‘Game-changing’ research could solve evolution mysteries

Stephanorhinus skull from Dmanisi. Photo credit: Mirian Kiladze, Georgian National Museum

Dr. Eske Willerslev (Chair of Geogenetics in D-IAS) and Associate Professor Enrico Cappellini from GLOBE Institute at University of Copenhagen has just published a new article in Nature – one of the most recognizable scientific journals in the world – and their findings involves an ancient rhino. 

By Susanne Siig Petersen

What can an ancient rhino tell us about our past?

An evolution revolution has begun after scientists extracted genetic information from a 1.7 million-year-old rhino tooth – the largest and oldest genetic data to ever be recorded. Researchers identified an almost complete set of proteins, a proteome, in the dental enamel of the rhino and the genetic information discovered is one million years older than the oldest DNA sequenced from a 700,000-year-old horse.

The findings has just been published in Nature – and they mark a breakthrough in the field of ancient biomolecular studies and could solve some of the biggest mysteries of animal and human biology by allowing scientists to accurately reconstruct evolution from further back in time than ever before.

Read the article in Nature 

Professor Enrico Cappellini, a specialist in Palaeoproteomics at the Globe Institute, University of Copenhagen, and first author on the paper, said:

“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. This new analysis of ancient proteins from dental enamel will start an exciting new chapter in the study of molecular evolution.”

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.

Scientists also don’t know what the genetic links are between us and extinct species such as Homo erectus – the oldest known species of human to have had modern human-like body proportions – because everything that is currently known is almost exclusively based on anatomical information, not genetic information.

Researchers have now used ancient protein sequencing – based on ground-breaking technology called mass spectrometry – to retrieve genetic information from the tooth of a 1.77 million year old Stephanorhinus – an extinct rhinoceros which lived in Eurasia during the Pleistocene. Researchers took samples of dental enamel from the ancient fossil which was discovered in Dmanisi, Georgia, and used mass spectrometry to sequence the ancient protein and retrieved genetic information previously unobtainable using DNA testing.

Tooth enamel is the hardest material present in mammals. In this study researchers discovered the set of proteins it contains lasts longer than DNA and is more genetically informative than collagen, the only other protein so far retrieved from fossils older than one million years.

Professor Jesper V. Olsen, head of the Mass Spectrometry for Quantitative Proteomics Group at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, and co-corresponding author on the paper, said:

“Mass spectrometry-based protein sequencing will enable us to retrieve reliable and rich genetic information from mammal fossils that are millions of years old, rather than just thousands of years old. It is the only technology able to provide the robustness and accuracy needed to sequence tiny amounts of protein this old.”

Professor Cappellini added:

“Dental enamel is extremely abundant and it is incredibly durable, which is why a high proportion of fossil records are teeth. We have been able to find a way to retrieve genetic information that is more informative and older than any other source before, and it’s from a source that is abundant in the fossil records so the potential of the application of this approach is extensive.”

Lead author on the paper Dr. Eske Willerslev, who holds positions at St John’s College, University of Cambridge, and is director of The Lundbeck Foundation Centre for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, at the University of Copenhagen, said:

“This research is a game-changer that opens up a lot of options for further evolutionary study in terms of humans as well as mammals. It will revolutionise the methods of investigating evolution based on molecular markers and it will open a complete new field of ancient biomolecular studies.”

This rearranging of the evolutionary lineage of a single species may seem like a small adjustment but identifying changes in numerous extinct mammals and humans could lead to massive shifts in our understanding of the way the world has evolved.

The team of scientists is already implementing the findings in their current research. The discovery could enable scientists across the globe to collect the genetic data of ancient fossils and to build a bigger, more accurate picture of the evolution of hundreds of species including our own.

Abstract on the article: ‘Early Pleistocene enamel proteome from the Dmanisi resolves Stephanorhinus phylogeny’

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5—although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7,8,9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck’s rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel—which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record—can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.

Read the whole article in Nature – or online at: https://www.nature.com/articles/s41586-019-1555-y

 

The following funding acknowledgements from the authors appear at the end of the paper:

E.C. and F.W. are supported by the VILLUM Fonden (grant number 17649) and by the European Commission through a Marie Skłodowska Curie (MSC) Individual Fellowship (grant number 795569). E.W. is supported by the Lundbeck Foundation, the Danish National Research Foundation, the Carlsberg Foundation, KU2016 and the Wellcome Trust. E.C., C.K., J.V.O., P.R. and D.S. are supported by the European Commission through the MSC European Training Network ‘TEMPERA’ (grant number 722606). M.M. and R.R.J.-C. are supported by the University of Copenhagen KU2016 (UCPH Excellence Programme) grant. M.M. is also supported by the Danish National Research Foundation award PROTEIOS (DNRF128). Work at the Novo Nordisk Foundation Center for Protein Research is funded in part by a donation from the Novo Nordisk Foundation (grant number NNF14CC0001). M.R.D. is supported by a PhD DTA studentship from NERC and the Natural History Museum (NE/K500987/1 & NE/L501761/1). K.P. is supported by the Leverhulme Trust (PLP -2012-116). L.R. and L.P. are supported by the Italian Ministry for Foreign Affairs (MAECI, DGSP-VI). L.P. was also supported by the EU-SYNTHESYS project (AT-TAF-2550, DE-TAF-3049, GB-TAF-2825, HU-TAF-3593 and ESTAF- 2997) funded by the European Commission. L.D. is supported by the Swedish Research Council (grant number 2017-04647) and FORMAS (grant number 2015-676). M.T.P.G. is supported by ERC Consolidator Grant ‘Extinction genomics’ (grant number 681396). L.O. is supported by the ERC Consolidator Grant ‘PEGASUS’ (grant agreement number 681605). B.S., J.K. and P.D.H. are supported by the Gordon and Betty Moore foundation. B.M.-N. is supported by the Spanish Ministry of Sciences (grant number CGL2016-80975-P). R.F. is supported by National Science Foundation (grant number 1025245). The authors acknowledge support from the Science for Life Laboratory, the National Genomics Infrastructure (Sweden) and UPPMAX for providing assistance with massive parallel sequencing and computational infrastructure. Research at Dmanisi is supported by the John Templeton Foundation (grant number 52935), and the Shota Rustaveli Science Foundation (grant number 18-27262).