All 20 Homo naledi skeletons found in South African cave are female, puzzling scientists

Deep in South Africa's Rising Star cave system lies a collection of bones that has been rewriting what we thought we knew about human ancestry since their discovery in 2013. Homo naledi—a small-brained relative of ours, with a brain closer in size to a gorilla's than to ours—has already forced scientists to reconsider whether such a creature could use fire, navigate treacherous underground passages, or even bury its dead. Now a new analysis has added something stranger still: every single skeleton recovered from that cave appears to be female.

The discovery came through an unexpected route. Researchers led by Palesa Madupe at the Max Planck Institute for Evolutionary Anthropology turned to proteins rather than DNA, a choice born of necessity. Ancient DNA rarely survives in warm African environments, but proteins embedded in tooth enamel can persist for millions of years and still carry the genetic information scientists need. Madupe's team focused on amelogenin genes, which code for proteins in dental enamel and vary between the sexes. All humans carry a gene variant called AMELX. Males carry a second variant, AMELY, found only on the Y chromosome. When the researchers examined twenty teeth from multiple H. naledi skeletons, they found AMELX proteins in every specimen. AMELY appeared in none of them. Across two dozen separate teeth from different individuals, not a single male marker showed up. The odds of that happening by chance in a genuinely mixed-sex population are vanishingly small.

The finding upends more than a decade of foundational work. When Lee Berger and his team first formally described H. naledi in 2015, they classified individuals based on skeletal size—the standard method in paleoanthropology, since males in many hominin species tend to be larger than females. The most complete skeleton, called DH1 and discovered in the Dinaledi Chamber, was designated male and became the primary reference specimen for the entire species. Another nearly complete skeleton, Neo, was also assumed male. If the protein analysis holds, both assumptions were wrong. Every skeleton, including these two, would be female. This does not erase earlier descriptions of the species, but it does mean that everything scientists currently understand about H. naledi's body proportions, brain size, and skeletal variation comes entirely from female anatomy. What a male H. naledi looked like remains completely unknown.

The finding gains additional weight from earlier hints. A 2024 study had already noted something unusual: the variation in H. naledi teeth was remarkably low, so low that researchers could not rule out the possibility that only one sex was represented in the sample. Madupe's work now provides a direct biological explanation for that pattern. The low variation may simply reflect the fact that the collection genuinely contains only females.

The implications extend to one of the most contested claims about H. naledi: whether these individuals were deliberately buried by members of their own species. Berger and colleagues have argued for intentional burial or body disposal, a behavior that would be extraordinary for a hominin with such a small brain. The all-female finding adds a new layer to that debate. John Hawks, a paleoanthropologist at the University of Wisconsin-Madison and co-author on the study, noted that many human societies throughout history have practiced sex-specific burial, placing men and women in separate locations or according to different rituals. If H. naledi did something similar, the Rising Star cave might represent a site reserved for females, while males could have been deposited elsewhere and simply not yet discovered. Berger himself suggested that "cultural selection after death for burial by sex and perhaps gender" is the most likely explanation, though he acknowledged the idea remains speculative.

Not all scientists are ready to accept the conclusion that no males were present. Elizabeth Sawchuk, curator of human evolution at the Cleveland Museum of Natural History, raised an important caveat: the absence of AMELY protein does not definitively prove the absence of males. A rare genetic condition exists in which the AMELY gene is simply deleted from an individual's genome, meaning even biological males would show no AMELY proteins in their tooth enamel. This condition has been documented in at least one Neanderthal male. Enrico Cappellini, a palaeoproteomics professor at the University of Copenhagen and co-author on the paper, acknowledged this possibility directly but argued it would be statistically extraordinary for such a deletion to appear in half or more of a twenty-individual sample, or to be a population-wide trait. Either scenario—whether males were genuinely absent or the entire species lacked the AMELY gene variant—would carry significant implications for understanding H. naledi biology.

The Cell paper revealed a second unexpected finding alongside the sex determination. Proteomic analysis showed that H. naledi shares a gene variant related to collagen production with Paranthropus robustus, a heavily built South African hominin that lived one to two million years ago and is not a direct ancestor of modern humans. This collagen variant differs from what appears in modern humans, Neanderthals, and Denisovans, suggesting it may represent an older trait retained in certain South African hominins. Whether this shared variant reflects a direct ancestral relationship, parallel evolution, or something else cannot yet be determined. Berger emphasized that building a larger protein database from other African hominins will be essential to understanding where H. naledi fits within the broader story of human evolution on the continent. The ability to determine biological sex from dental enamel proteins rather than relying on skeletal size opens a new avenue for revisiting sex classifications across fossil collections worldwide. As Sawchuk observed, the H. naledi findings continue to raise more questions than they answer—but each new question moves science closer to understanding one of the most unusual and poorly understood species in the human family tree.