Protein analysis of tooth enamel from Homo naledi fossils found in South Africa’s Rising Star cave suggests that 20 out of 20 individuals with usable data were female—an unusually consistent pattern that strengthens arguments that the species may have intentio
In the Rising Star cave system, the dead may have been treated differently than anyone expected. When Homo naledi fossils were discovered there 13 years ago. about 40 kilometres north-west of Johannesburg. researchers were left with a mystery: how did bodies end up in deep. difficult-to-access chambers?.
Now, a new analysis of proteins extracted from the fossils’ tooth enamel is pointing toward an even stranger twist. A team led by Palesa Madupe at the University of Copenhagen. Denmark. reports that all 20 Homo naledi individuals—out of 23 known individuals—that yielded recoverable amelogenin proteins show no trace of the male-linked signal typically found in enamel. The result suggests the individuals represented in the cave assemblage were all female.
The Rising Star story began in 2013. when a couple of cavers stumbled upon the Homo naledi remains while exploring the Rising Star cave system. The fossils were found in a series of deep and difficult-to-access cave chambers. Since then. researchers have been trying to solve the puzzle of how the bodies got there and what. if anything. Homo naledi may have done with them after death.
A prominent but controversial idea. first suggested in 2015. proposes that Homo naledi deliberately dragged its dead through the cave system and deposited them in the chambers. Over the following years. researchers working at the site—led by Lee Berger at the University of the Witwatersrand. South Africa—expanded that hypothesis. They argue that archaeological evidence inside the cave suggests Homo naledi dug graves in the dirt floor of the rock chambers. used flaming torches to light its way through the dark caves. and left rock art on the chamber cave walls. Those claims have met with extreme scepticism.
Madupe’s protein work adds a different kind of evidence to the debate. Proteins are built using information stored in DNA, so examining ancient proteins can offer a window into genetics. Homo naledi is thought to have existed between about 335,000 and 236,000 years ago. In this study. Madupe and colleagues extracted ancient proteins from Homo naledi tooth enamel and used those proteins to infer sex.
Tooth enamel contains just a dozen or so distinct protein types. Madupe says. which means it reveals relatively little about evolutionary history. But it can still reveal the sex of an ancient individual. Amelogenin proteins in enamel may carry a signal from the AMELX gene on the X chromosome or the AMELY gene on the Y chromosome. Female individuals carry only an AMELX signal in their tooth enamel. while male individuals typically carry both AMELX and AMELY signals.
Madupe and her colleagues analysed proteins from all 23 known Homo naledi individuals. For 20 of them, it was possible to recover amelogenin proteins. None of those 20 individuals carried any AMELY, suggesting all 20 individuals were female—an exceptionally unusual result.
Madupe describes the reaction in plain terms. “Honestly, it was very scary. I thought we were doing something wrong,” she says. Even after repeating the analysis, the outcome was the same. “Then we are like: OK, what is the story? Why is it that we’re not getting male individuals here?”
When a result is that one-sided. the next question is how it might be an artefact of preservation or chemistry rather than biology. One possibility is that the AMELY protein degrades more rapidly than AMELX. and so could have been present in some Homo naledi individuals but no longer detectable. Madupe thinks that explanation can be discounted. Last year. she and her colleagues published an analysis of enamel protein from 2-million-year-old hominin teeth also found in South Africa. and some of those contained AMELY.
Another possibility is that the Homo naledi population experienced a deletion of the AMELY gene. meaning male individuals wouldn’t necessarily express AMELY in their enamel. The team reviewed the literature and found that such deletions do occur in modern human populations. but they are exceptionally rare. Even when there is an AMELY deletion. it affects no more than 10 per cent of men and boys in the population.
Using that rate. the researchers calculated the odds that a random sample of 20 individuals—10 male and 10 female—would recover no AMELY. They say there is just a 0.0000954 per cent chance of that happening. With that possibility pushed to the margins. the study’s conclusion narrows sharply: the 20 ancient humans. it suggests. really are all female.
For Lee Berger, a collaborator on the study, the implication is uncomfortable for the “natural process” explanation. He argues it is no longer tenable to say the fossils ended up in the cave through a natural process. Instead, he thinks the result shows Homo naledi deliberately deposited dead female bodies in the cave.
Several other researchers are inclined to agree. “The explanations would likely be either that there are problems with this analytical approach or that there is some intentional selection here by other naledi individuals. ” says Emma Pomeroy at the University of Cambridge. Bernard Wood at the George Washington University in Washington DC offers a similar picture. but with emphasis on behaviour: “My guess is that there is a behavioural aspect to this. and for some reason they were putting the female cadavers into this cave and they weren’t putting any males in there.”.
Others remain cautious. and their counterarguments are rooted in the same stubborn problem that has followed the Rising Star fossils from the start: access. Kimberly Foecke at George Mason University in Virginia points out that the cave chambers may have been as difficult to access in the past as they are now. If so. it might have been more difficult for larger-bodied male Homo naledi to explore the caves. which could. in theory. explain a female bias in what was recovered.
Michael Petraglia at Griffith University in Brisbane, Australia, offers a different alternative explanation linked to ecology and group structure. “It is entirely possible that H. naledi. being a small-brained hominin and similar to non-human primates. had groups with high female-to-male sex ratios foraging in particular places on the landscape. ” he says. If the cave fossils came from such a group, it would naturally produce a large female proportion.
The complication for that idea is what the juvenile fossils appear to show. Other researchers make a similar point, although Eric Crubézy at the University of Toulouse, France, raises a specific concern. Even in primate social groups that contain many adult females and only one or two males. Crubézy says. infants include equal numbers of males and females. But the 10 or so juvenile Homo naledi individuals in the cave all appear to be female too. “If confirmed. a strongly female-biased assemblage spanning several age classes would be difficult to explain as a normal demographic slice of a living community. ” he says.
Berger argues the protein results fit his view that Homo naledi intentionally buried its dead. Other researchers insist that the evidence does not necessarily translate into elaborate burial practices. “To dump bodies through a crevice in a rock is not the same as burying them,” Wood says. And in his view. it doesn’t necessarily imply Homo naledi had any elaborate culture of the dead or developed a belief system. “I have no idea what this behaviour meant, and nor does Lee Berger.”.
As ever, the Rising Star fossils force scientists into hard choices between competing stories. “As ever, H. naledi surprises us and raises fascinating questions that are not easy to resolve,” Pomeroy says.
One of those questions is immediate and visceral: what did male Homo naledi look like?. Wood wonders whether males were similar in appearance to females, but he also suggests they may have been distinct. In some hominin species—particularly Paranthropus boisei—male individuals had larger skulls with a prominent bony crest. Wood says, “My guess is that these creatures didn’t have a sagittal crest, but I have no idea.”.
For now, the cave chambers remain silent on that point. But the protein evidence is loud in one direction: if these fossils truly represent 20 female individuals. then whatever happened in Rising Star wasn’t just accidental. It was selective enough to leave a genetic signature that still doesn’t add up to “nothing special”—even for researchers who want to be cautious.
Homo naledi Rising Star cave ancient proteins tooth enamel amelogenin AMELX AMELY sex determination paleoanthropology burial behavior Lee Berger Palesa Madupe