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When it comes to studying 2-million-year-old fossils found in hot, dry African climates, DNA analysis is not the ideal solution. Its simple structure does not allow it to survive intact for so long in such climates. Since current ancient DNA technologies have only been able to reveal genetic sequences up to around the last 200 000 years, a recent EU-backed study(opens in new window) turned to proteins to unravel the secrets of an ancient relative of humans called Paranthropus robustus.
P. robustus is an Early Pleistocene hominin species believed to have lived in southern Africa somewhere between 2 and 1 million years ago. Although well-documented as a species, it still lacked reported genetic evidence, a deficiency that an international research team set out to remedy with the support of six EU-funded projects: PUSHH(opens in new window), ApeGenomeDiversity, TEMPERA(opens in new window), BACKWARD, STAMP and COREX. In their study, the researchers analysed protein sequences preserved in fossilised tooth enamel to learn more about these ancient hominins, which were first discovered in South Africa in 1938.
The team analysed ancient proteins extracted 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,” write several of the study authors in an article(opens in new window) posted on ‘The Conversation’. “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.”
Tracing patterns of diversity
The protein analysis also revealed certain genetic differences. Two of the individuals were found to share 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,” report the scientists. Interestingly, one hominin even had both the amino acids – this being the first time two different versions of a gene have been documented in 2-million-year-old proteins.
While protein mutations are believed to point to different species, the authors were surprised to find a protein mutation that was variable within the P. robustus species, with some individuals having it and others not. “We realised that instead of seeing a single, variable species, we might be looking at a complex evolutionary puzzle of individuals with different ancestries,” the scientists conclude.
Using proteomics approaches, the study supported by PUSHH (Palaeoproteomics to Unleash Studies on Human History), ApeGenomeDiversity (Great ape genome variation now and then: current diversity and genomic relics of extinct primates), TEMPERA (Teaching Emerging Methods in Palaeoproteomics for the European Research Area), BACKWARD (Overcoming the frontiers of biomolecular studies on human history and adaptation using palaeoproteomics), STAMP (Spatiotemporal Analytical Modelling for Paleobiology) and COREX (From correlations to explanations: towards a new European prehistory) identified both the ancient individuals’ gender and patterns of diversity that point to the existence of multiple populations. The combined use of morphological and molecular data serves as a blueprint for future research.
For more information, please see:
PUSHH project website(opens in new window)
ApeGenomeDiversity project
TEMPERA project website(opens in new window)
BACKWARD
STAMP
COREX