Researchers from the Centre for Palaeogenetics have managed to analyse the genome from a 14,400-year-old woolly rhinoceros, recovered from a tissue sample found preserved inside the stomach of an ancient wolf. The study, published in Genome Biology and Evolution, 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 demographic decline.
"Sequencing the entire genome of an Ice Age animal found in the stomach of another animal has never been done before," says the study's last author, Camilo Chacón-Duque, until recently researcher at the Centre for Palaeogenetics. The Centre for Palaeogenetics 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," he says.
Unusual DNA source
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 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.
Genetic stability until the species died out
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," says Edana Lord, formerly a postdoctoral researcher at the Centre for Palaeogenetics.
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.
