Woolly rhino genome recovered from meat in frozen wolf pup’s stomach

A genome reconstructed from a tiny piece of flesh found in the stomach of a wolf pup that died 14,400 years ago suggests that woolly rhinos were still genetically healthy even as they faced imminent extinction.

No one will ever know how a young female wolf pup died at a site near what is now the town of Tumat in northern Siberia, Russia. But it is most likely that she and her sister, together known as the Tumat Puppies, had just been fed the meat of a woolly rhinoceros (Coelodonta antiquitatis) by their mother when their den collapsed, entombing the siblings in permafrost for 14,400 years.

The first of the puppies was found at the site in 2011 and the second in 2015. A dissection of the stomach contents of one of the puppies yielded a piece of woolly rhinoceros flesh.

Edana Lord at Stockholm University in Sweden, a member of the team that studied the fragment, says it looked pretty much “like a piece of jerky with a bit of fluff”.

“It had the hair on it still, which was quite unusual,” says Lord.

She says the fragment was preserved through an almost miraculous and vanishingly rare series of coincidences.

“For us, many, many, many thousands of years later to have uncovered these beautifully preserved mummified wolf puppies, looked into their stomach contents and found this piece of woolly rhinoceros tissue, which has then shed light on an entirely different species, is very unique and cool,” says Lord.

From that fragment, Lord and her colleagues were able to reconstruct the woolly rhino’s genome and determined that it was a female with no signs of inbreeding in the DNA.

This finding is very important, she says, because the species went extinct just a few centuries later and this is the first time that scientists have recovered genetic material from a woolly rhino so close to the date it vanished.

It has long been debated what led to the extinction of the woolly rhinoceros – human hunting pressure, climate change or simply that inbreeding meant that the species was no longer thriving.

Another member of the team, Love Dalén, also at Stockholm University, says that because the fur on the fragment was a yellowish colour, until the DNA work was done, it was thought to have been the remains of a cave lion (Panthera spelaea).

“To my knowledge, sequencing an entire ancient genome from a stomach content sample has never been done before,” says Dalén.

He says the team compared this new genome with two other woolly rhino genomes – one that is around 18,000 years old and the other that is at least 49,000 years old – and found no change in genetic diversity or inbreeding levels through time.

“If there had been a population decline, we would have seen lower diversity and higher inbreeding in the ‘stomach rhino’,” says Dalén.

Instead, the team says the most likely cause of extinction was a rapid period of climatic warming between 14,700 and 12,900 years ago called the Bølling–Allerød interstadial, which would have led to dramatic changes in the woolly rhino’s habitat.