Ancient protein fragments recovered using a new technique are 5 times older than any retrieved before. The fragments could help piece together how large mammals from 18 million years ago (mya) evolved and lived.
During the early part of the Miocene epoch (23 to 5.3 mya) East Africa was transforming. The warm, wet climate was gradually becoming drier. This saw the breaking up of extensive lowland rainforests which covered much of the continent.
More open habitats like savannah and grassland are believed to have been a key environmental driver in the evolution of bipedal apes that are ancestors to modern humans.
Other mammals which roamed the region during the early Miocene include ancient relatives of rhinoceroses and the proboscidean order which includes elephants. One prehistoric proboscidean which lived in early Miocene Kenya is Archaeobelodon – an animal with a trunk, tusk and large, forward facing, flat teeth. Archaeobelodon could grow to about 3.5 tonnes.
Studies of animals this far back in history are often restricted to the size and shape of fossilised remains.
Research based on ancient DNA or proteins has been confined to the Pleistocene (2.58 million to 11,700 years ago) or Pliocene (5.3–2.58 mya) due to the molecules breaking down over time.
The new research, published in Nature, opens a new window to studying earlier animals by demonstrating a technique to uncover proteins the fossilised teeth of early Miocene mammals found in Kenya.
Daniel Green examining fossils from a northern Kenyan site called
Napudet. Credit: Fred Horne.
“Teeth are rocks in our mouths,” says lead author Daniel Green, field program director at Harvard University’s Department of Human Evolutionary Biology (HEB). “They’re the hardest structures that any animals make, so you can find a tooth that is a hundred or a hundred million years old, and it will contain a geochemical record of the life of the animal.”
This record includes clues to the animal’s diet and environment.
“In the past we thought that mature enamel, the hardest part of teeth, should really have very few proteins in it at all,” Green says.
Green’s team used a new proteomics technique called liquid chromatography tandem mass spectrometry (LC-MS/MS) to detect a variety of proteins.
“The technique involves several stages where peptides are separated based on their size or chemistry so that they can be sequentially analysed at higher resolutions than was possible with previous methods,” explains corresponding author Kevin T. Uno, also from Harvard’s HEB.
“We and other scholars recently found that there are dozens – if not even hundreds – of different kinds of proteins present inside tooth enamel,” Green says.
The team tested the new technique on fossils from Kenya’s Turkana Basin in the Great Rift Valley where the 1.9-million-year-old hominin “Turkana Boy” was found. They focused on fossil teeth from large herbivores (rhino and elephant relatives) which can have enamel 2 to 3mm thick.
A view of the Turkwel River in Turkana, northern Kenya. Credit: Daniel Green.
They found peptide fragments, chains of amino acids, from proteins up to 18 million years old.
“Nobody’s ever found peptide fragments that are this old before,” Green says. The previous oldest peptide fragments retrieved are about 3.5 million years old.
The fragments are a small, but important piece of the organisms’ proteome – the entire set of proteins expressed by the genome.
The research “opens new frontiers in paleobiology, allowing scientists to go beyond bones and morphology to reconstruct the molecular and physiological traits of extinct animals and hominins”, says co-author Emmanuel K. Ndiema, a senior research scientist at the National Museum of Kenya.
The site of Buluk, formed approximately 16 million years ago. Credit: Ellen Miller.
“This provides direct evidence of evolutionary relationships,” Ndiema adds. “Combined with other characteristics of teeth, we can infer dietary adaptations, disease profiles, and even age at death – insights that were previously inaccessible.”
“We can use these peptide fragments to explore the relationships between ancient animals, similar to how modern DNA in humans is used to identify how people are related to one another,” Uno explains.
“Even if an animal is completely extinct – and we have some animals that we analyse in our study which have no living descendants – you can still, in theory, extract proteins from their teeth and try to place them on a phylogenetic tree,” says Green. This could “resolve longstanding debates between palaeontologists about what other mammalian lineages these animals are related to using molecular evidence”.