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Accessing genetic information from the past is crucial

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Published on Monday, 07 October 2019

Aurélien Ginolhac, bioinformatician at the University of Luxembourg, has contributed to the recent publication “Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogenyin” in the prestigious scientific journal Nature. In this paper, they have demonstrated how the recovery of peptide sequences inside enamel enables to understand the evolution of species.

Retrieving DNA from a horse to a rhino 

The oldest genome available until now was from the DNA of a 700,000-year-old horse that Aurélien Ginolhac, researcher within the Life Sciences Research Unit (LSRU) at the University of Luxembourg co-published in 2013 when he was working at the University of Copenhagen. This DNA was still preserved, despite being extremely fragmented thanks to the location of the fossil: a permanently frozen soil (permafrost) in Yukon, Canada. Most fossils of interest are not conserved in those frozen conditions and DNA is unlikely to be informative when more degraded and fragmented. 

In the Dmanisi cave (Georgia), Dr. Enrico Cappellini, a specialist in Palaeoproteomics at the Globe Institute, University of Copenhagen and first author on the paper, managed to retrieve protein sequences from an extinct rhino tooth. Using ground-breaking technology called mass spectrometry, Enrico and collaborators retrieved genetic information from the tooth of a 1.77 million year old Stephanorhinus specimen which lived in Eurasia during the Pleistocene. 

Using high performance computing 

Extraction of ancient DNA was also performed and sequences were analysed at the University of Luxembourg thanks to the High Performance Computing (HPC) facility. “We demonstrated that no genuine DNA templates were present by comparing the obtained sequences to different modern mammals genomes since this extinct rhino genome is not known. The conclusion was that genetic information for such old specimens is still preserved only in the proteins contained in the enamel of teeth, the hardest material in vertebrates bodies”, explains Aurélien. 

Dr. Enrico Cappellini commented: “For 20 years ancient DNA has been used to address questions about the evolution of extinct species, adaptation and human migration but it has limitations. Now for the first time we have retrieved ancient genetic information which allows us to reconstruct molecular evolution way beyond the usual time limit of DNA preservation.” 

New ways to study extinct species 

DNA data that genetically tracks human evolution only covers the last 400,000 years. But the lineages that led to modern humans and to the chimp – the living species genetically closest to humans – branched apart around six to seven million years ago which means scientists currently have no genetic information for more than 90 per cent of the evolutionary path that led to modern humans. Using paleoproteomics is opening an exciting area where scientists can now study extinct species such as Homo erectus, which remains are present in the Dmanisi cave, because everything that is currently known is almost exclusively based on anatomical information, not genetic information.

Further collaboration 

Collaboration between researchers Enrico and Aurélien will continue, since Enrico was recently awarded an Innovative Training Networks (ITN) project (Call: H2020-MSCA-ITN-2019) named Palaeoproteomics to Unleash Studies on Human History (PUSHH). One of the future recruited PhD student will spend 3 months at the University of Luxembourg to be supervised by Aurélien Ginolhac and Sébastien Varrette (Deputy Head HPC for research) to set-up a computational workflow to analyse ancient proteins data.

In addition, Enrico Cappellini will give a talk entitled: "Palaeoproteomic analysis for cultural heritage and molecular phylogeny beyond the limits of ancient DNA" at the University of Luxembourg on 25 November 2019.

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Article: "Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny", Nature, September 2019

Picture: Stephanorhinus skull from Dmanisi © Mirian Kiladze, Georgian National Museum