Groundbreaking study reveals biological sex and genetic diversity in Paranthropus robustus

Researchers from the University of Cape Town (UCT) and the University of Copenhagen have achieved a scientific first by using 2-million-year-old protein traces to determine the biological sex and uncover previously hidden genetic variation in Paranthropus robustus, an extinct close relative of modern humans.

Published in the journal Science, the research analysed ancient proteins extracted from fossilised teeth discovered in South Africa's Cradle of Humankind.

The remarkable discovery represents some of the oldest human genetic data ever recovered from Africa and challenges established understandings of this early hominin.

The study’s co-lead, Dr Palesa Madupe, a research associate at UCT’s Human Evolution Research Institute (HERI) and postdoctoral fellow at the University of Copenhagen’s Globe Institute, is part of a powerful  African cohort transforming palaeoanthropology from within. 

"Because we can sample multiple African Pleistocene hominin individuals classified within the  same group, we’re now able to observe not just biological sex, but for the first time genetic  differences that might have existed among them," said Madupe. 

UCT’s HERI played a central role in the research, with co-director Professor Rebecca  Ackermann as a senior author, and contributions from co-director Robyn Pickering and multiple HERI research associates. 

The team used cutting-edge palaeoproteomic techniques and mass spectrometry to identify sex-specific variants of amelogenin, a protein found in tooth enamel.

Two of the ancient individuals were conclusively male; the others, inferred through novel quantitative methods, were female. 

Paper co-lead and postdoctoral researcher at the Center for Protein Research, University of Copenhagen, Claire Koenig, explained: “Enamel is extremely valuable because it provides information about both biological sex and evolutionary relationships. However, since identifying females relies on the absence of specific protein variants, it is crucial to rigorously control our methods to ensure confident results.” 

The university explained that unexpectedly, another enamel protein – enamelin, revealed genetic diversity among the four individuals.

Two shared a particular variant, a third had a distinct one, and a fourth displayed both. 

Co-lead and postdoctoral research fellow at the University of Copenhagen’s Globe Institute  Ioannis Patramanis said while studying proteins, specific mutations are thought to be  characteristic of a species.

“We were thus quite surprised to discover that what we initially thought was a mutation uniquely describing Paranthropus robustus was actually variable within that group,” said Patramanis.

The university added that this revelation forces a rethink of how ancient hominin species are identified, showing genetic variation, not just skeletal traits, must be considered in understanding their  complexity. 

According to the researchers, Paranthropus lived in Africa between 2.8 and 1.2 million years ago, walking upright and likely coexisting with early members of Homo.

Though on a different evolutionary path, its story remains central to understanding human origins. 

Madupe added that this study not only advances palaeoproteomics in Africa, but also highlights the vital role of  African scholars in rewriting human history. 

“As a young African researcher, I’m honoured to have significantly contributed to such a high-impact publication as its co-lead. But it’s not lost on me that people of colour have a long journey to go before it becomes commonplace more of us need to be leading  research like this,” said Madupe.

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Ackermann detailed that HERI was actively leading that shift and the institute launched programmes introducing palaeoproteomic techniques to a new generation of African scientists and is expanding training across the continent. 

“We are excited about the capacity building that has come out of this collaboration. The  future of African-led palaeoanthropology research is bright,” Ackerman said. 

Cape Argus