DNA breakthrough expected to reveal fresh insights into evolutionary past

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The 1.77-million-year-old Stephanorhinus skull from Dmanisi. Photo: Mirian Kiladze, Georgian National Museum

The rich evolutionary history of the horse could be revealed in greater detail than ever imagined after scientists took a major stride in detecting ancient DNA.

The breakthrough was announced after scientists extracted genetic information from a 1.77 million-year-old rhino tooth – the largest genetic data set this old to ever be confidently recorded

The method opens the door for studying the evolutionary history of fossil species dating back millions of years.

Until now, the oldest DNA sequenced was from a 700,000-year-old horse recovered from permafrost, which means the latest technique pushes back DNA recovery back another million years.

Researchers say they identified an almost complete set of proteins – a proteome – in the dental enamel of the now-extinct rhino.

The findings by scientists from the University of Copenhagen and the University of Cambridge have been described in a paper published in the journal Nature.

They mark a breakthrough in the field of ancient molecular studies and could solve some of the biggest mysteries of ancient animal and human biology by allowing scientists to accurately reconstruct evolution from further back in time than ever before.

This is especially tantalizing for those who study the storied evolution of the horse, species of which ranged across the globe before nearly all became extinct.

“For 20 years ancient DNA has been used to resolve questions about the evolution of extinct species, adaptation and human migration, but it has limitations,” said Professor Enrico Cappellini, Associate Professor in Palaeoproteomics at the Globe Institute, part of the University of Copenhagen.

“For the first time, we have retrieved ancient genetic information which allows us to reconstruct evolution way beyond the usual time limit of DNA preservation.”

Cappellini, who is first author on the paper, says the ability to investigate ancient proteins from dental enamel will start a new chapter in the study of molecular evolution.

The reliance on DNA analysis has allowed scientists to genetically track the processes of evolution behind the origins of our species that occurred in the last 400,000 years or so.

However, it means that researchers have no genetic information for 90% or more of the evolutionary journey of species, including our own.

In humans, for example, researchers still don’t know our genetic relationship to Homo erectus – the oldest known species of humans to have had modern human-like body proportions – or between us and the Australopithecus group of species, which includes the iconic fossil commonly referred to as Lucy.

The DNA at the centre of the research was recovered from a Stephanorhinus – an extinct rhinoceros which lived in Eurasia during the Pleistocene.

The study team extracted protein remains of dental enamel from a fossil tooth discovered in Dmanisi, Georgia. The researchers used mass spectrometry to sequence the ancient proteins and retrieve genetic information previously unobtainable using DNA sequencing.

Tooth enamel is the hardest material present in the mammal body. In their study, researchers discovered that the set of proteins it contains lasts longer than DNA and is genetically more informative than collagen, the only other ancient protein so far retrieved in fossils older than a million years.

Ultimately, mass spectrometry-based ancient protein sequencing expands the possibilities of retrieving reliable and rich genetic information from mammal fossils to those which are millions, rather than just thousands, of years old.

“With the new, protein-sequencing-based method the possibilities of genetic information have been stretched beyond ancient DNA,” professor and co-corresponding author, Jesper Velgaard Olsen, from the Novo Nordisk Foundation Center for Protein Research, explains.

“Basically, this approach can tell us not only the species and the gender of an ancient fossil, but we can also draw an evolutionary line – all from a single tooth,” he says.

“Dental enamel is extremely abundant and it is highly durable, which is why a high proportion of fossil records are teeth,” Cappellini adds.

“We have been able to find a way to retrieve genetic information that is more informative and reliable than any other source of comparable age before, and it’s from a material that is abundant in the fossil records so the potential of the application of this approach is extensive.”

The sequencing of the ancient proteome from the Stephanorhinus fossil cemented its place in the evolutionary tree with other extinct and existing rhinoceros species, and defined its genetic relationship with them.

Professor Eske Willerslev, who holds positions at the University of Cambridge and is director of The Lundbeck Foundation Centre for GeoGenetics at the University of Copenhagen, describes the research as a game-changer.

“There are extinct species of early humans that we haven’t been able to get any DNA from – species like Homo Erectus. The remains we have are too old and too poorly preserved for the DNA to survive,” he says.

The new technique opens up many opportunities for further evolutionary studies in terms of humans as well as mammals.

“It will revolutionize the methods of investigating evolution based on molecular markers and it will open a complete new field of ancient molecular studies.”

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

The scientists say they are already implementing the findings in their current research.

The findings should allow scientists to analyse proteins from ancient fossils and build a bigger, more accurate picture of the evolution of hundreds of species.

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