croatia to the Meuse basin — as “barbarians,” defining themselves in opposition to them.

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