The largest ancient-protein study of any extinct hominin found no trace of a Y-chromosome protein, and scientists are split on what that means

None of the 20 Homo naledi individuals sampled from South Africa's Rising Star cave system carried a protein marker linked to the male Y chromosome. The finding comes from the largest analysis of ancient proteins ever done for an extinct human relative, published in Cell. It leaves two very different explanations on the table: a burial site used only for females, or a population in which the male marker had simply disappeared.

The study first appeared in June. It is back in the news this week after the University of York, one of the partner institutions, publicized it again, as reported by ScienceDaily. Since publication, independent commentary has leaned more cautiously than the early headlines — and that debate is now the real story.

The stakes go beyond one cave. If H. naledi sorted its dead by sex, that would be the earliest known example of such a practice in any species other than our own. If a gene was lost instead, the result says more about the biology of a small, isolated population than about burial customs.

Reading Sex From Enamel Without Destroying the Fossils

Homo naledi lived roughly 335,000 to 241,000 years ago and has puzzled researchers since its remains were found in 2013 deep inside the Rising Star cave system, in the Cradle of Humankind near Johannesburg. Adult fossils from the Dinaledi Chamber look unusually alike in size and shape, which has made it hard to tell males from females.

DNA does not survive well at that age in South Africa's climate, so the team turned to proteins locked inside tooth enamel. Using a minimally destructive acid-etching method, researchers removed tiny amounts of enamel from 23 teeth representing at least 20 individuals and analyzed the recovered protein fragments, called peptides, with mass spectrometry.

The key protein is amelogenin. Females carry only the X-linked version, while males also produce a Y-linked form called amelogenin-Y. Finding that Y-linked peptide marks a tooth as male. A University of York chemistry lab confirmed the proteins were ancient rather than modern contamination by measuring how much their amino acids had broken down.

Lead author Palesa Madupe, who did the work as a postdoctoral researcher at the University of Copenhagen, said enamel makes these proteins "ideal carriers of genetic information from deep time."

A Female-Only Chamber or a Vanished Y-Linked Gene

No amelogenin-Y turned up in any sample. The sample included adults, children and an infant, according to coauthor John Hawks, and the team's statistics placed 19 individuals as female with high confidence and the remaining one as consistent with female.

Corresponding author Lee Berger of the National Geographic Society favors a cultural reading. He said the most likely explanation is "a sex-bias in mortuary practice," according to the project's announcement. The team argues that H. naledi deliberately placed its dead in the cave, a claim that remains disputed among paleoanthropologists.

The second explanation is genetic. In a small, isolated population, the gene for amelogenin-Y could have mutated or been deleted, so males would test as female. Deletions of this gene are known in some present-day men, according to the Max Planck Society, which took part in the work.

An independent research highlight in Nature Ecology & Evolution gave that second option real weight. Writer Devin Ward noted that the authors ruled out many technical explanations and concluded it is more likely the individuals "simply do not carry the male-specific amelogenin Y peptide," according to Nature Ecology & Evolution. In other words, the absence of a marker is not the same as proof that every individual was female.

Where the Evidence Is Strong and Where It Stops

The evidence is strong on one point: the male marker was not detected, and contamination and poor preservation were checked. It is much weaker on why. The study is a laboratory proteomics analysis of 23 teeth from a single cave system, published in a peer-reviewed journal. It found an absence, not a cause, and both leading explanations fit the data.

Sample size also matters. Twenty individuals is large for ancient proteins, but small for concluding how an entire species treated its dead. The fossils may also represent burials spread over a long period, which complicates any reading of a single cultural rule.

University of York chemist Marc Dickinson called the absence of male markers fascinating, and the team says the next step is new protein tools that can tell a missing gene from a missing sex. Finding even one male marker in another H. naledi tooth would change the picture quickly.

A New Tool for Fossils Where DNA Has Vanished

For most readers, the practical lesson is about how science handles a striking result. The finding is real, but its meaning is unsettled, and responsible coverage should keep both explanations in view rather than declaring an all-female burial ground as fact.

The method is the lasting win — reading biological sex from a speck of enamel, without grinding up a rare fossil, gives researchers a tool for other sites where DNA has long since vanished. That could help answer old questions about who was buried where across early human history.

Further enamel studies, including teeth from other Rising Star chambers, are the next development to watch. Until then, the safest summary is that Homo naledi's known remains carry no male protein marker, and nobody yet knows why.

What Readers Want to Know

What did the study find? Enamel proteins from at least 20 Homo naledi individuals showed no amelogenin-Y, the protein linked to the male Y chromosome.

Does this prove they were all female? No. A female-only burial is one explanation. The other is that the male-linked gene had mutated or been lost in this population.

How old are the fossils? Homo naledi lived roughly 335,000 to 241,000 years ago.

How were the proteins collected? Researchers used gentle acid etching to remove tiny amounts of enamel, then identified peptides with mass spectrometry.

Why does this matter? If confirmed, sex-based burial would be the earliest known outside Homo sapiens. Either way, the method lets scientists sex fossils without DNA.

What happens next? Researchers want more enamel samples and new protein tools that can separate a missing gene from a missing sex.