Denisovans

Is the “million-year-old” skull from China a Denisovan or something else?

anthropology, Archaeology, Denisovans, hominins, homo longi, paleoanthropology, Science, skulls / Shannon Garcia / September 30, 2025

Homo longi by any other name

Now that we know what Denisovans looked like, they’re turning up everywhere.

This digital reconstruction makes Yunxian 2 look liess like a Homo erectus and more like a Denisovan (or Homo longi, according to the authors). Credit: Feng et al. 2025

A fossil skull from China that made headlines last week may or may not be a million years old, but it’s probably closely related to Denisovans.

The fossil skull, dubbed Yunxian 2, is one of three unearthed from a terrace alongside the Han River, in central China, in a layer of river sediment somewhere between 600,000 and 1 million years old. Archaeologists originally identified them as Homo erectus, but Hanjiang Normal University paleoanthropologist Xiaobo Feng and his colleagues’ recent digital reconstruction of Yunxian 2 suggests the skulls may actually have belonged to someone a lot more similar to us: a hominin group defined as a species called Homo longi or a Denisovan, depending on who’s doing the naming.

The recent paper adds fuel—and a new twist—to that debate. And the whole thing may hinge on a third skull from the same site, still waiting to be published.

A front and a side view of a digitally reconstructed hominin skull — This digital reconstruction makes Yunxian 2 look less like a *Homo erectus* and more like a Denisovan (or *Homo longi*, according to the authors). Credit: Feng et al. 2025

Denisovan or Homo longi?

The Yunxian skull was cracked and broken after hundreds of thousands of years under the crushing weight of all that river mud, but the authors used CT scans to digitally put the pieces back together. (They got some clues from a few intact bits of Yunxian 1, which lay buried in the same layer of mud just 3 meters away.) In the end, Feng and his colleagues found themselves looking at a familiar face; Yunxian 2 bears a striking resemblance to a 146,000-year-old Denisovan skull.

That skull, from Harbin in northeast China, made headlines in 2021 when a team of paleoanthropologists claimed it was part of an entirely new species, which they dubbed Homo longi. According to that first study, Homo longi was a distinct hominin species, separate from us, Neanderthals, and even Denisovans. That immediately became a point of contention because of features the skull shared with some other suspected Denisovan fossils.

Earlier this year, a team of researchers, which included one of the 2021 study’s authors, took samples of ancient proteins preserved in the Harbin skull; of the 95 proteins they found, three of them matched proteins only encoded in Denisovan DNA. While the June 2025 study suggested that Homo longi was a Denisovan all along, the new paper draws a different conclusion: Homo longi is a species that happens to include the population we’ve been calling Denisovans. As study coauthor Xijun Ni, of the Chinese Academy of Sciences, puts it in an email to Ars Technica, “Given their similar age range, distribution areas, and available morphological data, it is likely that Denisovans belong to the Homo longi species. However, little is known about Denisovan morphology.”

Of course, that statement—that we know little about Denisovan morphology (the shapes and features of their bones)—only applies if you don’t accept the results of the June 2025 study mentioned above, which clocked the Harbin skull as a Denisovan and therefore told us what one looks like.

And Feng and his colleagues, in fact, don’t accept those results. Instead, they consider Harbin part of some other group of Homo longi, and they question the earlier study’s methods and results. “The peptide sequences from Harbin, Penghu, and other fossils are too short and provide conflicting information,” Ni tells Ars Technica. Feng and his colleagues also question the results of another study, which used mitochondrial DNA to identify Harbin as a Denisovan.

In other words, Feng and his colleagues are pretty invested in defining Homo longi as a species and Denisovans as just one sub-group of that species. But that’s hard to square with DNA data.

Alas, poor Yunxian 2, I knew him well

Yunxian 2 has a wide face with high, flat cheekbones, a wide nasal opening, and heavy brows. Its cranium is higher and rounder than Homo erectus (and the original reconstruction, done in the 1990s), but it’s still longer and lower than is normal for our species. Overall, it could have held about 1,143 cubic centimeters of brain, which is in the ballpark of modern people. But its shape may have left less room for the frontal lobe (the area where a lot of social skills, logic, motor skills, and executive function happen) than you’d expect in a Neanderthal or a Homo sapiens skull.

Feng and his colleagues measured the distances between 533 specific points on the skull: anatomical landmarks like muscle attachment points or the joints between certain bones. They compared those measurements to ones from 26 fossil hominin skulls and several-dozen modern human skulls, using a computer program to calculate how similar each skull was to all of the others.

Yunxian 2 fits neatly into a lookalike group with the Harbin skull, along with two other skulls that paleoanthropologists have flagged as belonging to either Denisovans or Homo longi. Those two skulls are a 200,000- to 260,000-year-old skull found in Dali County in northwestern China and a 260,000-year-old skull from Jinniushi (sometimes spelled Jinniushan) Cave in China.

Those morphological differences suggest some things about how the individuals who once inhabited these skulls might have been related to each other, but that’s also where things get dicey.

front and side views of 3 skulls. — An older reconstruction of the Yunxian 2 skull gives it a flatter look. Credit: government of Wuhan

Digging into the details

Most of what we know about how we’re related to our closest extinct hominin relatives (Neanderthals and Denisovans) comes from comparing our DNA to theirs and tracking how small changes in the genetic code build up over time. Based on DNA, our species last shared a common ancestor with Neanderthals and Denisovans sometime around 750,000 years ago in Africa. One branch of the family tree led to us; the other branch split again around 600,000 years ago, leading to Neanderthals and Denisovans (or Homo longi, if you prefer).

In other words, DNA tells us that Neanderthals and Denisovans are more closely related to each other than either is to us. (Unless you’re looking at mitochondrial DNA, which suggests that we’re more closely related to Neanderthals than to Denisovans; it’s complicated, and there’s a lot we still don’t understand.)

“Ancient mtDNA and genomic data show different phylogenetic relationships among Denisovans, Neanderthals and Homo sapiens,” says Ni. So depending on which set of data you use and where your hominin tree starts, it can be possible to get different answers about who is most closely related to whom. The fact that all of these groups interbred with each other can explain this complexity, but makes building family trees challenging.

It is very clear, however, that Feng and his colleagues’ picture of the relationships between us and our late hominin cousins, based on similarities among fossil skulls in their study, looks very different from what the genomes tell us. In their model, we’re more closely related to Denisovans, and the Neanderthals are off on their own branch of the family tree. Feng and his colleagues also say those splits happened much earlier, with Neanderthals branching off on their own around 1.38 million years ago; we last shared a common ancestor with Homo longi around 1 million years ago.

That’s a big difference from DNA results, especially when it comes to timing. And the timing is likely to be the biggest controversy here. In a recent commentary on Feng and his colleagues’ study, University of Wisconsin paleoanthropologist John Hawks argues that you can’t just leave genetic evidence out of the picture.

“What this research should have done is to put the anatomical comparisons into context with the previous results from DNA, especially the genomes that enable us to understand the relationships of Denisovan, Neanderthal, and modern human groups,” Hawks writes.

(It’s worth a side note that most news stories describe Yunxian 2 as being a million years old, and so do Feng and his colleagues. But electron spin resonance dating of fossil animal bones from the same sediment layer suggests the skull could be as young as 600,000 years old or as old as 1.1 million. That still needs to be narrowed down to everyone’s satisfaction.)

What’s in a name?

Of course, DNA also tells us that even after all this branching and migrating, the three species were still similar enough to reproduce, which they did several times. Many groups of modern people still carry traces of Neanderthal and Denisovan DNA in their genomes, courtesy of those exchanges. And some ancient Neanderthal populations were carrying around even older chunks of human DNA in the same way. That arguably makes species definitions a little fuzzy at best—and maybe even irrelevant.

“I think all these groups, including Neanderthals, should be recognized within our own species, Homo sapiens,” writes Hawks. Hawks contends that the differences among these hominin groups “were the kind that evolve among the populations of a single species over time, not starkly different groups that tread the landscape in mutually unrecognizeable ways.”

But humans love to classify things (a trait we may have shared with Neanderthals and Denisovans), so those species distinctions are likely to persist even if the lines between them aren’t so solid. As long as that’s the case, names and classifications will be fodder for often heated debate. And Feng’s team is staking out a position that’s very different from Hawks’. “‘Denisovan’ is a label for genetic samples taken from the Denisova Cave. It should not be used everywhere. Homo longi is a formally named species,” says Ni.

Technically, Denisovans don’t have a formal species name, a Latinized moniker like Homo erectus that comes with a clear(ish) spot on the family tree. Homo longi would be a more formal species name, but only if scientists can agree on whether they’re actually a species.

an archaeologist kneels in front of a partially buried skull — An archaeologist comes face to face with the Yunxian 3 skull Credit: government of Wuhan

The third Yunxian skull

Paleoanthropologists unearthed a third skull from the Yunxian site in 2022. It bears a strong resemblance to the other two from the area (and is apparently in better shape than either of them), and it dates to about the same timeframe. A 2022 press release describes it as “the most complete Homo erectus skull found in Eurasia so far,” but if Feng and his colleagues are right, it may actually be a remarkably complete Homo longi (and/or Denisovan) skull. And it could hold the answers to many of the questions anthropologists like Feng and Hawks are currently debating.

“It remains pretty obvious that Yunxian 3 is going to be central to testing the relationships of this sample [of fossil hominins in Feng and colleagues’ paper],” writes Hawks.

The problem is that Yunxian 3 is still being cleaned and prepared. Preparing a fossil is a painstaking, time-consuming process that involves very carefully excavating it from the rocky matrix it’s embedded in, using everything from air-chisels to paintbrushes. And until that’s done and a scientific report on the skull is published, other paleoanthropologists don’t have access to any information about its features—which would be super useful for figuring out how to define whatever group we eventually decide it belongs to.

For the foreseeable future, the relationships between us and our extinct cousins (or at least our ideas about those relationships) will keep changing as we get more data. Eventually, we may have enough data from enough fossils and ancient DNA samples to form a clearer picture of our past. But in the meantime, if you’re drawing a hominin family tree, use a pencil.

Science, 2025. DOI: 10.1126/science.ado9202 (About DOIs).

Kiona is a freelance science journalist and resident archaeology nerd at Ars Technica.

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Oldest wooden tools in East Asia may have come from any of three species

ancient people did stuff, Archaeology, Denisovans, hominins, homo erectus, Homo heidelbergensis, Science, wooden tools / DJ Henderson / July 7, 2025

That leaves a few possibilities: Denisovans, Homo heidelbergensis (the common ancestor of Neanderthals, Denisovans, and our species), or Homo erectus. All three species could have lived in the area at the time. But nobody at Gantangqing left behind any convenient, readily identifiable bones along with their wooden tools, stone tools, and butchered animal bones (so inconsiderate of them), making it hard to pin down exactly which species these 300,000-year-old hunter-gatherers belonged to.

Homo erectus had been in Asia for more than a million years by the time Gantangqing’s lakeshore was occupied; the oldest Homo erectus fossils in Asia are from Indonesia and date back 1.8 million years. They also stuck around until quite recently. In caves at a site called Zhoukoudian, outside Beijing in eastern China, Homo erectus remains date to sometime between 700,000 and 200,000 years ago (there’s still a lot of debate on exactly how old the site is).

All of that means that Homo erectus’ presence in the region overlaps the age of the wood tools at Gantangqing. And the stone tools found nearby are fairly simple cores and flakes that don’t rule out Homo erectus as their makers. Archaeologists haven’t unearthed evidence of Homo erectus making or using sophisticated wooden tools like this, but for a species that managed to harness fire and cross miles of ocean, it’s not too wild a speculation.

On the other hand, we know that Denisovans were probably in the area, too, or at least not too far away. A recently identified Denisovan skull from Harbin, China, is 146,000 years old but bears a striking resemblance to other hominin skulls from sites all over China, which range from 300,000 to 200,000 years old. And making finely crafted wooden tools fits with everything we know about Denisovan capabilities.

Then there’s Homo heidelbergensis, the direct ancestor of Denisovans. In fact, it’s a little hard to tell where hominins stop being Homo heidelbergensis and start being Denisovans, or even whether the distinction matters. It’s a problem paleoanthropologists refer to as the “muddle in the Middle,” since both species date to the Middle Pleistocene. So if Homo erectus and Denisovans are in the running, so is Homo heidelbergensis, by default.

And unless someone finds a telltale skull nearby or another very similar toolkit at a site with telltale skulls to consult, we may not know for sure.

Science, 2023. DOI: 10.1126/science.adr8540 (About DOIs).

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We’ve had a Denisovan skull since the 1930s—only nobody knew

ancient DNA, ancient proteins, anthropology, Archaeology, Denisovans, hominins, Neanderthals, paleoanthropology, paleoproteomics, proteomics, Science, skeletons and skeleton accessories, skulls / Mike M. / June 18, 2025

It’s a Denisovan? Always has been.

After years of mystery, we now know what at least one Denisovan looked like.

A 146,000-year-old skull from Harbin, China, belongs to a Denisovan, according to a recent study of proteins preserved inside the ancient bone. The paleoanthropologists who studied the Harbin skull in 2021 declared it a new (to us) species, Homo longi. But the Harbin skull still contains enough of its original proteins to tell a different story: A few of them matched specific proteins from Denisovan bones and teeth, as encoded in Denisovan DNA.

So Homo longi was a Denisovan all along, and thanks to the remarkably well-preserved skull, we finally know what the enigmatic Denisovans actually looked like.

Two early-human skulls against a black background. — Credit: Ni et al. 2021

The Harbin skull (left) and the Dali skull (right).

Unmasking Dragon Man

Paleoanthropologist Qiang Ji, of the Chinese Academy of Sciences, and colleagues tried to sequence ancient DNA from several samples of the Harbin skull’s bone and its one remaining tooth, but they had no luck. Proteins tend to be hardier molecules than DNA, though, and in samples from the skull’s temporal bone (the ones on the sides of the head, just behind the cheekbones), the researchers struck pay dirt.

They found fragments of a total of 95 proteins. Four of these had variations that were distinct to the Denisovan lineage, and the Harbin skull matched Denisovans on three of them. That’s enough to confidently say that the Harbin skull had belonged to a Denisovan. So for the past few years, we’ve had images of an almost uncannily well-preserved Denisovan skull—which is a pretty big deal, especially when you consider its complicated history.

While the world is now aware of it, until 2021, only one person had known what the skull looked like since its discovery in the 1930s. It was unearthed in Harbin, in northeast China, during the Japanese occupation of the area. Not wanting it to be seized by the occupying government, the person who found the skull immediately hid it, and he kept it hidden for most of the rest of his life.

He eventually turned it over to scientists in 2018, who published their analysis in 2021. That analysis placed the Harbin skull, along with a number of other fossils from China, in a distinct lineage within our genus, Homo, making them our species’ closest fossil relatives. They called this alleged new species Homo longi, or “Dragon Man.”

The decision to classify Homo longi as a new species was largely due to the skull’s unique combination of features (which we’ll discuss below). But it was a controversial decision, partly because paleoanthropologists don’t entirely agree about whether we should even call Neanderthals a distinct species. If the line between Neanderthals and our species is that blurry, many in the field have questioned whether Homo longi could be considered a distinct species, when it’s even closer to us than the Neanderthals.

Meanwhile, the 2021 paper also left room for debate on whether the skull might actually have belonged to a Denisovan rather than a distinct new species. Its authors acknowledge that one of the fossils they label as Homo longi had already been identified as a Denisovan based on its protein sequences. They also point out that the Harbin skull has rather large molars, which seem to be a common feature in Denisovans.

The paper’s authors argued that their Homo longi should be a separate branch of the hominin lineage, more closely related to us than to Denisovans or Neanderthals. But if the Harbin skull looked so much like Denisovan fossils and so little like fossils from our species, the alleged relationship begins to look pretty dubious. In the end, the 2021 paper’s authors dodged the issue by saying that “new genetic material will test the relationship of these populations to each other and to the Denisovans.”

Which turned out to be exactly what happened.

A ghost lineage comes to life

Denisovans are the ghost in our family tree. For scientists, a “ghost lineage” is one that’s known mostly from genetic evidence, not fossils; like a ghost, it has a presence we can sense but no physical form we can touch. With the extremely well-preserved Harbin skull identified as a Denisovan, though, we’re finally able to look our “ghost” cousins in the face.

Paleogeneticists have recovered Denisovan DNA from tiny fragments of bone and teeth, and even from the soil of a cave floor. Genomics researchers have found segments of Denisovan DNA woven into the genomes of some modern humans, revealing just how close our two species once were. But the handful of Denisovan fossils paleoanthropologists have unearthed are mostly small fragments—a finger bone here, a tooth there, a jawbone someplace else—that don’t reveal much about how Denisovans lived or what they looked like.

We know they existed and that they were something slightly different from Homo sapiens or Neanderthals. We even know when and where they lived and a surprising amount about their genetics, and we have some very strong hints about how they interacted with our species and with Neanderthals. But we didn’t really know what they looked like, and we couldn’t hope to identify their fossils without turning to DNA or protein sequences.

Until now.

Neanderthals and Denisovans probably enjoyed the view from Denisova Cave, too. Credit: loronet / Flickr

The face of a Denisovan

So what did a Denisovan look like? Harbin 1 has a wide, flattish face with small cheekbones, big eye sockets, and a heavy brow. Its upper jaw juts forward just a little, and it had big, robust molars. The cranium itself is longer and less dome-like than ours, but it’s roomy enough for a big brain (about 1,420 millimeters).

Some of those traits, like the large molars and the long, low cranium, resemble those of earlier hominin species such as Homo erectus or Homo heidelbergensis. Others, like a relatively flat face, set beneath the cranium instead of sticking out in front of it, look more like us. (Early hominins, like Australopithecus afarensis, don’t really have foreheads because their skulls are arranged so their brains are right behind their faces instead of partly above them, like ours.)

In other words, Harbin’s features are what paleoanthropologists call a mosaic, with some traits that look like they come from older lineages and some that seem more modern. Mosaics are common in the hominin family tree.

But for all the detail it reveals about the Denisovans, Harbin is still just one skull from one individual. Imagine trying to reconstruct all the diversity of human faces from just one skull. We have to assume that Densiovans—a species that spanned a huge swath of our planet, from Siberia to Taiwan, and a wide range of environments, from high-altitude plateaus in Tibet to subtropical forests—were also a pretty diverse species.

It’s also worth remembering that the Harbin skull is exactly that: a skull. It can’t tell us much about how tall its former user was, how they were built, or how they moved or worked during their life. We can’t even say for sure whether Harbin is osteologically or genetically male or female. In other words, some of the mystery of the Denisovans still endures.

What’s next?

In the 2021 papers, the researchers noted that the Harbin skull also bears a resemblance to a 200,000- to 260,000-year-old skull found in Dali County in northwestern China, a roughly 300,000-year-old skull found in Hualong Cave in eastern China, and a 260,000-year-old skull from Jinniushi (sometimes spelled Jinniushan) Cave in China. And some fossils from Taiwan and northern China have molars that look an awful lot like those in that Tibetan jawbone.

“These hominins potentially also belong to Denisovan populations,” write Ji and colleagues. That means we might already have a better sample of Denisovan diversity than this one skull suggests.

And, like the Harbin skull, the bones and teeth of those other fossils may hold ancient DNA or proteins that could help confirm that intriguing possibility.

Science, 2023 DOI: 10.1126/science.adu9677 (About DOIs).

Kiona is a freelance science journalist and resident archaeology nerd at Ars Technica.

We’ve had a Denisovan skull since the 1930s—only nobody knew Read More »

High-altitude cave used by Tibetan Buddhists yields a Denisovan fossil

ancient proteins, Archeology, Denisovans, human evolution, Science / DJ Henderson / July 3, 2024

Eating in —

Cave deposits yield bones of sheep, yaks, carnivores, and birds that were butchered.

John Timmer – Jul 3, 2024 6: 27 pm UTC

Image of a sheer cliff face with a narrow path leading to a cave opening. — Enlarge / The Baishiya Karst Cave, where the recently analyzed samples were obtained.

Dongju Zhang’s group (Lanzhou University)

For well over a century, we had the opportunity to study Neanderthals—their bones, the items they left behind, their distribution across Eurasia. So, when we finally obtained the sequence of their genome and discovered that we share a genetic legacy with them, it was easy to place the discoveries into context. In contrast, we had no idea Denisovans existed when sequencing DNA from a small finger bone revealed that yet another relative of modern humans had roamed Asia in the recent past.

Since then, we’ve learned little more. The frequency of their DNA in modern human populations suggest that they were likely concentrated in East Asia. But we’ve only discovered fragments of bone and a few teeth since then, so we can’t even make very informed guesses as to what they might have looked like. On Wednesday, an international group of researchers described finds from a cave on the Tibetan Plateau that had been occupied by Denisovans, which tell us a bit more about these relatives: what they ate. And that appears to be anything they could get their hands on.

The Baishiya Karst Cave

The finds come from a site called the Baishiya Karst Cave, which is perched on a cliff on the northeast of the Tibetan Plateau. It’s located at a high altitude (over 3,000 meters or nearly 11,000 feet) but borders a high open plain, as you can see in the picture below.

Oddly, it came to the attention of the paleontology community because the cave was a pilgrimage site for Tibetan monks, one of whom discovered a portion of a lower jaw that eventually was given to a university. There, people struggled to understand exactly how it fit with human populations until eventually analysis of proteins preserved within it indicated it belonged to a Denisovan. Now called the Xiahe mandible, it remains the most substantial Denisovan fossil we’ve discovered to date.

Enlarge / The Ganjia Basin borders the cliffs that contain the Baishiya Karst Cave.

Dongju Zhang’s group (Lanzhou University)

Since then, excavations at the site had turned up a large collection of animal bones, but none that had been identified as Denisovan. Sequencing of environmental DNA preserved in the cave, however, revealed that the Denisovans had occupied the cave regularly for at least 100,000 years, meaning they were surviving at altitude during both of the last two glacial cycles.

The new work focuses in on the bones, many of which are too fragmentary to be definitively assigned to a species. To do so, the researchers purified fragments of proteins from the bones, which contain large amounts of collagen. These fragments were then separated according to their mass, a technique called mass spectrometry, which works well even with the incredibly small volumes of proteins that survive over hundreds of thousands of years.

Mass spectrometry relies on the fact that there are only a limited number of combinations of amino acids—often only one—that will produce a protein fragment of a given mass. So, if the mass spectrometry finds a signal at that mass, you can compare the possible amino acid combinations that produce it to known collagen sequences to find matches. Some of these matches will end up being in places where collagens from different species have distinct sequences of amino acids, allowing you to determine what species the bone came from.

When used this way, the technique is termed zooarchaeology by mass spectrometry, or ZooMS. And, in the case of the work described in the new paper, it identified nearly 80 percent of the bone fragments that were tested.

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