Scientists have pushed back the frontiers of how far into the past we can trace the history of life. For the first time, they have succeeded in extracting proteins more than 20 million years old from the teeth of a long-extinct species of rhinoceros from Canada. A researcher says that the discovery could reshape understanding of how life on Earth took form.
Over the past decade, researchers have gradually extended how far back they can look using genetic methods to study ancient life.
First, they showed that they could peer tens of thousands of years into the past by analysing ancient DNA from animals preserved in the Siberian permafrost — and in recent years, DNA has even been successfully retrieved from specimens up to 2 million years old in ideal conditions.
Later, they turned to proteins — which are more stable than DNA — to explore relationships between animals that lived more than a million years ago.
Now they have pushed the boundary again by successfully extracting proteins from the teeth of a rhinoceros that lived in Canada between 21 and 24 million years ago.
According to a researcher behind the study, this opens entirely new opportunities to study the relationships between species of animals that became extinct millions of years ago, other extinct animal species and animals living today.
“This enables us to place extinct species on the family tree of life and determine which animals they are actually related to. When we can extract genetic material from an animal this old, we can much better map how life has evolved and how various species have emerged over the past 30 million years,” says Ryan Sinclair Paterson, Postdoctoral Fellow, Section for GeoGenetics, Globe Institute, University of Copenhagen, Denmark.
The research has been published in Nature.
How DNA and proteins reveal animal relationships
When researchers look back in time, genetic material such as DNA and proteins has proven to be an invaluable resource.
In the past, the relationships between extinct animal species could only be determined by examining their bones, which has major limitations.
For example, both birds and bats have developed the ability to fly but are not closely related in any way.
With genetic material, researchers can determine whether two species are truly related – and when they began to diverge in their evolutionary paths.
DNA breaks down relatively quickly, whereas proteins can survive for millions of years, especially in tooth enamel.
Proteins carry less genetic information than DNA and change more slowly, but these slow shifts make them useful for tracing lineages.
The oldest known DNA was previously from a mammoth more than 2 million years old, and the oldest identified proteins were 3.7 million years old.
Proteins stored in rhinoceros teeth for 20 million years
In the new study, the researchers aimed to determine how far back in time identifiable proteins can be found.
To do this, they examined enamel from the teeth of an extinct rhinoceros species that lived in Arctic Canada between 21 and 24 million years ago.
Ryan Sinclair Paterson explains that the fossil of the extinct rhinoceros was found in Arctic Canada, where the dry, cold climate created ideal conditions for preserving proteins.
Tooth enamel is the hardest animal tissue — like armour shielding tiny protein traces for millions of years.
“We examined a sample from a tooth found in Haughton Crater, which, in addition to being an interesting place to find fossils, is also used to simulate missions to Mars. It is the perfect place to preserve proteins over time,” explains Ryan Sinclair Paterson.
Revealing the ancient proteins
To find ancient proteins in the enamel of a tooth that has been around for 20 million years, researchers dissolved a tiny sample in acid.
The sample was then analysed using a mass spectrometer — a device that breaks proteins into tiny fragments and weighs them individually. Using these weights, the researchers identified which amino acids and peptides were present — and thereby which proteins the tooth once contained.
The researchers pieced together the fragments and reconstructed how they had once been assembled into whole proteins.
They compared the fragments with databases of known proteins to reconstruct what their original structure.
“Mapping such ancient proteins is difficult because we cannot compare them directly with proteins from living animals. But we can do this anyway by identifying amino acids and peptides,” says Ryan Sinclair Paterson.
What the discovery can reveal about the evolution of life and the climate
How can identifying proteins from a long-extinct species of rhinoceros be used?
According to Ryan Sinclair Paterson, the study should first be used to validate that proteins this old can be found.
Second, it opens new opportunities to determine how long-extinct species are related.
This perspective is perhaps especially relevant today, when climate change is causing permafrost to disappear in many parts of the world. Studying extinct animals from these regions requires acting soon — before both the fossils and their proteins vanish in a warmer climate.
“The great potential lies in understanding evolution — how species arose and became extinct in the past. Twenty million years ago, the Arctic was a completely different place: warm, green and full of life. It was warmer, perhaps closer to the climate we are heading towards. If we better understand what once lived in the Arctic, and when and how the animals disappeared, we may also be able to better predict what may happen in the Arctic in the future,” concludes Ryan Sinclair Paterson.
