First-ever protein analysis of Homo naledi fossils finds zero male markers

HERI’s Dr Palesa Madupe with study co-authors dressed in full body clean lab suits. Photo credit: Enrico Cappellini

An international team of researchers, led by HERI Research Associate Dr Palesa Madupe, has successfully extracted and analysed the first-ever protein fragments from fossil teeth of Homo naledi, an extinct human relative found in the Cradle of Humankind World Heritage Site in South Africa. 

“Our results demonstrate that protein analysis of Pleistocene hominins is not just possible, in some cases, it can be done in a minimally destructive way,” says Madupe, who published findings in the journal Cellwith colleagues from the University of Copenhagen, the National Geographic Society’s Rising Star project and 13 collaborating global institutions. 

“This means potentially opening the door to a whole new way of sustainably investigating the differences between sexes in groups of extinct hominins and other animals without causing visible damage to these priceless fossils,” she says.

Protein analysis of Pleistocene hominins 

In the study, researchers analysed 23 teeth representing at least 20 Homo naledi individuals - the largest extinct hominin sample to ever be examined using ancient protein analysis. To determine the biological sex of each individual, researchers looked for Amelogenin-Y, a protein that is uniquely coded onto the male Y chromosome, within the tooth enamel. 

Thorough examination of ancient proteins from the enamel of 23 Homo naledi teeth revealed a complete absence of the marker, indicating a strong likelihood that each of these individuals discovered in the Rising Star Cave system was biologically female. 

Among hominins, like most other mammals, females typically exhibit two X chromosomes and males carry an X and a Y chromosome. Because only males have a Y chromosome, finding amelogenin-Y tells researchers with certainty that the tooth belonged to a male. 

“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,” said Madupe.

Madupe is a South African-born molecular scientist. She was a PhD student at the University of Copenhagen, co-supervised by HERI Co-director Prof Rebecca Ackermann, at the time of the study. She is currently a postdoctoral researcher at Max Planck Institute for Evolutionary Anthropology in Germany.

“Dr Madupe is herself a ‘rising star’ and a great example of how South African talent can thrive given opportunities and resources,” says Ackermann.

Featured photo credit: Alberto Taurozzi