DNA from mammoth remains reveals the history of the last surviving population

A small group of woolly mammoths became trapped on Wrangel Island around 10,000 years ago when rising sea levels separated the island from mainland Siberia. Small, isolated populations of animals lead to inbreeding and genetic defects, and it has long been thought that the Wrangel Island mammoths ultimately succumbed to this problem about 4,000 years ago.

A paper in Cell on Thursday, however, compared 50,000 years of genomes from mainland and isolated Wrangel Island mammoths and found that this was not the case. What the authors of the paper discovered not only challenges our understanding of this isolated group of mammoths and the evolution of small populations, it also has important implications for conservation efforts today.

A severe bottleneck

It’s the culmination of years of genetic sequencing by members of the international team behind this new paper. They studied 21 mammoth genomes—13 of which were newly sequenced by lead author Marianne Dehasque; others had been sequenced years prior by co-authors Patrícia Pečnerová, Foteini Kanellidou, and Héloïse Muller. The genomes were obtained from Siberian woolly mammoths (Mammuthus primigenius), both from the mainland and the island before and after it became isolated. The oldest genome was from a female Siberian mammoth who died about 52,300 years ago. The youngest were from Wrangel Island male mammoths who perished right around the time the last of these mammoths died out (one of them died just 4,333 years ago).

It’s a remarkable and revealing time span: The sample included mammoths from a population that started out large and genetically healthy, went through isolation, and eventually went extinct.

Mammoths, the team noted in their paper, experienced a “climatically turbulent period,” particularly during an episode of rapid warming called the Bølling-Allerød interstadial (approximately 14,700 to 12,900 years ago)—a time that others have suggested might have led to local woolly mammoth extinctions. However, the genomes of mammoths studied through this time period don’t indicate that the warming had any adverse effects.

Adverse effects only appeared—and drastically so—once the population was isolated on that island.

The team's simulations indicate that, at its smallest, the total population of Wrangel Island mammoths was fewer than 10 individuals. This represents a severe population bottleneck. This was seen genetically through increased runs of homozygosity within the genome, caused when both parents contribute nearly identical chromosomes, both derived from a recent ancestor. The runs of homozygosity within isolated Wrangel Island mammoths were four times as great as those before sea levels rose.

Despite that dangerously tiny number of mammoths, they recovered. The population size, as well as inbreeding level and genetic diversity, remained stable for the next 6,000 years until their extinction. Unlike the initial population bottleneck, genomic signatures over time seem to indicate inbreeding eventually shifted to pairings of more distant relatives, suggesting either a larger mammoth population or a change in behavior.

Within 20 generations, their simulations indicate, the population size would have increased to about 200–300 mammoths. This is consistent with the slower decrease in heterozygosity that they found in the genome.

Long-lasting negative effects

The Wrangel Island mammoths may have survived despite the odds, and harmful genetic defects may not have been the reason for their extinction, but the research suggests their story is complicated.

At about 7,608 square kilometers today, a bit larger than the island of Crete, Wrangel Island would have offered a fair amount of space and resources, although these were large animals. For 6,000 years following their isolation, for example, they suffered from inbreeding depression, which refers to increased mortality as a result of inbreeding and its resulting defects.

That inbreeding also boosted the purging of harmful mutations. That may sound like a good thing—and it can be—but it typically occurs because individuals carrying two copies of harmful mutations die or fail to reproduce. So it’s good only if the population survives it.

The team’s results show that purging genetic mutations can be a lengthy evolutionary process. Lead author Marianne Dehasque is a paleogeneticist who completed her PhD at the Centre for Palaeogenetics. She explained to Ars that, “Purging harmful mutations for over 6,000 years basically indicates long-lasting negative effects caused by these extremely harmful mutations. Since purging in the Wrangel Island population went on for such a long time, it indicates that the population was experiencing negative effects from these mutations up until its extinction.”

Co-author Love Dalén is a professor of evolutionary genomics at the Centre for Palaeogenetics in Stockholm. He said “When individuals have a double copy of harmful mutations (e.g., inherited from both parents that are related) these individuals become sick. And this subsequently means that these mutations are removed from the population through natural selection.” In other words, they die, but they take harmful mutations with them.

“We also see that mildly harmful mutations accumulate in the population up until its extinction,” Dehasque added. “The higher the amount of mildly harmful mutations, the bigger the potential negative fitness effects.” These might have ultimately led to the population’s end, either directly or by making it more vulnerable to environmental changes.

Vincent Lynch, associate professor at the University of Buffalo, was also not involved in the research, but he was part of a team that did earlier genetic research on Wrangel Island mammoths.

He was surprised by the results of this paper, noting that even with the persistent genetic impacts of inbreeding depression, they continued to survive. And, he said, he liked the two suggestions the team made about what may have caused their eventual extinction. In one, “the accumulation of many [harmful] mutations of small effects added up to a burden they couldn’t afford,” a scenario he compared to the straw that broke the horse’s back. In the other, “it is also possible they didn’t have the genetic diversity needed to deal with a sudden change in the climate or the introduction of an infectious disease (like white-nose syndrome in little brown bats); or some combination of these,” he explained.

And then they were gone

While the results of the research don’t elucidate the reason behind the Wrangel Island mammoth extinction, they do indicate it happened remarkably fast.

“From archeological evidence, we know that humans only arrived after mammoths went extinct,” Dehasque said,  “Something sudden like disease or a fire could have definitely caused the population to collapse, but this remains very speculative. With more research we will hopefully unravel in the near future what caused the mammoth’s final extinction.”

Are there lessons for current populations in this data? This bird’s-eye view of genetic changes over thousands of years is in stark contrast to current conservation studies of similarly isolated populations, where scientists have access to only a handful of generations’ worth of genetics to study.  This is significant because the long-term genetic effects of these mammoths show that “just restoring population size may not be sufficient to ensure a viable population,” Dehasque said.

At a time when the habitats for many forms of life are shrinking, climate change is impacting the world, and there are increasing numbers of endangered species, it is more important than ever to understand possible extinction risks.

“Conservation biologists have, in the past, thought that as long as one brings the population size up to a level where inbreeding doesn’t increase (and genetic diversity stops going down), then the genetic threat has been largely removed,” Dalén said. “But our results show that even when inbreeding/diversity has been stabilized, the population will still continue to be affected by inbreeding depression for hundreds of generations.”

“This is not good news for endangered species. However, when we now know this, we can factor this into models that predict extinction risks,” he continued. “Moreover, we can in some cases take actions such as facilitating gene flow between populations in order to bring inbreeding levels down.”

Jacqueline Robinson is an evolutionary geneticist at the University of California San Francisco. She was not involved in the research, but her work on island foxes was referenced in this paper. She told Ars that she was “fascinated and impressed” by this research, noting that it’s “a valuable study for how this process—bottleneck and long-term isolation—has played out over time. We can study contemporary populations all we want, but we’re not going to be able to see what the impacts of their population decline will be in the future. We can make predictions. But that’s different than being able to actually look at something that has happened in the past and directly observe those effects.”

She finds it “very encouraging” that the Wrangel Island mammoths stabilized after a severe population bottleneck, as it indicates species in similar circumstances today might do the same. “To me,” she said, “it’s a sign that species and populations are more resilient than we would expect. I just feel like it gives us more hope and greater reasons to invest in protecting species that have declined to unfortunately small numbers.”

Robinson says this research “will hopefully further boost the message that we shouldn’t give up on populations” even if their numbers are tiny.

A near miss?

For Dalén, who started working on Wrangel Island mammoth DNA more than 20 years ago, there are two key takeaways from this research, the first of which is “that bottlenecks cause a genetic debt in the form of harmful mutations, and that it can take many thousands of years for this debt to be paid.”

The other key takeaway, he suggested, is “that the mammoth’s extinction seems likely to have been caused by some random environmental event, meaning that perhaps they simply were unlucky. If it hadn’t been for that, we may still have had mammoths living today.”

The idea of their potential continued existence is one that Dehasque considered as well, wondering, “If the mammoths had survived until now, would the harmful mutations have kept accumulating? And how bad would their combined fitness effects have been by now?”

Cell, 2024.  DOI: 10.1016/j.cell.2024.05.033