Scientists have recovered and analysed the genes of a 14,400-year-old woolly rhinoceros preserved inside the stomach of an ancient wolf.
The study, by researchers from Stockholm University, Norwegian University of Science and Technology, Cardiff University, University of Copenhagen, and North-Eastern Federal University, shows that woolly rhinos remained genetically healthy until the end of the last Ice Age. The species therefore probably died out due to a rapid collapse of the population, rather than a slow decline.
"Sequencing the entire genome of an Ice Age animal found in the stomach of another animal has never been done before," says Camilo Chacón-Duque, a researcher at the Centre for Palaeogenetics, which is a collaboration between Stockholm University and the Swedish Museum of Natural History.
Recovering genomes from individuals that lived right before extinction is challenging, but it can provide important clues on what caused the species to disappear, which may also be relevant for the conservation of endangered species today.
The analysed rhinoceros sample comes from the frozen remains of an Ice Age wolf discovered in permafrost near the village of Tumat in north-eastern Siberia. When the ancient wolf was autopsied, the researchers identified a small fragment of preserved tissue in its stomach. Radiocarbon dating revealed the tissue to be approximately 14,400 years old, and DNA sequencing identified it as a woolly rhinoceros (Coelodonta antiquitatis) – one of the youngest specimens of woolly rhinoceros ever discovered.
Mapping the genome from this type of material is extremely difficult. Ancient DNA is typically degraded and occurs in very small amounts, and the presence of predator DNA further complicates the analyses.
"It was a very unusual specimen to work on in the lab," says Dr David Stanton, a researcher at Cardiff University's School of Biosciences, who was working at the Swedish Museum of Natural History at the time.
"It was initially identified as a piece of cave lion tissue, so it was quite a surprise when the genetic analysis showed that it was actually a woolly rhinoceros.
"When the radiocarbon date came back, we realised how unique the specimen was. The date estimate, very close to when woolly rhinos went extinct, made it incredibly valuable for understanding how and why so many species went extinct at the time."
"It was really exciting, but also very challenging, to extract a complete genome from such an unusual sample," says student Sólveig Guðjónsdóttir, the study's lead author, who carried out the work as part of her master's thesis at Stockholm University.
The research team compared the Tumat rhinoceros' genome with two other high-quality genomes from older specimens, dated to around 18,000 and 49,000 years ago, respectively. These comparisons allowed the researchers to examine how genome diversity, inbreeding levels, and the number of harmful mutations changed through time during the last Ice Age. They found no signs of genetic deterioration as the species approached extinction. This indicates that the woolly rhinoceros probably maintained a stable and relatively large population until just before the species disappeared.
Our analyses showed a surprisingly stable genetic pattern with no change in inbreeding levels through tens of thousands of years prior to the extinction of woolly rhinos.
The researchers saw no signs in the genome that would indicate a long-term gradual population decline. The extinction therefore appears to have occurred relatively quickly, probably caused by global warming at the end of the Ice Age.
"Our results show that the woolly rhinos had a viable population for 15,000 years after the first humans arrived in northeastern Siberia, which suggests that climate warming rather than human hunting caused the extinction," says Love Dalén, professor of evolutionary genomics at the Centre for Palaeogenetics.
The research, Genome shows no recent inbreeding in near-extinction woolly rhinoceros sample found in ancient wolf's stomach, was published in Genome Biology and Evolution.
