Ancient human genetic material found preserved in 2-million-year-old teeth

Paranthropus robustus possessed unusually huge teeth with thick enamel.
Mrigakshi Dixit
Skull of a 1.8 million years old Paranthropus robustus
Skull of a 1.8 million years old Paranthropus robustus

CC BY-SA 4.0/Collection of the Transvaal Museum 

Archeologists discovered the earliest preserved human genetic material in two million-year-old tooth fossils. 

The specimen is most likely from the African hominid Paranthropus robustus (P. robustus). These prehistoric humans possessed unusually huge teeth with thick enamel. 

As per Nature, it is noted to be the earliest genetic information ever gathered about any ancient hominid. 

Protein sequencing of the enamel 

Enrico Cappellini, a protein chemist at the University of Copenhagen, led a team that studied four P. robustus teeth samples collected from Swartkrans cave, roughly 40 kilometers northwest of Johannesburg. 

They sequenced the proteins in the collected fossils to learn more about the early human species. 

The amino acids found in each sample's enamel (the outer layer of teeth) were thoroughly examined using a method known as mass spectrometry. Through this method, they were able to pinpoint the sex to which the fossils belonged.

In two samples, they discovered the existence of amelogenin-Y, a protein generated by a gene on the Y chromosome. The presence of this protein in two of the enamel samples confirmed that the teeth belonged to males.

While the other two teeth lacked amelogenin-Y, they did contain the X-chromosome variant of the protein, indicating that the specimens were most likely from a female.

All four tooth samples were analyzed, and 400 amino acids were sequenced. 

Evolutionary relationship

The sequencing process resulted in forming a "simple evolutionary tree." 

This demonstrated that Homo sapiens, Neanderthals, and Denisovan hominins living in Siberia in the last 200,000 years are more closely connected than the Paranthropus

According to the study, which has been uploaded to the pre-print server, creating an evolutionary tree based on genetic material from fossils "can be considered a potentially transformative breakthrough for palaeoanthropology."

Authors say that studying ancient proteins might help researchers determine where species like Australopithecus afarensis fit in the hominin family tree. Over the last few decades, researchers have found many fossil remains of this species, including the nearly complete specimen famously known as Lucy.

The study has been uploaded to the pre-print server bioRxiv. 

Study abstract:

The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. For Paranthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa 1,2 and the nature of intraspecific variation are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically to P. robustus, from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern African Paranthropus, as previously suggested based on morphology alone. Finally, the molecular data also confirm the taxonomic placement of Paranthropus within the hominin clade. This study demonstrates the feasibility of recovering informative Early Pleistocene hominin enamel proteins from Africa. Crucially, it also shows how the analysis of these proteins can contribute to understanding whether hominin morphological variation is due to sexual dimorphism or to taxonomic differences. We anticipate that this approach can be widely applied to geologically-comparable sites within South Africa, and possibly more broadly across the continent.

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