An international team of researchers has sequenced and analyzed a complete nuclear genome and 14 mitochondrial genomes from the extinct woolly rhinoceros (Coelodonta antiquitatis) and found that its population remained stable and diverse until only a few thousand years before it disappeared from Siberia, when temperatures likely rose too high for the cold-adapted species.
The woolly rhinoceros was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene epoch.
This species first appeared some 350,000 years ago and became extinct approximately 14,000 years ago.
The woolly rhinoceros fossils are fairly common and have been discovered throughout Europe and Asia. Well-preserved remains have been found frozen in ice and buried in oil-saturated soils.
In Ukraine, a complete carcass of a female woolly rhinoceros was discovered buried in the mud. The combination of oil and salt prevented the remains from decomposing, allowing the soft tissues to remain intact.
While humans and climate change have been proposed as potential causes of its extinctions, knowledge is limited on how this ancient creature was impacted by human arrival and climatic fluctuations.
“It was initially thought that humans appeared in northeastern Siberia 14,000-15,000 years ago, around when the woolly rhinoceros went extinct,” said Professor Love Dalén, a researcher at the Centre for Palaeogenetics, a joint venture between Stockholm University and the Swedish Museum of Natural History.
“But recently, there have been several discoveries of much older human occupation sites, the most famous of which is around thirty thousand years old.”
“So, the decline towards extinction of the woolly rhinoceros doesn’t coincide so much with the first appearance of humans in the region.”
“If anything, we actually see something looking a bit like an increase in population size during this period.”
To investigate the demographic history of the woolly rhinoceros leading up to its extinction, Professor Dalén and colleagues studied DNA from tissue, bone, and hair samples of 14 individuals.
“We sequenced a complete nuclear genome to look back in time and estimate population sizes, and we also sequenced fourteen mitochondrial genomes to estimate the female effective population sizes,” said Edana Lord, a Ph.D. student at the Centre for Palaeogenetics.
By looking at the heterozygosity, or genetic diversity, of these genomes, the researchers were able to estimate the woolly rhino populations for tens of thousands of years before their extinction.
“We examined changes in population size and estimated inbreeding,” said Dr. Nicolas Dussex, a postdoctoral researcher at the Centre for Palaeogenetics.
“We found that after an increase in population size at the start of a cold period some 29,000 years ago, the woolly rhino population size remained constant and that at this time, inbreeding was low.”
This stability lasted until well after humans began living in Siberia, contrasting the declines that would be expected if the woolly rhinos went extinct due to hunting.
“That’s the interesting thing. We actually don’t see a decrease in population size after 29,000 years ago,” Lord said.
“The data we looked at only goes up to 18,500 years ago, which is approximately 4,500 years before their extinction, so it implies that they declined sometime in that gap.”
The DNA data also revealed genetic mutations that helped the woolly rhinoceros adapt to colder weather.
One of these mutations, a type of receptor in the skin for sensing warm and cold temperatures, has also been found in woolly mammoths.
Adaptations like this suggest the woolly rhinoceros, which was particularly suited to the frigid northeast Siberian climate, may have declined due to the heat of a brief warming period, known as the Bølling-Allerød interstadial, that coincided with their extinction towards the end of the last Ice Age.
“We’re coming away from the idea of humans taking over everything as soon as they come into an environment, and instead elucidating the role of climate in megafaunal extinctions,” Lord said.
“Although we can’t rule out human involvement, we suggest that the woolly rhinoceros’ extinction was more likely related to climate.”
The results were published in the journal Current Biology.
Edana Lord et al. Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros. Current Biology, published online August 13, 2020; doi: 10.1016/j.cub.2020.07.046