A team of international researchers has analyzed fossilized teeth from a cave in South Africa, uncovering remarkable insights into the biology and diversity of ancient human relatives. Published on May 29, 2025, in the journal Science, the study focuses on proteomic data extracted from four Paranthropus robustus individuals who lived approximately 2.2 million years ago. This marks a significant leap forward in the study of early hominins, revealing that our evolutionary story may be more complex than previously understood.

A Breakthrough In Ancient Protein Analysis

Until recently, ancient DNA analysis was the primary method for extracting genetic information from fossils. But in Africa’s warm climate, DNA rarely survives beyond 20,000 years. The new research overcomes this barrier using paleoproteomics, a method that analyzes long-preserved proteins found in tooth enamel, one of the most durable biological substances. This approach allowed researchers to extract and sequence proteins from the enamel of the four hominin fossils discovered in the Swartkrans cave, a site located in the Cradle of Humankind World Heritage area.

“Figuring out the human family tree using proteins is the goal,” explained Claire Koenig, postdoctoral researcher at the University of Copenhagen. She co-authored the study with Palesa Madupe and Ioannis Patramanis. But the team acknowledges that “our ability to distinguish between different species is limited by the small number of different proteins present in enamel.” Despite this limitation, the study opens a new frontier for identifying and classifying early human relatives based on biological evidence far older than DNA can provide.

A replica of a Paranthropus robustus skull discovered at Kromdraai in South Africa in 1938. (Image credit: Alamy)

Unexpected Diversity in Paranthropus Robustus

One of the study’s most surprising discoveries came from sex determination. By analyzing AMELY and AMELX proteins, which are sexually dimorphic, the team found that two specimens were male and two were female. However, the molecular analysis contradicted previous assumptions based on tooth size and morphology. One individual, believed to be female due to its small teeth, was identified as male through its protein profile.

“Our results thus indicate that measurements of dental size are not necessarily accurate for correct sex estimation,” the researchers wrote in the study. This finding has profound implications for paleoanthropology, as it challenges a long-standing method used to interpret the fossil record. The ability to correctly sex individuals using protein data offers a more reliable alternative, potentially revising past assumptions about sexual dimorphism and social structures among extinct hominin species.

Are We Looking At A New Species?

While analyzing the protein sequences, the team observed genetic variation among the individuals that couldn’t be explained by sex alone. One individual — labeled SK-835 — was especially intriguing. Its amino acid profile showed it was more distantly related to the other three, raising the possibility that it belonged to a distinct species of hominin previously unrecognized by scientists.

Although it is “premature to classify SK-835 as a member of the newly proposed Paranthropus [capensis] taxa,” as Koenig emphasized, the variation still suggests a deeper phylogenetic complexity. Another explanation could be microevolutionary differences among geographically or temporally separated populations. As study co-author Rebecca Ackermann from the University of Cape Town noted, “We need to analyse more Paranthropus material from different sites to get a better handle on the variation within southern African Paranthropus.”

The Limits And Promise Of Paleoproteomics

Despite the success of the study, the researchers caution that paleoproteomics is still in its infancy. Koenig explained that “proteomics is inherently a destructive technique, but we take great care to minimize impact, especially when working with rare or precious specimens.” Fortunately, ongoing innovations aim to reduce the invasiveness of the process, such as acid etching that removes only an ultra-thin enamel layer.

The future of this field lies in finer analytical tools and higher-throughput sequencing, which may eventually distinguish between closely related hominin species. “It remains to be seen, for example, whether or not we can molecularly tell apart a Paranthropus robustus from an Australopithecus africanus,” Koenig said, “because these species are closely related and therefore their proteins are going to look very similar.” Still, as methods improve, paleoproteomics may become a cornerstone of early human ancestry studies, reshaping our understanding of evolution at a molecular level.