Protein evidence reveals hidden variation in P. robustus. The species may be more complex than once believed.
For close to a hundred years, researchers have examined puzzling fossils belonging to a distant and unusually robust relative of early humans, known as Paranthropus robustus. This upright-walking species was adapted for powerful chewing, equipped with large jaws and oversized teeth covered in thick enamel. Evidence suggests it lived between approximately 2.25 million and 1.7 million years ago.
Today, the human lineage includes a wide range of ancient relatives and ancestors that lived millions of years in the past. Fossil evidence from South Africa spans early hominins such as Australopithecus prometheus, A. africanus (including the Taung child), A. sediba, and P. robustus, as well as early members of the genus Homo (H. erectus/ergaster, H. habilis), and later hominins like H. naledi and modern Homo sapiens.
Unanswered questions about Paranthropus robustus
Fossil evidence traces the development of these early relatives as far back as Australopithecus africanus, which lived 3.67 million years ago. These remains also mark key evolutionary milestones, such as the shift to bipedal walking, the emergence of tool use, and the growth of brain size. Eventually, modern humans (Homo sapiens) appeared in South Africa around 153,000 years ago.
The first fossils of Paranthropus robustus were unearthed in South Africa in 1938, yet many fundamental questions persisted. How much variation existed within the species? Were size differences the result of sexual dimorphism, or did they indicate the presence of multiple species? How was P. robustus connected to other hominins and early members of the genus Homo? And what genetic features set it apart?
Definitive answers have remained out of reach. Our team—comprising African and European researchers in molecular science, chemistry, and paleoanthropology—sought to address these questions, but ancient DNA analysis was not an option. While ancient DNA has transformed research on later hominins like Neanderthals and Denisovans, it deteriorates quickly in Africa’s warm climate due to its fragile molecular structure.
Fortunately, certain proteins can survive for millions of years because they stick to teeth and bones, remaining stable despite high temperatures. One such protein can determine the biological sex of fossil specimens. Using this method, we discovered that two of the individuals were male and two were female.
These results offer a fresh perspective on human evolution, potentially changing how scientists interpret diversity among early ancestors. They also provide some of the oldest human genetic data recovered from Africa, paving the way for a deeper understanding of the relationships between individuals and raising the possibility of identifying whether the fossils represent different species.
More than one kind of Paranthropus?
The analysis of protein sequences revealed subtle but potentially important genetic differences among the fossils. One particularly notable variation occurred in a gene responsible for producing enamelin, a key protein involved in forming tooth enamel. Two of the individuals shared an amino acid found in modern and early humans, as well as in chimpanzees and gorillas. The other two possessed an amino acid that, among African great apes, has so far been identified only in Paranthropus.
Even more striking, one individual carried both amino acids, providing the first recorded example of heterozygosity (the presence of two different versions of a gene) in proteins dating back 2 million years.
In protein studies, certain mutations are often taken as indicators of distinct species. Initially, we believed the amino acid difference was unique to Paranthropus robustus. However, we discovered that this variation occurred within the group itself—some individuals possessed it, while others did not. This marks the first time a protein mutation has been documented in ancient proteins, as such findings are typically identified through ancient DNA.
These results suggest that what appears to be a single, variable species might instead represent a more intricate evolutionary pattern involving individuals with diverse ancestries. By integrating morphological analysis (the study of organismal form and structure) with ancient protein research, we can build a more accurate understanding of the evolutionary relationships among these early hominins.
However, to confirm that P. robustus fossils have different ancestry, we will need to take samples of tooth enamel protein from more of their teeth. To do this, we plan to sustainably sample more P. robustus from other sites in South Africa where they’ve been found.
Preserving Africa’s fossil heritage
Our team was careful to balance scientific innovation with the need to protect irreplaceable heritage. Fossils were sampled minimally, and all work followed South African regulations. We also involved local laboratories in the analysis. Many of the authors were from the African continent. They were instrumental in guiding the research agenda and approach from the early stages of the project.
Doing this kind of high-end science on African fossils in Africa is an important step toward transformation and decolonization of paleontology. It builds local capacity and ensures that discoveries benefit the regions from which the fossils come.
By combining data on molecules and morphology, our study offers a blueprint for future research – one that could clarify whether early hominins were more or less diverse than we’ve known.
For now, the Paranthropus puzzle just got a little more complex – and a lot more exciting. As paleoproteomic techniques improve and more fossils are analyzed, we can expect more surprises from our ancient relatives.
Reference: “Enamel proteins reveal biological sex and genetic variability in southern African Paranthropus” by Palesa P. Madupe, Claire Koenig, Ioannis Patramanis, Patrick L. Rüther, Nomawethu Hlazo, Meaghan Mackie, Mirriam Tawane, Johanna Krueger, Alberto J. Taurozzi, Gaudry Troché, Job Kibii, Robyn Pickering, Marc R. Dickinson, Yonatan Sahle, Dipuo Kgotleng, Charles Musiba, Fredrick Manthi, Liam Bell, Michelle DuPlessis, Catherine Gilbert, Bernhard Zipfel, Lukas F. K. Kuderna, Esther Lizano, Frido Welker, Pelagia Kyriakidou, Jürgen Cox, Catherine Mollereau, Caroline Tokarski, Jonathan Blackburn, Jazmín Ramos-Madrigal, Tomas Marques-Bonet, Kirsty Penkman, Clément Zanolli, Lauren Schroeder, Fernando Racimo, Jesper V. Olsen, Rebecca R. Ackermann and Enrico Cappellini, 29 May 2025, Science.
DOI: 10.1126/science.adt9539
This research project was funded by the European Union’s Marie Skłodowska-Curie training network “PUSHH” under the Horizon 2020 research and innovation program, the European Research Council (ERC) Advanced Grant “BACKWARD,” and the ERC Proof of Concept Grant under the EU’s Horizon Europe program. The work at the Novo Nordisk Foundation Center for Protein Research was funded in part by a donation from the Novo Nordisk Foundation.
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2 Comments
Such structures of living creatures were often existed,encircled with like other nether living organisms and the warhead system matching,the story goes like that;whatever found at the end platue region of the Eastern Ghats mountains in the India.
Enamelin focused in as a protein that supposedly links humans with these ‘assumed’ human ancestors is found in other creatures including dogs so I’m not sure how this can be used to confirm human lineage from such creatures?