Last week’s DNA Science post considered the ebb and flow of treatment possibilities for Alzheimer’s disease. This week, it’s Huntington’s disease. Like…
Two views of the forces behind extinction of the woolly rhino elegantly illustrate how scientific thinking shifts to embrace new knowledge – a phenomenon that reverberates as new findings about COVID-19 pour in.
Several large animal species (“megafauna”) vanished with the last ice age, including woolly rhinos and mammoths, huge armadillos, cave lions, and sabertooth tigers. The prevailing view of the extinctions blamed overhunting by humans, a scenario that once roughly fit broad timelines. But in a new report in Current Biology, DNA data from preserved rhinos open a window into the past onto climate change. The new view charts the ebb and flow of long-ago rhino populations, while identifying specific gene variants that flesh out how well the animals had been adapted to the cold – putting them at a disadvantage when the climate warmed.
It’s interesting to contrast how different types of data support different conclusions.
The Old View, From Statistics
Five years ago, researchers from the universities of Exeter and Cambridge compared extinction times for megafauna, approximate dates of human settlements in specific geographical areas, and high‐resolution climate reconstructions extending back 90,000 years. The decline of the giant mammals began about 80,000 years ago and all were extinct by 10,000 years ago. The woolly rhinos were gone by about 14,000 years ago.
“Early humans were the dominant cause of the extinction of a variety of species of giant beasts,” the researchers concluded in a news release about their article in the journal Ecography.
Their certainty is disturbing. Said co-author Lewis Bartlett: “As far as we are concerned, this research is the nail in the coffin of this 50-year debate – humans were the dominant cause of the extinction of megafauna.” He added, however, that the study didn’t reveal how, exactly, the extinctions happened.
Did people have mammoth roasts? Set fires? Drive the animals from their habitats in other ways? “Our analysis doesn’t differentiate, but we can say that it was caused by human activity more than by climate change. It debunks the myth of early humans living in harmony with nature,” Bartlett maintained.
I think it’s a jump from being in the same place and time as an event to causing the event.
The New View, From Genomes
In the just-published report, a team from Stockholm University and the Swedish Museum of Natural History scrutinized DNA from tissue, bone, and hair from 14 woolly rhinoceroses preserved in Siberia. “We sequenced a complete nuclear genome to look back in time and estimate population sizes, and we also sequenced 14 mitochondrial genomes to estimate the female effective population sizes,” said co-first author Edana Lord, from the Centre for Palaeogenetics at the museum. “Mitogenomes” are passed only from females, and are used to trace lineages across time and geography.
The complete genome sequence came from a rhino that perished 18,500 years ago, about 4,500 years before the extinction. The investigators searched among the nearly 20,000 genes for variants (caused by mutation) that replace one amino acid with another, changing a function, or that remove DNA, leading to a “loss-of-function.”
The variants hailed from 89 genes that reveal the marks of positive natural selection: changes that confer an advantage, such as adaptation to environmental stress. The 89 genes partake in basic requirements for life, including cell division, development, metabolism, and response to stimuli.
One gene stood out as a beacon of climate change: TRPA1, which encodes an ion channel. Woolly rhinos and mammoths have a loss-of-function mutation that controls perception of, and tolerance to, cold. So when temperatures warmed across Eurasia during a brief period 14,690 to 12,890 years ago called the Bølling-Allerød interstadial, just as the last ice age was sputtering out, the woolly rhinos found themselves ill-adapted to the encroaching fledgling forests.
Modern rhinos can’t sweat and they become lethargic in the heat, so perhaps their hairy ancestors couldn’t survive the warming period, ushering in their extinction as the glaciers melted.
Comparing genome regions among the rhino samples revealed as much genetic diversity as seen in non-African humans today, and more than in mammoths or in modern northern or southern white rhinoceroses. That indicates minimal inbreeding, with presumably populations large and healthy enough to roam about and mate. The mitogenome findings support that view: 781,000 to 126,000 years ago, woolly rhino populations diverged and coalesced repeatedly. (Mutation rates of certain well-studied genes are used as evolutionary “clocks” to estimate time.)
A narrative emerged from the DNA data. About 29,000 years ago a cold period ensued. The cold-adapted woolly rhino populations grew and then remained constant, the animals numerous, mobile, and healthy enough to not have to procreate with their close relatives. Their numbers remained strong until long after people came to Siberia, arguing against the overhunting hypothesis.
“It was initially thought that humans appeared in northeastern Siberia 14,000 or 15,000 years ago, around when the woolly rhinoceros went extinct. But recently, there have been several discoveries of much older human occupation sites, the most famous around 30,000 years old. So the decline towards extinction of the woolly rhinoceros doesn’t coincide with the first appearance of humans in the region. We actually see an increase in population size during this period,” said author Love Dalén, a professor of evolutionary genetics.
“We’re coming away from the idea of humans taking over everything as soon as they come into an environment. Although we can’t rule out human involvement, we suggest that the woolly rhinoceros’ extinction was more likely related to climate,” said Lord. That’s an appropriately-qualified “conclusion.”
The researchers are digging up more rhinos, and probing the genomes of other cold-adapted megafauna, to see if, and how, climate change might have affected them.