Parathropus robustus (Artist's impression)
Bary Davies, RCA
Human evolution isn’t a tidy staircase; it’s a branching, tangled tree full of transitional forms. And now, cutting-edge protein analysis from two-million-year-old teeth has revealed that Paranthropus robustus — one of our distant cousins — carried mixed ancestry, adding powerful new evidence to the evolutionary story creationists work so hard to deny.
If there is anything guaranteed to send a creationist into a fit of denial — desperately trying to redefine basic terms such as “transitional”, “species”, and “evolution”, and, as a last resort, claiming palaeontologists must have faked the evidence — it is the discovery of a transitional species in human evolutionary history.
But the hominin fossil record, like the evolutionary record for most living species, is absolutely packed with transitional forms. In fact, there are so many in human palaeontology that it can be difficult to single out one that is clearly more ‘transitional’ than the rest, because they form a fairly smooth continuum from the australopiths through to the genus Homo, just as we would expect of a slow process unfolding over tens of thousands or millions of years.
However, one species, Paranthropus robustus, stands out for its mosaic of features consistent with a lineage intermediate between the common ancestor of chimpanzees and hominins and the australopiths that followed.
And this mosaic has now been expanded to include genetic-level evidence, thanks to advances in palaeoproteomics. Proteins can persist far longer than DNA, yet they retain a direct correspondence to DNA via RNA, which encodes their amino-acid sequences. Once ancient proteins have been recovered and analysed, researchers can work backwards to reconstruct the RNA, and therefore the DNA, that produced them.
Using proteins extracted from the tooth enamel of four P. robustus fossils, researchers led by the University of Copenhagen have shown that these individuals themselves had mixed ancestry — indicating interbreeding with contemporaneous relatives, just as we now know happened among later hominin species, and almost certainly among the australopiths too.
The findings of the team were published in Science in May 2025, and are the subject of a recent article in The Conversation by three of the team.
New clues from 2 million-year-old tooth enamel tell us more about an ancient relative of humans
Proteins were taken from the enamel of this Paranthropus robustus’ tooth.
For nearly a century, scientists have been puzzling over fossils from a strange and robust-looking distant relative of early humans: Paranthropus robustus. It walked upright, and was built for heavy chewing with relatively massive jaws, and huge teeth with thick dental enamel. It’s thought to have lived between 2.25 million and 1.7 million years ago.
Humans today have a diverse array of hominin distant relatives and ancestors from millions of years ago. The South African fossil record ranges from early hominins such as Australopithecus prometheus, A. africanus (Taung child), A. sediba and P. robustus, to early members of the genus Homo (H. erectus/ergaster, H. habilis), to later hominins such as H. naledi and Homo sapiens (humans).
Fossils show how these early relatives evolved from as far back as A. africanus, 3.67 million years ago. They also document milestones in evolution, including the transition to walking on two legs, tool making and increased brain development. Ultimately, our species – Homo sapiens – appeared in South Africa 153,000 years ago.
Fossils of P. robustus were first discovered in South Africa in 1938. But crucial questions remained. How much variation was there within the species? Were the size differences related to sex, or did they reflect the presence of multiple species? How was P. robustus related to the other hominins and early Homo? And what, genetically, made it distinct?
Until now, answers to these questions have been elusive. As a team of African and European molecular science, chemistry and palaeoanthropology researchers, we wanted to find answers but we couldn’t use ancient DNA to help us. Ancient DNA has been a game-changer in studying later hominins like Neanderthals and Denisovans but it doesn’t survive well in Africa’s climate because of its simple structure.
We experienced a breakthrough when we decided to use palaeoproteomics – the analysis of ancient proteins. We extracted these from the enamel of the 2-million-year-old teeth of four P. robustus fossils from Swartkrans Cave in South Africa’s Cradle of Humankind.
Luckily, proteins that are millions of years old preserve well because they stick to teeth and bones and are not affected by the warm weather. One of these proteins tells us the biological sex of the fossils. This is how we found that two of the individuals were male and two were female.
These findings open a new window into human evolution – one that could reshape how we interpret diversity in our early ancestors by providing some of the oldest human genetic data from Africa. From there, we can understand more about the relationships between the individuals and potentially even whether the fossils come from different species.
More than one kind of Paranthropus?
The protein sequences also revealed other subtle but potentially significant genetic differences. One standout difference was found in a gene which makes enamelin, a critical enamel-forming protein. We found that two of the individuals shared an amino acid with modern and early humans, chimpanzees and gorillas. The other two had an amino acid that among African great apes is, so far, unique to Paranthropus.
What’s even more interesting is that one of the individuals had both the distinct amino acids. This is the first documented time we can show heterozygosity (a state of having two different versions of a gene) in proteins that are 2 million years old.
When studying proteins, specific mutations are thought to indicate different species. We were quite surprised to discover that what we initially thought was a mutation unique to Paranthropus robustus was actually variable within that group – some individuals had it while others did not. Again, this was the first time anyone had observed a protein mutation in ancient proteins (these mutations are usually observed in ancient DNA).
We realised that instead of seeing a single, variable species, we might be looking at a complex evolutionary puzzle of individuals with different ancestries. This shows that combining analyses of morphology (the study of the form and structure of organisms) and the study of ancient proteins, we can create a clearer evolutionary picture of the relationships among these early hominin individuals.
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 towards transformation and decolonisation of palaeontology. 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 palaeoproteomic techniques improve and more fossils are analysed, we can expect more surprises from our ancient relatives.
(Jesper V. Olsen, Rebecca R. Ackermann and Enrico Cappellini were also the principal investigators on this project.)
Palesa P. Madupe, Postdoctoral Researcher, University of Copenhagen; Claire Koenig, Post doc researcher, University of Copenhagen, and Ioannis Patramanis, Postdoctoral Researcher, University of Copenhagen
This article is republished from The Conversation under a Creative Commons license. Read the original article.
Abstract
Paranthropus robustus is a morphologically well-documented Early Pleistocene hominin species from southern Africa with no genetic evidence reported so far. In this work, we describe the mass spectrometric sequencing of enamel peptides from four ~2 million–year-old dental specimens attributed morphologically to P. robustus from the site of Swartkrans in South Africa. The identification of AMELY-specific peptides enabled us to assign two specimens to male individuals, whereas semiquantitative mass spectrometric data analysis attributed the other two to females. A single amino acid polymorphism and the enamel-dentine junction shape variation indicated potential subgroups present within southern African Paranthropus. This study demonstrates how palaeoproteomics can help distinguish sexual dimorphism from other sources of variation in African Early Pleistocene hominins.
Palesa P. Madupe et al.
Enamel proteins reveal biological sex and genetic variability in southern African Paranthropus.
Science 388, 969-973 (2025). DOI: 10.1126/science.adt9539
© 2025 American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.
Once again, the evidence aligns from every direction: anatomy, geology, developmental biology, genetics, and now ancient proteins all tell the same story. Human evolution is a messy, branching, experimentally rich process — and *Paranthropus robustus* sits right where we would expect a transitional form to sit, complete with the genetic fingerprints of interbreeding and divergence.
Creationists often demand “transitional forms” as though evolution should be obliged to produce museum-ready half-and-half creatures on command. Yet when the fossil record delivers precisely what any honest inquirer would recognise as transitional, the response is denial, distortion, and conspiracy theories about forged fossils. It is not evidence they lack; it is the willingness to accept it.
Science advances not by clinging to comforting myths, but by following data wherever it leads. And as our tools improve — from classical morphology to whole-genome sequencing and now ancient protein reconstruction — the picture of human origins becomes richer, more detailed, and entirely consistent with evolution by natural processes. The real story of our species is far more fascinating than any manufactured pseudoscience: we are the product of deep time, branching ancestries, and countless experiments in survival — a lineage written in bone and now, quite literally, in protein.
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