Ancient proteins found no male marker in Homo naledi, deepening a cave burial mystery

Twenty individuals, 23 teeth, and not a trace of the protein that marks a male. That was the result when an international team dissolved microscopic layers of enamel from Homo naledi fossils and went looking for amelogenin-Y, the tooth protein encoded on the Y chromosome. The remains all came from a single South African chamber, and the silence is now a puzzle about how the dead got there.

Read next on Morning Overview: Zero Motorcycles unveiled an electric motorcycle targeted at under $8K and a street-legal dirt bike at EICMA

The work appeared in the journal Cell on June 24, 2026, and a University of York summary was recirculated by ScienceDaily on Nov. 11, putting the question back in front of readers. The finding does not settle the matter, and its own authors lay out two very different explanations.

Amelogenin-Y and 23 teeth from the Dinaledi Chamber

The paper, “Proteomic analysis of dental enamel from 20 Homo naledi individuals shows no male markers”, was led by Palesa Madupe, who did the work as a postdoctoral researcher at the University of Copenhagen. It lists 21 authors, among them Lee Berger, John Hawks and senior author Enrico Cappellini. The fossils come from the Dinaledi Chamber of the Rising Star Cave system, where Homo naledi was first described after discoveries beginning in 2013.

The team used a gentle acid etch to pull peptides, small protein fragments, from the tooth enamel, a method that limits damage to irreplaceable fossils. They examined 23 teeth belonging to at least 20 individuals. Specialists at York’s chemistry facility then analyzed the amino acids to confirm the proteins were ancient rather than modern contamination, according to the ScienceDaily write-up of the York release.

The reason to look in the first place is an older oddity. Adult fossils from the Dinaledi Chamber show little of the size and shape variation normally seen between males and females, and the York release says the study is the largest set of individuals from an extinct hominin species examined with ancient protein analysis.

An all-female chamber, or a missing gene

Marc Dickinson of York’s Department of Chemistry called the lack of male markers in the group “truly fascinating,” in the University of York news release. Madupe said the pattern may mean the individuals could all have belonged to one sex. If the chamber was in fact reserved for females, the release says, it could be the earliest known burial place restricted to one sex by a relative of humans other than Homo sapiens, pointing to symbolic funeral customs once thought unique to modern people.

The second explanation is biological. In a highly isolated population, the Y-linked amelogenin gene could have mutated or been deleted, leaving males present but invisible to this particular test. The authors state plainly that the cultural reading is not the only one.

Berger, the corresponding author, argued the odds favor culture. In an account of the study in Daily Maverick, he said the chance of sampling 20 individuals and finding all of them from one sex is quite literally one in a million. Hawks added that the team reads the pattern as some kind of cultural practice, while also conceding that the researchers do not know where the males are.

Cappellini’s argument is about the gene. Deleting the whole amelogenin-Y gene, he said, is very unlikely to have happened in even half of the 20 individuals studied, though he regards either outcome, no males or a systematic deletion, as intriguing. Rebecca Ackermann, another co-author, said more work is needed to establish whether every sampled individual is truly female.

Limits of enamel evidence on burial

A cave full of one sex does not prove anyone chose to put them there. Homo naledi lived roughly 335,000 to 241,000 years ago, a span in which few fossils and tools have been recovered, and Popular Science notes that conclusions about the species’ culture remain tentative. Teeth also cannot reveal who carried a body, or whether the chamber was used for one purpose over a long time.

Madupe stressed that enamel is the hardest tissue in the body and shields proteins from contamination for millions of years, which is why the method can reach so far back and why the absence of Y-linked protein reads as a real signal rather than decay. Berger went further, saying the field has grossly underestimated the cultural capacity of ancient human relatives, a view the team’s data support only if the cultural reading holds.

The burial angle itself is the team’s inference, not a measurement. Researchers recovered no direct evidence of why the bodies are in the Dinaledi Chamber from the proteins, only a pattern in who is represented, and the York release frames the all-female site as something that could be true if the biology holds up. That conditional wording matters, because the same data would look identical under a lost gene.

The open question is a testable one. If more teeth or other tissues from the same chamber turn up male-specific peptides, the all-female idea collapses; if they do not, the choice between a sex-restricted burial ground and a vanished gene becomes harder to avoid.

This article was produced with the assistance of AI and reviewed by Morning Overview editors prior to publication.