"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."
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.
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.
The result is surprising because there are no known ancient human cemeteries or collections of nonhuman primate skeletons that contain only females.
A partial jawbone with teeth from Homo naledi lies was found in the Rising Star cave system. (Image credit: Mathew Berger / Rising Star Program)
The discovery that everything we know about H. naledi comes from female skeletons has surprised paleoanthropologists.
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.
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
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.
"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.
"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."
Study lead author Palesa Madupe has pioneered techniques to extract proteins from fossils. (Image credit: Alberto Taurozzi / Rising Star Program)What does sex change?
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.
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.
RELATED STORIES"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 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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