How a dime-sized fossil rewrote the story of human evolution

2010 was a seismic year for human prehistory.

That year, scientists made not one but two discoveries that rewrote the story of our species. First, in May, researchers from the Max Planck Institute for Evolutionary Anthropology sequenced the Neanderthal genome and found that Neanderthals, long considered an evolutionary dead end, had interbred with Homo sapiens. Their DNA lives on in many modern-day humans, especially people of European descent. (I’m as Slavic as they come and probably have 1–3% Neanderthal DNA.)

The second discovery came in December and was even more stunning. The same team extracted ancient DNA from a tiny fingertip found in the Denisova Cave, nestled in the Altai Mountains of Siberia. The results showed that the DNA didn’t belong to a Neanderthal or a modern human. Instead, it came from an entirely different lineage. Soon, journalists began calling this enigmatic group of humans the “Denisovans” — after the cave in which they were discovered. (Just as Neanderthals were named after Germany’s Neander Valley). 

It wasn’t just what they found that shook the field. It was how. 

Paleoanthropology, the study of prehistoric humans and their relatives, had long relied on painstaking digs, careful reconstruction of bones, and conservative interpretation. Now, DNA was fast outpacing fossil discoveries, and the discovery of the Denisovans represented a new milestone: They were the first group of humans to be identified through DNA alone.

When these results came out, Silvana Condemi, a seasoned paleoanthropologist and research director of the National Centre for Scientific Research (CNRS), the largest French public scientific research organization, was shocked, even skeptical. Like many of her colleagues, she had trained her eye to spot anatomical nuance — a Neanderthal ear canal, a sapiens jaw — but now she was being asked to trust a genetic readout pulled from a sliver of finger no bigger than a coin.

But when I spoke with her recently, she said the doubt eventually turned to wonder. “Everything I learned in school — from how to study prehistory to the actual facts — was being rewritten. And the story turned out to be much more exciting than I ever imagined.”

She turned to her longtime friend and collaborator, François Savatier, a science journalist, to talk about the discoveries. The two already had a habit of discussing prehistory simply for what Savatier called “the pleasure of thinking.” Their conversations eventually led them to coauthor two previous books (A Pocket History of Human Evolution and Neanderthal, My Brother). Together, they bring a unique dynamic: Condemi offers the deep expertise and trained skepticism of a researcher, while Savatier brings a curious, if still cautious, outsider’s perspective. The combination allows them to pursue ideas that stretch beyond the boundaries of their individual perspectives. 

Now, they turned their attention to this mysterious third lineage.

In their new book, The Secret World of the Denisovans, Condemi and Savatier bring together everything we know about this enigmatic human, allowing readers to get to know our ancient cousin species. The result is part primer, part detective story. But more than that, it’s a reminder that even our oldest assumptions about human history can be overturned and rewritten.

Who were the Denisovans?

Condemi and Savatier start where the story first broke: the Denisova Cave.

This region was already known to researchers as a prehistoric crossroads. During interglacial periods, warmer intervals between Ice Ages, various hominin groups, including Neanderthals and modern humans, moved through or inhabited the area as they migrated between Asia and Europe.

The Denisova Cave, in particular, has an unusual advantage that caught the attention of researchers: Its average temperature hovers just below freezing, which makes it an ideal vault for preserving ancient DNA. Unfortunately, the cave wasn’t just inhabited by humans, but also other species (from hyenas to horses) that trampled the cave floor and pulverized what might have been bigger fossils into smaller fragments. 

Still, scientists had been visiting the cave for years, suspecting it might have fossils that contain preserved DNA. And in 2008, a Russian team sent a small fingertip bone they had found to the lab of Svante Pääbo, a pioneering geneticist at the Max Planck Institute in Leipzig who was at the forefront of advances in sequencing ancient DNA. 

When Pääbo’s team announced they had identified a new species, it sent shockwaves through the field. Researchers rushed back to Denisova Cave, hoping to confirm or complicate the picture. The sudden and intense interest yielded significant discoveries, among them the DNA of a 13-year-old girl with a Neanderthal mother and a Denisovan father. 

In other words, the Denisova Cave wasn’t home to just one kind of ancient human; it was a shared space. Evidence from the Denisova cave and beyond now reveals every possible pairing: sapiens with Neanderthals, sapiens with Denisovans, and Neanderthals with Denisovans. All produced fertile offspring.

This raises an important question: Were these truly separate species, or regional variants of the same species?

In biology, one standard definition of species is based on reproductive isolation — whether two groups can produce fertile offspring. By that standard, these ancient humans might be seen as one species. (For comparison, horses and donkeys can mate, but their offspring, mules, are sterile.) However, Condemi notes, there’s more to species classification than genetics alone. Denisovans were genetically and anatomically distinct, and the consensus among scientists is that they represent a separate paleontological species. But they weren’t isolated. They belonged to a complex, overlapping human lineage that challenges simple categories.

As Condemi told me, “Humans like to think in terms of categories. The word species helps us make sense of it. But when we’re writing a book like this, while we agree it is a separate paleontological species, we also want to show how fragile those lines can be.”

“Denisovation”

After walking readers through the discovery of the first Denisovan, Condemi and Savatier zoom out to ask a bigger question: What does this discovery change about how we understand human evolution?

Quite a lot, it turns out. The more scientists looked, the further Denisovan traces extended. In 2011, just a year after the group was formally named, a genetic study revealed that modern-day Melanesians and some Micronesians carry up to 5% Denisovan DNA. That was an astonishing number, especially given that no Denisovan fossils had been found anywhere near the Pacific. It suggested that Denisovans had spread far beyond Siberia, likely interbreeding with H. sapiens somewhere in Southeast Asia or Oceania.

Then came physical evidence. One of the most critical clues was the Xiahe mandible, a jawbone discovered in the 1980s by a Tibetan monk in the Baishiya Karst Cave, a sacred site. The monk gave the jawbone to Chinese researchers, but it didn’t have clear features that researchers could use to link it to a particular species, so it remained unclassified in a collection for decades. Then, in 2019, scientists reanalyzed it using modern techniques to detect ancient proteins (the DNA hadn’t survived. They confirmed it belonged to a Denisovan.

As Condemi describes, this body of evidence points to at least two distinct populations: Northern and Southern Denisovans.

“These groups are closely tied to the environments where they evolved,” she explains. “Neanderthals and northern Denisovans adapted to cold and temperate climates, while southern Denisovans lived in tropical regions. Denisovans likely developed regional adaptations that gave them greater phenotypic diversity [i.e., different appearance] than Neanderthals. In the end, Denisovans and Neanderthals are like Eurasian siblings — more closely related to each other than to their African cousin, Homo sapiens.”

This ecological flexibility, surviving in high-altitude plateaus, tropical forests, and northern steppe, is what Savatier calls “spectacular.” It suggests that Denisovans weren’t just hardy; they were adaptable in ways that may have helped them thrive for hundreds of thousands of years.

Based on these findings, Condemi and Savatier offer a new evolutionary timeline.

The outdated timeline many people learned was fairly simple: Homo erectus, often described as the first human ancestor to walk fully upright and leave Africa, spread across Eurasia. Then another species, Homo heidelbergensis, came out of Africa and gave rise to the Neanderthals in western Eurasia (though not eastern Eurasia). In this version of events, Denisovans didn’t exist at all.

The updated timeline centers more solidly on H. heidelbergensis. According to the latest evidence, Neanderthals and Denisovans likely evolved from H. heidelbergensis in Western and Eastern Eurasia (respectively). Here’s the story: 

• Around 750,000 years ago, a population of H. heidelbergensis left Africa.
• By 400,000 years ago, this lineage had split into Neanderthals in the west and Denisovans in the east.
• By 200,000 years ago, Denisovans and Neanderthals were thriving — Denisovans mostly in Asia, Neanderthals in Europe, with the two meeting in areas like the Siberian steppe.
• Around 70,000 years ago, a population of H. sapiens began leaving Africa. As they spread through Eurasia, they encountered and interbred with both Neanderthals and Denisovans.

In Europe, this evolutionary process led to what the authors call “Neanderthalization.” In Asia, a parallel but distinct process took place, which Condemi and Savatier called “Denisovation.” And the Denisovan legacy wasn’t just symbolic. The DNA they passed on to modern humans had real, biological effects.

For example, in some modern-day populations, Denisovan genes help humans resist pathogens found in tropical environments. Meanwhile, Tibetans inherited the EPAS1 gene from Denisovans, which helps the body use oxygen more efficiently at high altitudes, where oxygen levels are about 40% lower than at sea level. This gene likely allowed both ancient Denisovans and modern Tibetans to survive and thrive on the high-elevation Tibetan Plateau.

A fragmented fossil record

Even though Denisovan DNA appears across Asia and Oceania, there are few fossil remains of Denisovans. In fact, until recently, nearly all confirmed Denisovan fossils came from just two sites: the Denisova Cave in Siberia and Baishiya Karst Cave on the Tibetan Plateau. Both offered unusually cold or high-altitude conditions, which help preserve fossils and ancient DNA. 

That doesn’t mean their fossils aren’t out there.

In the final chapters of the Secret World of the Denisovans, Condemi and Savatier focus on the Denisovan individual — what they might have looked like, how they hunted, and what they ate. They also discuss the possibility that some Denisovan fossils may have been misidentified for decades and make a call to action that we need to re-examine some specimens in light of our new understanding of a third lineage. 

Specifically, Condemi and Savatier address the long-standing dominance of a single species in the Asian fossil record: H. erectus, which arrived in Asia around 1.8 million years ago.  

“For decades, every ancient fossil found in Asia was simply labeled Homo erectus,” Condemi explains. “The same name was used to describe all the forms that existed between 1.3 million and 100,000 years ago. 

“But that became a problem, because people started stretching the term to cover everything — ‘archaic Homo erectus,’ ‘evolved Homo erectus,’ even ‘Homo erectus sapiens.’ It created a mess. You could be talking about a fossil from a million years ago or one from 400,000 years ago, and still call it Homo erectus, with no clarity about what that actually meant.”

Yet, as Condemi notes, the idea that all those fossils represent a single species doesn’t add up. “If all those fossils really did belong to the same species, it would mean Homo erectus survived in Asia for over a million years without much evolutionary change; while in Europe, hominins were evolving into Neanderthals. Why wouldn’t something similar have happened in Asia?”

The discovery of the Denisovans offers a different perspective. As summarized, their existence supports a branching evolutionary model in which H. heidelbergensis (not H. erectus) gave rise to Neanderthals in Europe and Denisovans in Asia, while H. erectus may have disappeared earlier. This model reflects a more realistic view of human evolution: not a single line, but a tree with diverging branches and regionally adapted populations.

This timeline suggests that some fossils discovered before 2010, when H. erectus and Neanderthals were thought to be the only hominin species in Eurasia, may need a second look. Condemi and Savatier point to fossils like “Dali Man” from China and the “Solo Man”  from Indonesia as examples of fossils identified as H. erectus that might really be Denisovan. 

Still, not everyone is eager to rewrite that story — especially in China, where fossils like Peking Man, a landmark discovery classified as H. erectus pekinensis, hold deep cultural and national significance. Reclassifying such fossils as Denisovan, or even suggesting Denisovan admixture, means challenging a powerful origin narrative, one that links ancient and modern humans in China through a direct evolutionary line.

Savatier and Condemi are quick to note that this kind of scientific nationalism is not unique to China; it has roots in European intellectual traditions, where ideas about human origins were long shaped by national pride and regional biases. Still, the situation highlights a crucial point: Prehistory is not free from bias. The interpretation of ancient human remains is often influenced not only by evidence but also by cultural narratives and modern identity politics.

The secret world remains (mostly) a secret

Savatier emphasizes that there’s likely more to discover, and that linking fossils to Denisovan DNA is essential. “From most researchers’ perspectives, the discovery of Denisovan DNA alone didn’t amount to identifying a new species,” he explains. “Connecting that enigmatic genetic signal to actual fossil remains was crucial — and that’s what we’ve been doing. Since then, geneticists have detected Denisovan DNA in fossils we had already suspected were Denisovan.”

Still, he and Condemi both acknowledge that there is a significant gap in the fossil record, especially in tropical regions where Denisovans likely lived and, in some cases, are known to have lived. 

“Fossilization in the tropics is rare, and finding ancient DNA is even rarer,” he says. “But if you look hard enough, you’ll probably find something. We need to explore caves across the Asian tropics as well as India. In other words, there’s plenty of work for the young scientists.”

By the end of The Secret World of the Denisovans, Condemi and Savatier cover far more than I can capture here: what Denisovans may have looked like, how they lived, where they traveled, and how shifting climates and ancient landmasses (some now submerged) shaped their migrations. They sketch a remarkably adaptable person, surviving in both cold highlands and tropical rainforests. I found myself able to picture their faces, body, their tools, the way they hunted, and more.

However, when I asked Condemi what she most hoped readers would take from the book, she didn’t point to a single fossil or breakthrough. She pointed to a broader truth:

“If we humans, Homo sapiens, are today the only human species on Earth, this was not always the case. Other humans have inhabited our planet, and they were well adapted to their environment. These hunter-gatherer populations moved through the territory, they encountered other humans, they exchanged techniques of survival and also sometimes their genes.”

Her comment struck me as highlighting an important broader truth: Humans are used to being the dominant species, but that wasn’t always the case. As they write at the end of their book, Neanderthals and Denisovans may have been the last “animal-humans” of Eurasia, populations that lived in ecological balance, taking what they needed and adapting without overrunning.

The contrast is hard to miss. Modern humans are the ones who broke that balance and, in doing so, became something different. We multiplied, migrated, and transformed every environment we touched. And ironically, our ability to dominate may have come from what we inherited through coexistence and contact.

At least, that’s the story so far. Check back in a decade.