Text settings Story text Size Small Standard Large Width * Standard Wide Links Standard Orange * Subscribers only Learn more Minimize to nav All the Homo naledi skeletons in Rising Star Cave are female, and that probably didn’t happen by accident.
In 2013, a team of anthropologists led by Lee Berger unearthed the remains of more than 20 small-bodied hominins (ancient relatives of humans), all 335,000 to 236,000 years old, from the Rising Star Cave System in South Africa. Excavations at Rising Star have sparked debate about whether these little hominins had all ended up in the caves by tragic accident, or whether they’d been carefully placed there by other members of their enigmatic species, dubbed Homo naledi.
Now there’s a plot twist that may speak to how the remains got there: All of the hominins in Rising Star are female, at least according to the proteins in their dental enamel.
Max Planck Institute for Evolutionary Anthropology molecular scientist Palesa Madupe and her colleagues recently analyzed the proteins in dental enamel from 23 Homo naledi teeth unearthed in four different cave chambers deep in the Rising Star system. Those 23 teeth came from at least 20 different individuals, ranging from babies with their first tiny teeth to older adults with teeth worn down from decades of chewing.
All of the samples contained a protein called amelogenin-X, or AMELX, which is encoded in the DNA of the X-chromosome. But not a single sample contained the male version, AMELY, which is encoded on the Y-chromosome.
In genetically male humans, dental enamel usually contains about a tenth as much AMELY as AMELX, and Madupe and her colleagues say that given the level of AMELX in their samples, they should have been able to detect AMELY if it was there. But it seemingly wasn’t. It appears that every single skeleton in the cave system, meaning every known Homo naledi (except the ones for whom the anthropologists found only bones, not teeth), is genetically female.
The odds of that being a coincidence are about the same as the odds of flipping a coin 20 times and landing on the same side every time: 0.0000954 percent, according to Madupe and her colleagues. In other words, the metaphorical coin must be weighted—in this case, by hominins doing things on purpose, like laying their dead to rest in the narrow, twisting darkness of Rising Star.
“This was no longer chance, at this point,” Berger (also a co-author of the recent study) tells Ars Technica.
It’s technically possible that the code for AMELY just got deleted from the DNA; that happens sometimes in humans, and it has happened in at least one Neanderthal. But it’s extremely rare—so rare that it’s unlikely to explain what’s going on with Homo naledi. It’s much more likely that the dead hominins in Rising Star actually are all genetically female.
It’s not unusual to find mostly female groups of primates in nature: Chimpanzees and gorillas both live in groups where nearly all of the adults are female. Even so, the group inevitably includes children of both sexes. But even the babies in Rising Star are all female.
“It is rarely the case that we have such clear evidence of culture as this case is,” University of Wisconsin paleoanthropologist John Hawks, another co-author of the recent study, tells Ars Technica. “It’s like, there is no other process that can make this happen.”
It’s technically possible, perhaps, that Homo naledi divided up the work of hunting and gathering, or even some kind of ritual activity, in a way that meant females were the ones venturing deep into the cave and getting lost or trapped. But if they took the children with them, then we should see males among the tiny skeletons that make up half the sample. The most likely option now looks like Homo naledi buried its dead.
Berger and his colleagues have been arguing in favor of that point for years, but now there’s more: It also looks like Homo naledi, with its chimp-sized brain, even had a concept of gender as a part of an individual’s identity that mattered even in death.
The protein analysis also offers some hope of answering one of the many lingering questions about Homo naledi: how are they related to us and the other members of the hominin family tree? The bones themselves offer more questions than answers.
It turns out that five of the 20 Homo naledi in the study have a version of a particular protein in common with Paranthropus robustus, an even earlier hominin relative that lived between 2 million and 1 million years ago. And in 15 of the Homo naledi teeth, Madupe and her colleagues found another protein version that’s apparently unique to Homo naledi. That’s not quite enough to build a hominin family tree with, but it’s a tantalizing hint, and an indication that ancient proteins in teeth could reveal even more about extinct hominins.
University of Copenhagen paleoproteomics researcher Enrico Cappellini, also a co-author of the study, hopes the team will sequence proteins from other South African hominins, as well as species from Kenya, Tanzania, and Ethiopia in east Africa. That could reveal whether that protein variant is actually unique to Homo naledi; if so, it could be used to identify other fossils. And comparing the protein variants of Homo naledi to those in species like Homo erectus and Australopithecus africanus could help shed light on how all of these species are related.
“That’s the aspiration, to start to have molecular evidence that is rich enough to be informative for reconstruction of early hominin evolution in Africa and outside Africa,” Cappellini tells Ars Technica.
Getting that kind of evidence is going to require not just sampling more hominins from more species, but taking a risk on sampling that requires cutting deeper into fossil teeth. Dentin, the material inside teeth, contains more proteins than enamel, which means it might offer more answers—but at the cost of damaging rare and irreplaceable fossils.
“For now, we wanted to deliver these results and see the feedback from the scientific community,” says Cappellini. “Based on that, we will continue with further analysis.”
Some of that analysis may eventually include ancient DNA. Scientists have sequenced the genomes of our closest hominin relatives, Neanderthals and Denisovans, but the Homo naledi remains at Rising Star are older, and South Africa’s heat breaks down DNA faster and more thoroughly than where those other remains were found. A decade ago, Berger’s team tried sequencing Homo naledi DNA, but the material in the bones had broken down too much to get a sample. Since then, Hawks says, the team has unearthed other bones that might be better preserved, and sampling and sequencing technologies have also improved.
“We are assessing whether it’s now promising to do DNA sampling, and I am hopeful,” says Hawks. “I can’t yet predict what outcome we might get.”
Meanwhile, where are all the Homo naledi males? Hominins are a long, long way from reproducing by parthenogenesis, so they must be somewhere.
When Berger and his colleagues discovered the species—and up until they got the results of the protein analysis back in 2024—they assumed that male and female Homo naledi just happened to be very similar in size and build, since all the skeletons looked so much alike. Many ape species, like gorillas, have drastic size differences between the sexes, which scientists call sexual dimorphism. Homo naledi was, Berger thought, the least sexually dimorphic hominin anyone had ever seen.
So much for that idea! “Our study helps resolve the long-standing mystery of why Homo naledi lacked significant variation,” says Madupe in a recent press release about the study. “It’s probably because they could have all belonged to one sex.”
No one actually knows what a male Homo naledi looks like, and that opens up some interesting possibilities. There could, of course, be a chamber in Rising Star or at another nearby site where Homo naledi laid its menfolk to rest. But Hawks has another suspicion.
“I do think that there are other fossils from other sites that we have previously ruled out as naledi, in some cases, because they’re bigger than naledi,” he says. “If the males are much larger, differently developed, we don’t know that we don’t already have a male that we haven’t recognized as Homo naledi, because we’re looking for something that looks much more like our small female sample.”
The case for burial in the Rising Star system has been contentious for years. Part of the challenge is that it’s hard to know for sure when something counts as a grave, given the wide diversity in how our own species deals with its dead. Where is the line between laying the dead to rest and simply disposing of the body?
But part of the contention comes because the scientific community tends to set a very high bar for accepting evidence that other species (even other hominins) actually do the things that we’ve always thought make humans special. Hominins have been making stone tools for at least 3 million years, but anthropologists and animal behavior researchers still put tool-making in a different category of behavior than, say, painting a cave wall or imagining an afterlife. And for many anthropologists, earlier hominins with those capabilities—once considered uniquely human—are a hard sell.
There’s an ongoing debate about Neanderthal art and abstract thought despite a growing pile of evidence. And that sort of debate rises in intensity when the early hominins in question have brains as relatively small as Homo naledi’s, which is about the size of a chimpanzee’s.
“There is a divide in the field between those that think that humans evolved from cultural species that were before us, and those that believe that culture originated with modern humans,” says Hawks, “so they resist any claims of culture earlier unless they have some sort of extraordinary evidence.”
But the existence of culture in the hominins that preceded (and sometimes overlapped with) us isn’t really such an extraordinary claim anymore. That’s partly thanks to the evidence from other species like Neanderthals and partly thanks to other evidence at Rising Star that suggest that Homo naledi used fire, something that our species and Neanderthals were also doing by this point in prehistory. They even left behind engravings on the rock, which Berger, Hawks, and their colleagues described in a 2023 paper.
Those engravings in Rising Star stayed on Berger’s mind for months afterwards. “Those symbols weren’t meant for us. Whatever they’re meant for, it certainly wasn’t for a Homo sapiens,” he says. “They were meant either for them to come back to, their descendants to come back to, or some other purpose, but they weren’t meant for us.”
“This is our first contact with a—and I think it’s important to repeat this—a non-human species. Their brains are not human brains,” says Berger. And he’s deeply concerned about how humanity navigates that first contact.
Homo naledi’s protein results, with their grave implications (not sorry), prompted Berger and his team to pause their excavations in the cave system, although analysis in the lab continues. He hopes the protein study will prompt anthropologists and Homo sapiens in general to seriously think about the ethics of digging up the graves of an intelligent and cultured but non-human species.
“It certainly will mean we have to stop digging hominins like dinosaurs,” Berger says. “I think that we have the responsibility to be respectful, but we also have a responsibility to also be real. This is more like a Star Trek episode, you know? I know what we do if it’s a human culture, but it isn’t one.” The first step, he points out, is understanding more about Homo naledi and their culture, which will require more excavation and more lab work.
Cell, 2026. DOI: 10.1016/j.cell.2026.05.044 (About DOIs).
