A team of researchers examined 23 teeth from at least 20 individuals from South Africa‘s Rising Star Cave system and found no evidence of the male-specific Amelogenin-Y protein.
A recent study, published in Cell, marks the first ancient protein analysis of Homo naledi and raises the possibility that the Dinaledi Chamber may contain predominantly, or possibly exclusively, female individuals. If confirmed, Homo naledi would become the first known non-human species to practice sex-specific burial.
A Decade-Old Puzzle
Since its discovery in 2013, Homo naledi has puzzled paleoanthropologists. This extinct human relative lived between 335,000 and 241,000 years ago and combined ape-like anatomy with distinct human features. So far, Homo naledi remains have only been found in the Rising Star Cave system in South Africa.
For over a decade, scientists noted that the adult fossils from the Dinaledi Chamber were nearly identical, lacking the skeletal variation usually seen between males and females. The reason for this similarity remained unclear.
Proteins Where DNA Fails
To investigate further, a team from the University of York, the University of Copenhagen, and additional institutions analyzed the remains at the molecular level. They used a minimally destructive acid-etching method to extract protein fragments, or peptides, from the enamel of the 23 teeth.
“Unlike those found in other remains like bone fragments, proteins in tooth enamel are preserved because dental enamel—the hardest tissue in the human body—shields proteins from environmental contamination even for millions of years. This makes them ideal carriers of genetic information from deep time. Our study helps explain the long-standing mystery of why Homo naledi lacked significant variation; it’s probably because they could have all belonged to one sex,” said Palesa Madupe, who conducted the research during her postdoctoral fellowship at the University of Copenhagen.
A Missing Male Marker
The researchers specifically searched for Amelogenin-Y, a protein produced only by the male Y chromosome, but detected none of it in the sampled teeth. To make sure the results were not due to modern contamination, a specialized chemistry team at the University of York independently confirmed that the amino acids were genuinely ancient. The findings remained consistent.
“The lack of male markers within the group is truly fascinating. It is incredibly exciting to gain a window not only into the biology of our ancestors, but also into how they lived. These findings offer rare insights into a culture that has, until now, been difficult to access directly. Advances in ancient protein analysis are opening the door to a far richer and more nuanced understanding of ancient hominins,” said Dr. Marc Dickinson from the university’s Department of Chemistry.
Ritual or Genetic Fluke?
The findings allow for two possible explanations. One is cultural: if the chamber were reserved for females, it could indicate that Homo naledi practiced sex-specific, symbolic mortuary behavior, a trait previously thought to be unique to modern humans.
The second explanation is biological. The researchers note that a small, isolated Homo naledi population could have lost or mutated the Amelogenin-Y gene, leaving males without the protein marker typically used to identify male remains.
Either explanation could reshape what scientists know about Homo naledi. If researchers confirm the site as an all-female burial chamber, it would suggest that symbolic behavior emerged earlier in the human lineage than previously believed. On the other hand, a genetic change across the population would show how isolation can shape a species’ biology in ways that fossils alone cannot reveal. This study shows how ancient protein analysis from teeth can open new windows into human evolution.
Austin Burgess is a writer and researcher with a background in sales, marketing, and data analytics. He holds an MBA, a Bachelor of Science in Business Administration, and a data analytics certification. His work focuses on breaking scientific developments, with an emphasis on emerging biology, cognitive neuroscience, and archaeological discoveries.