What can a predator’s last meal reveal that a fossil shelf cannot? In the Siberian steppe, a small accident had created an exceptionally rich fossil record. A grey wolf pup, only weeks old, had eaten flesh from a woolly rhinoceros and died so quickly that digestion had hardly begun. When the pup was found near the village of Tumat, still frozen in permafrost, its stomach held a piece of tissue with hair strands still intact an unlikely time capsule from the end of the Ice Age.
However, this fragment was more than just a prey identifier. By isolating genetic material from the undigested flesh, scientists were able to reconstruct an entire woolly rhinoceros genome from within another creature’s stomach, an achievement that was celebrated as the first complete genome to be extracted from stomach contents. “Sequencing the entire genome of an Ice Age animal found in the stomach of another animal has never been done before,” said Camilo Chacón-Duque. The problem was not simply one of age, as both predator and prey were ancient. Therefore, approaches that are common in distinguishing DNA, such as differences in damage patterns to distinguish between sources, were less relevant. Instead, the team used comparative genomics, using the Sumatran rhinoceros as a “living guide” to reconstruct the genetic code of the woolly rhinoceros, filtering out wolf DNA in the process.
Permafrost makes such a reconstruction possible because it prevents the degradation of the molecules, which would otherwise happen. In the coldest parts of the northern deposits, DNA has been found that is 2 million years old, but the issue of engineering is not so much survival as it is contamination, degradation, and mixture. A stomach is a very complex record because it includes predator cells, prey tissue, microbes, and environmental debris, all of which are mixed together and then frozen in the midst of all this activity. The Tumat pup’s diet was just what was needed because the collapse of the den appears to have been so sudden that the tissue was barely changed, so that a genome-quality signal was retained.
With the genome on the table, the most fascinating thing about this research was not the new picture of a shaggy herbivore but rather the new insight into the mechanism of extinction itself. By comparing this individual, who lived about 14,400 years ago, to two other genomes of the woolly rhino that were 18,000 and 49,000 years old, the researchers were able to observe how the levels of diversity and inbreeding changed over tens of thousands of years. The expectation would be that a species on the brink of extinction would be genetically stressed, says Nathan Wales, who studied the pups but did not contribute to the rhino analysis. “one might assume the last lineages would have small populations and were highly inbred. But this well-established analysis shows that at a genetic level, the population looked stable.”
This makes the question of why the woolly rhinoceros became extinct take on a whole new meaning. The genome indicates not a gradual extinction but a more sudden one a rapid extinction, despite the fact that the species was genetically sound almost until the very end. The implications of this discovery were encapsulated by Love Dalén in the following words of the study itself: “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.”
The bigger picture is encapsulated in the process. The Tumat pups also included plants, insects, and bird tissue, which indicated that permafrost mummies could potentially link genetics to diet and environment in the same individual, rather than simply linking these to genetics based on fossil evidence. For evidence engineers, researchers who build datasets from noisy, mixed, and small signals, the wolf pup’s stomach contents demonstrate how an unusual dataset could potentially fill the missing time point that fossils so often cannot.
