‘A weird result from an already weird hominin’: Archaeologists discover all Homo naledi skeletons found in South African cave are female

For the first time, archaeologists have analyzed the genetic material of Homo naledi, a mysterious 300,000-year-old relative of modern humans discovered deep in a South African cave system. What they found is unique in human evolution studies: Every skeleton known from the species is female.

“I think it is fair to say that they surprised us,” Lee Berger, a National Geographic explorer-in-residence, told Live Science in an email, but H. naledi “has always been an enigmatic discovery.”

Since 2013, Berger has headed the Rising Star project, which discovered nearly two dozen skeletons of small-brained, two-legged creatures, which the research team named H. naledi, within a cave system in South Africa’s Cradle of Humankind.

Research over the past decade has revealed that H. naledi was unusual for having a small brain and upper body, similar to earlier australopithecines like Lucy, but a face, hands and lower limbs that were more human-like. In 2023, the Rising Star team suggested H. naledi may have used fire in the cave, and in 2025, they advanced the controversial claim that H. naledi buried their dead — a complex behavior unexpected for a human relative with such a small brain.

But a new study of H. naledi teeth published Wednesday (June 24) in the journal Cell may bolster the team’s interpretation of the Rising Star cave as a burial site.

An international team of experts studied 20 teeth from H. naledi skeletons using proteomic analysis, a minimally destructive technique that sequences genetic material from ancient proteins. Proteomics is a burgeoning field, especially because these proteins can last longer than DNA. The team focused on amelogenin genes (AMEL), which code for proteins in dental enamel and vary by sex. While the gene variant called AMELX is found in both males and females, another one, AMELY, is found only in biological males.

In analyzing the H. naledi teeth, the team found no AMELY genes but plenty of AMELX ones, suggesting that all of the skeletons were from females. These included the nearly complete skeleton of Neo and DH1, the main representative of the species, both originally assumed to be male.

The result is surprising because there are no known ancient human cemeteries or collections of nonhuman primate skeletons that contain only females.

“The most likely reason for these robust results are, in my opinion, cultural selection after death for burial by sex and perhaps gender,” Berger said. “There are many past human societies with sex-specific burial practices,” study co-author John Hawks, a paleoanthropologist at the University of Wisconsin-Madison, said in a statement, but the H. naledi skeletons “are older than any known Neanderthal or modern human burial site, and it’s remarkable to see that they may all be female.”

“An already weird hominin”

The discovery that everything we know about H. naledi comes from female skeletons has surprised paleoanthropologists.

“The bottom line is this is a weird result from an already weird hominin,” Elizabeth Sawchuk, curator of human evolution at the Cleveland Museum of Natural History, who was not involved in the study, told Live Science in an email. “The key thing to remember is that failure to detect evidence of AMELY does not mean there are no males in the sample — it just means that none were detected.”

One possible reason for the lack of this gene in H. naledi skeletons is an AMELY gene deletion that is known to occur very rarely in some modern-human populations and that has been found in one Neanderthal male. If the AMELY gene doesn’t exist in this H. naledi group, then the protein profiles of males would look identical to the profiles of females.

However, “it’s very unlikely that this would be the case among even half of the 20 individuals we studied or for an entire population,” study co-author Enrico Cappellini, a paleoproteomics professor at the University of Copenhagen in Denmark, said in the statement. “Either scenario, namely the absence of H. naledi males in the Rising Star cave system or a systematic deletion of their AMELY gene, is fascinating and would have deep implications for a better understanding of the biology and evolution of this species.”

Studies of H. naledi, a species known from a single site, “continue to yield more questions than answers,” Sawchuk said. “As the authors point out, this is a surprising result that requires more investigation.”

Other hominins in South Africa

A second surprising result in the proteomic analysis was that H. naledi shares a gene variant with Paranthropus robustus, a human relative with a massive face and teeth that lived in South Africa around 1 million to 2 million years ago.

Proteomic analysis of four P. robustus skeletons in 2025 proved that limited genetic material could be recovered from ancient human relatives in Africa. The new study has revealed that some members of this species and H. naledi shared a gene variant related to collagen production, which is different from the genes found in modern humans, Neanderthals and Denisovans.

While H. naledi and P. robustus inhabited the same general geographic area, it is unclear if they lived there at the same time and overlapped or if they may have had an ancestor-descendant relationship.

“It is early days for sampling fossil hominins with ancient proteins, and until we build a better, bigger sample, we just don’t know” what the shared genetic variant means, Berger said.

Building a larger database of ancient proteins from other human relatives that evolved in Africa, such as Australopithecus africanus and Homo erectus, may clarify where H. naledi fits into the picture of human evolution.

“Key data are missing from H. erectus and A. africanus that would help put this evidence into context,” Sawchuk said. “For now, this is another curious finding that bears further investigation.”

What does sex change?

In 2015, Berger and colleagues named the new hominin H. naledi and described what they presumed to be male and female variants of the species based on the skeletons’ sizes. In many groups of human relatives and in modern humans, males are physically larger than females, on average. This assumption led the researchers to classify the presumed male individual DH1, discovered in the Dinaledi chamber of the cave, as the main representative of the new species.

But a 2024 study was the first to question the assumption that the H. naledi skeletons came from two sexes. In that study, researchers found variation in the teeth of H. naledi that was “so low that the possibility that one sex is represented by few or no individuals in the sample cannot be excluded,” they wrote.

“Our study helps resolve the long-standing mystery of why Homo naledi lacked significant variation,” study first author Palesa Madupe, a researcher at the Max Planck Institute for Evolutionary Anthropology in Germany, said in the statement. “It’s probably because they could have all belonged to one sex.”

If the proteomic sex analysis is correct and H. naledi does not have AMELY deletion issues, it means everything we know about the species comes from females. But this doesn’t mean interpretations of the species are wrong.

“The only thing that has changed is that we have never seen a male!” Berger said. “When and if we do, we will have to extend the description to include male sex characters and the likely extension of certain aspects of variation.”

The researchers hope their study paves the way for more proteomic analyses of human relatives in the future.

The new analysis proves that protein analysis of fossils from the Pleistocene (2.58 million years ago to 11,700 years ago) can be done in a minimally destructive way, Madupe said. “This means potentially opening the door to a whole new way of sustainably investigating the differences between sexes in groups of extinct hominins and other animals without causing visible damage to these priceless fossils.”

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