Ancient Enamel Proteins Uncover Biological and Genetic Diversity in Paranthropus robustus

Paranthropus robustus is a well-documented species within the Hominin group that has yet to be associated with genetic evidence. This species thrived in what is now South Africa between 2 million and 1.2 million years ago. In a recent study, paleontologists extracted enamel protein sequences from a dental specimen, believed to be 2 million years old, discovered at the Swartkrans site in South Africa. The results indicate a greater diversity than previously recognized for Paranthropus robustus and support the potential existence of multiple species within the genus.

Advancements in ancient DNA (aDNA) sequencing have provided essential insights into the evolutionary connections among mid- to late Pleistocene hominins. However, our understanding of the earlier Pliocene-Pleistocene species, including Paranthropus robustus, remains limited.

This limitation is primarily due to the poor preservation of aDNA in African hominin fossils older than 20,000 years.

Paranthropus robustus has traditionally been regarded as a singular evolutionary line.

Yet, morphological overlaps between Paranthropus robustus and Australopithecus raise questions about their possible evolutionary links.

Moreover, variations in dental morphology suggest either an undiscovered diversity within Paranthropus robustus or the existence of multiple distinct species.

In this study, researchers from the University of Copenhagen, the University of Cape Town, and Dr. Paresa Madupe employed more durable ancient proteins to explore the variation within this ancient human species.

Four tooth enamel proteins were analyzed using high-resolution mass spectrometry and paleontological techniques, focusing on Paranthropus robustus fossils from the Swartkrans cave.

These specimens, dating from 2.2 to 1.8 million years ago, are among the earliest known hominins.

Molecular analysis of the protein sequences revealed significant variation at the molecular level among Paranthropus robustus individuals, including evidence from both male and female fossils, challenging the reliability of tooth size as a sole indicator of sexual dimorphism and suggesting that this variance cannot be attributed exclusively to sexual differences.

Notably, one individual appears to be genetically distinct from the others, highlighting considerable intraspecies variability within Paranthropus robustus.

The results align with recent morphological evidence, indicating previously unrecognized taxonomic diversity within the genus, including the proposed species Paranthropus capensis.

“Our study illustrates how paleobiological traits can assist in distinguishing sexual dimorphism from other forms of variation in the early Pleistocene human lineage in Africa,” the authors concluded.

The study is published in the journal Science.

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Paresa P. Madupe et al. 2025. Enamel proteins reveal biological and genetic variation in southern Africa Paranthropus robustus. Science 388 (6750): 969-973; doi: 10.1126/science.adt953