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‘Moon landings of genomics’: Genetic code of ancient bear recreated by Cambridge scientists from faeces and urine samples in Mexican cave





The entire genetic code of a bear that died out 12,000 years ago has been reconstructed using samples of faeces and droplets of urine from soil samples in a remote Mexican cave.

The extraordinary achievement, involving University of Cambridge scientists, has been described as the “moon landings of genomics”.

Team members entering the Chiquihuite cave. Picture: Devlin A Gandy (39116337)
Team members entering the Chiquihuite cave. Picture: Devlin A Gandy (39116337)

They also recreated the genomes of other animals, plants and bacteria from the microscopic fragments of DNA found in the Chiquihuite Cave, which sits 2,750 metres above sea level.

It is the first time ancient DNA has been reconstructed from soil and sediment and will greatly enhance the study of animal, plant and microorganism evolution. It means scientists no longer have to rely on finding and testing fossils to determine genetic ancestry and connections.

Giant short-faced bear eating a bison on the Pleistocene tundra landscape: Picture: Ronaldino and Grant Zazula, Yukon Beringia Interpretation Centre (46358811)
Giant short-faced bear eating a bison on the Pleistocene tundra landscape: Picture: Ronaldino and Grant Zazula, Yukon Beringia Interpretation Centre (46358811)

Professor Eske Willerslev, from Cambridge’s Department of Zoology and the Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, said: “When an animal or a human urinates or defecates, cells from the organism are also excreted.

“We can detect the DNA fragments from these cells in the soil samples and have now used these to reconstruct genomes for the first time.

“We have shown that hair, urine and faeces all provide genetic material which, in the right conditions, can survive for much longer than 10,000 years.

Researchers at Chiquihuite Cave. Picture: Supplied by St John's College
Researchers at Chiquihuite Cave. Picture: Supplied by St John's College

“Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change – fossils will no longer be needed.”

The full genetic code of two ancestors of the American black bear were reconstructed from the traces: the Stone Age American black bear and a short-faced bear called Arctodus simus that died out 12,000 years ago.

Prof Willerslev said: “Imagine the stories those traces could tell. It’s a little insane – but also fascinating – to think that, back in the Stone Age, these bears urinated and defecated in the Chiquihuite Cave and left us the traces we’re able to analyse today.”

The enormous predatory short-faced bear stood at nearly two metres while on all fours and could weigh up to 1,000 kilos. It also lived in North America.

Assistant professor Mikkel Winther Pedersen from the University of Copenhagen sampling the cave sediments for DNA. Picture: Devlin A Gandy (39116326)
Assistant professor Mikkel Winther Pedersen from the University of Copenhagen sampling the cave sediments for DNA. Picture: Devlin A Gandy (39116326)

DNA of mice, voles, kangaroo rats and bats was also found.

Being able to work with highly fragmented DNA from soil means scientists will no longer require samples from bone or teeth to extract sufficient genetic material to recreate a profile of ancient DNA.

“All over the world, everyone scientifically involved in the study of ancient DNA recognised the need to reconstruct genomes from fragments found in soil or sediment,” added Prof Willersleve, a fellow of St John’s College. “Being able to do that for the first time means we have opened up a new frontier. Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change – this is the moon landing of genomics because fossils will no longer be needed.”

Fragments of DNA in sediment from many former Stone Age settlements around the world will now be tested, say the scientists, who reported their findings in the journal Current Biology.

Researchers heading to Chiquihuite Cave. Picture: Supplied by St John's College (39116322)
Researchers heading to Chiquihuite Cave. Picture: Supplied by St John's College (39116322)

Assistant Professor Mikkel Winther Pedersen, first author of the paper, said the sequencing represents “the dawn of an entirely new era” of population genomics.

“The short-faced bears that lived in northern Mexico were distinctly different from the population of black bears living in north-western Canada,” said Prof Pedersen. “This is an excellent example of the new knowledge that suddenly becomes available when you reconstruct genomes based on DNA fragments extracted from soil.

“Studies of ancient environmental DNA have been very limited until now. Fragmented DNA from a soil sample could only tell us whether a specific species lived in a certain locality at a certain time, but it gave us no concrete details about the individual in question.

“So, we couldn’t compare this individual with present-day individuals of the same species. But we can now. We have published for the first time a DNA profile of an American black bear that lived in a mountain cave in northern Mexico in the Stone Age.

“I’m not exaggerating when I say that the potential to extract this type of information from a soil sample of a mere few grams will revolutionise our field.”

Researchers at Chiquihuite Cave. Picture: Supplied by St John's College
Researchers at Chiquihuite Cave. Picture: Supplied by St John's College

The Cambridge Independent has previously reported how the work of Prof Willerslev and colleagues at the remote cave uncovered evidence of people in the Americas 15,000 years earlier than thought.

The researchers slept in the high-altitude cave and needed an armed escort to protect them from Mexican drug cartels during their paintstaking 10-year study.

Nearly 2,000 stone tools and small tool fragments, known as flakes, were discovered during the work.

Read more

How dangerous mission to Mexican cave uncovered evidence of people in Americas 15,000 years earlier than thought



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