Neanderthals

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.

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Studies pin down exactly when humans and Neanderthals swapped DNA

ancient DNA, ancient genomics, ancient people did stuff, anthropology, Archaeology, Neanderthals, out of africa, Science / 9u50fv / December 12, 2024

We may owe our tiny sliver of Neanderthal DNA to just a couple of hundred Neanderthals.

The artist’s illustration shows what the six people buried at the Ranis site, who lived between 49, 500 and 41,000 years ago, may have looked like. Two of these people are mother and daughter, and the mother is a distant cousin (or perhaps a great-great-grandparent or great-great-grandchild) to a woman whose skull was found 130 kilometers away in what’s now Czechia. Credit: Sumer et al. 2024

Two recent studies suggest that the gene flow (as the young people call it these days) between Neanderthals and our species happened during a short period sometime between 50,000 and 43,500 years ago. The studies, which share several co-authors, suggest that our torrid history with Neanderthals may have been shorter than we thought.

Pinpointing exactly when Neanderthals met H. sapiens

Max Planck Institute of Evolutionary Anthropology scientist Leonardo Iasi and his colleagues examined the genomes of 59 people who lived in Europe between 45,000 and 2,200 years ago, plus those of 275 modern people whose ancestors hailed from all over the world. The researchers cataloged the segments of Neanderthal DNA in each person’s genome, then compared them to see where those segments appeared and how that changed over time and distance. This revealed how Neanderthal ancestry got passed around as people spread around the world and provided an estimate of when it all started.

“We tried to compare where in the genomes these [Neanderthal segments] occur and if the positions are shared among individuals or if there are many unique segments that you find [in people from different places],” said University of California Berkeley geneticist Priya Moorjani in a recent press conference. “We find the majority of the segments are shared, and that would be consistent with the fact that there was a single gene flow event.”

That event wasn’t quite a one-night stand; in this case, a “gene flow event” is a period of centuries or millennia when Neanderthals and Homo sapiens must have been in close contact (obviously very close, in some cases). Iasi and his colleagues’ results suggest that happened between 50,500 and 43,000 years ago. But it’s quite different from our history with another closely related hominin species, the now-extinct Denisovans, with whom different Homo sapiens groups met and mingled at least twice on our way to taking over the world.

In a second study, Arev Sümer (also of the Max Planck Institute) and her colleagues found something very similar in the genomes of people who lived 49,500 to 41,000 years ago in what’s now the area around Ranis, Germany. The Ranis population, based on how their genomes compare to other ancient and modern people, seem to have been part of one of the first groups to split off from the wave of humans who migrated out of Africa, through the Levant, and into Eurasia sometime around 50,000 years ago. They carried with them traces of what their ancestors had gotten up to during that journey: about 2.9 percent of their genomes were made up of segments of Neanderthal ancestry.

Based on how long the Ranis people’s segments of Neanderthal DNA were (longer chunks of Neanderthal ancestry tend to point to more recent mixing), the interspecies mingling happened about 80 generations, or about 2,300 years, before the Ranis people lived and died. That’s about 49,000 to 45,000 years ago. The dates from both studies line up well with each other and with archaeological evidence that points to when Neanderthal and Homo sapiens cultures overlapped in parts of Europe and Asia.

What’s still not clear is whether that period of contact lasted the full 5,000 to 7,000 years, or if, as Johannes Krause (also of the Max Planck Institute) suggests, it was only a few centuries—1,500 years at the most—that fell somewhere within that range of dates.

Natural selection worked fast on our borrowed Neanderthal DNA

Once those first Homo sapiens in Eurasia had acquired their souvenir Neanderthal genes (forget stealing a partner’s hoodie; just take some useful segments of their genome), natural selection got to work on them very quickly, discarding some and passing along others, so that by about 100 generations after the “event,” the pattern of Neanderthal DNA segments in people’s genomes looked a lot like it does today.

Iasi and his colleagues looked through their catalog of genomes for sections that contained more (or less) Neanderthal ancestry than you’d expect to find by random chance—a pattern that suggests that natural selection has been at work on those segments. Some of the segments that tended to include more Neanderthal gene variants included areas related to skin pigmentation, the immune response, and metabolism. And that makes perfect sense, according to Iasi.

“Neanderthals had lived in Europe, or outside of Africa, for thousands of years already, so they were probably adapted to their environment, climate, and pathogens,” said Iasi during the press conference. Homo sapiens were facing selective pressure to adapt to the same challenges, so genes that gave them an advantage would have been more likely to get passed along, while unhelpful ones would have been quick to get weeded out.

The most interesting questions remain unanswered

The Neanderthal DNA that many people carry today, the researchers argue, is a legacy from just 100 or 200 Neanderthals.

“The effective population size of modern humans outside Africa was about 5,000,” said Krause in the press conference. “And we have a ratio of about 50 to 1 in terms of admixture [meaning that Neanderthal segments account for about 2 percent of modern genomes in people who aren’t of African ancestry], so we have to say it was about 100 to maybe 200 Neanderthals roughly that mixed into the population.” Assuming Krause is right about that and about how long the two species stayed in contact, a Homo sapiens/Neanderthal pairing would have happened every few years.

So we know that Neanderthals and members of our species lived in close proximity and occasionally produced children for at least several centuries, but no artifacts, bones, or ancient DNA have yet revealed much of what that time, or that relationship, was actually like for either group of people.

The snippets of Neanderthal ancestry left in many modern genomes, and those of people who lived tens of thousands of years ago, don’t offer any hints about whether that handful of Neanderthal ancestors were mostly male or mostly female, which is something that could shed light on the cultural rules around such pairings. And nothing archaeologists have unearthed so far can tell us whether those pairings were consensual, whether they were long-term relationships or hasty flings, or whether they involved social relationships recognized by one (or both) groups. We may never have answers to those questions.

And where did it all happen? Archaeologists haven’t yet found a cave wall inscribed with “Og heart Grag,” but based on the timing, Neanderthals and Homo sapiens probably met and lived alongside each other for at least a few centuries, somewhere in “the Near East,” which includes parts of North Africa, the Levant, what’s now Turkey, and what was once Mesopotamia. That’s one of the key routes that people would have followed as they migrated from Africa into Europe and Asia, and the timing lines up with when we know that both Homo sapiens and Neanderthals were in the area.

“This [same] genetic admixture also appears in East Asia and Australia and the Americas and Europe,” said Krause. “If it would have happened in Europe or somewhere else, then the distribution would probably look different than what we see.”

Science, 2023 DOI: 10.1126/science.adq3010;

Nature, 2023 DOI: 10.1038/s41586-024-08420-x;

(About DOIs ).

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

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Much of Neanderthal genetic diversity came from modern humans

Biology, evolution, Genetics, Genomics, human evolution, Neanderthals, Science / DJ Henderson / July 12, 2024

The basic outline of the interactions between modern humans and Neanderthals is now well established. The two came in contact as modern humans began their major expansion out of Africa, which occurred roughly 60,000 years ago. Humans picked up some Neanderthal DNA through interbreeding, while the Neanderthal population, always fairly small, was swept away by the waves of new arrivals.

But there are some aspects of this big-picture view that don’t entirely line up with the data. While it nicely explains the fact that Neanderthal sequences are far more common in non-African populations, it doesn’t account for the fact that every African population we’ve looked at has some DNA that matches up with Neanderthal DNA.

A study published on Thursday argues that much of this match came about because an early modern human population also left Africa and interbred with Neanderthals. But in this case, the result was to introduce modern human DNA to the Neanderthal population. The study shows that this DNA accounts for a lot of Neanderthals’ genetic diversity, suggesting that their population was even smaller than earlier estimates had suggested.

Out of Africa early

This study isn’t the first to suggest that modern humans and their genes met Neanderthals well in advance of our major out-of-Africa expansion. The key to understanding this is the genome of a Neanderthal from the Altai region of Siberia, which dates from roughly 120,000 years ago. That’s well before modern humans expanded out of Africa, yet its genome has some regions that have excellent matches to the human genome but are absent from the Denisovan lineage.

One explanation for this is that these are segments of Neanderthal DNA that were later picked up by the population that expanded out of Africa. The problem with that view is that most of these sequences also show up in African populations. So, researchers advanced the idea that an ancestral population of modern humans left Africa about 200,000 years ago, and some of its DNA was retained by Siberian Neanderthals. That’s consistent with some fossil finds that place anatomically modern humans in the Mideast at roughly the same time.

There is, however, an alternative explanation: Some of the population that expanded out of Africa 60,000 years ago and picked up Neanderthal DNA migrated back to Africa, taking the Neanderthal DNA with them. That has led to a small bit of the Neanderthal DNA persisting within African populations.

To sort this all out, a research team based at Princeton University focused on the Neanderthal DNA found in Africans, taking advantage of the fact that we now have a much larger array of completed human genomes (approximately 2,000 of them).

The work was based on a simple hypothesis. All of our work on Neanderthal DNA indicates that their population was relatively small, and thus had less genetic diversity than modern humans did. If that’s the case, then the addition of modern human DNA to the Neanderthal population should have boosted its genetic diversity. If so, then the stretches of “Neanderthal” DNA found in African populations should include some of the more diverse regions of the Neanderthal genome.

Much of Neanderthal genetic diversity came from modern humans Read More »