Ancient genetic data reveals biological sex and genetic variability of Paranthropus robustus
A team of researchers, spearheaded by the University of Copenhagen and the University of Cape Town (UCT), have revealed the biological sex of four ancient pre-human relatives after successfully retrieving ~2-million-year-old protein remains from teeth belonging to Paranthropus robustus.
The work, published in the journal Science, marks a significant breakthrough in human evolution studies by providing some of the oldest human genetic data from Africa and reveals previously undetected genetic variability.
“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,” says the study’s co-lead Palesa Madupe.
Madupe is a postdoctoral research fellow at the Globe Institute at the University of Copenhagen, and research associate at the Human Evolution Research Institute (HERI) at UCT. HERI Co-director Professor Rebecca Ackermann was a senior author on the study, with contributions from Co-director Robyn Pickering and several HERI research associates.
The researchers used a technique called palaeoproteomics to retrieve ancient protein sequences from the teeth of four P. robustus fossils recovered from the cave site Swartkrans, in the Cradle of Humankind, South Africa. Using state-of-the-art mass spectrometry techniques, they were able to partially reconstruct the ancient enamel protein sequences from the teeth.
Detecting specific variants of one protein called amelogenin, the team identified a male-specific variant assigning two of the Paranthropus specimens as male individuals. A novel quantitative approach allowed the researchers to infer that the other two specimens were female.
Study co-leads Dr Palesa Madupe, Dr Claire Koenig and Dr Ioannis Patramanis with a replica of Paranthropus robustus.
Photo credit: Victor Yan Kin Lee
“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.” says Claire Koenig, paper co-lead and a Postdoctoral Researcher at the Center for Protein Research, University of Copenhagen.
A single genetic variant in another protein, enamelin, was also identified that differentiated the four Paranthropus specimens among themselves. Two specimens carried one version of the protein, a third carried another, and a fourth specimen appeared to be carrying both.
“When studying proteins, specific mutations are thought to be characteristic of a species and, as such, used to identify it. 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; some individuals had it while others did not,” says paper co-lead Ioannis Patramanis, a Postdoctoral Research Fellow at the Globe Institute, University of Copenhagen.
The findings not only challenge long-held assumptions around P. robustus based solely on skeletal morphology, or the study of form and structure of the skeletal system. It also opens new avenues for understanding the complex evolutionary history of our ancient relatives.
“With this data, we shed light on how evolution worked in the deep-past and how recovering these mutations might help us understand genetic differences we see today,” says Madupe.
Paranthropus is an extinct hominin genus that emerged and evolved in Africa between 2.8 and 1.2 Ma. Considered to be a side branch of our evolutionary tree, Paranthropus walked on two legs and coexisted with early species of Homo in Africa, possibly interacting.
This breakthrough research represents a shift toward more robust palaeoproteomic studies, where existing African hominin fossils that were previously considered beyond the reach of genetic analysis may be able to yield critical biomolecular data. It also demonstrates the potential for that work to be driven by African researchers.
“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,” Madupe says.
The Human Evolution Research Institute (HERI) at UCT, where Madupe is a member, actively encourages that shift. It led a programme introducing palaeoproteomic applications to a pan-African group of young researchers. Other projects are also in progress to support skills development for researchers interested in integrating the approach into their work.
“We are excited about the capacity building that has come out of this collaboration. The future of African-led palaeoanthropology research is bright,” says Ackermann.