Genomic study of extinction in progress may give insights into modern conservation.
Isolated on an island in the Arctic Ocean, not only were the world’s last woolly mammoths on their way out, but they were also swamped with ‘bad genes’, possibly losing their sense of smell and acquiring strange translucent coats.
A study1 published today gives a rare insight into how genomes change as a population is dying out. Towars the end of the last Ice Age, around11,700 years ago, woolly mammoths ranged through Siberia and the colder stretches of North America. But by about 4,000 years ago, the mainland mammoths had gone and only a small population remained on Wrangel Island off the Siberian coast. In a paper in PLOS Genetics, biologists Rebekah Rogers and Montgomery Slatkin at the University of California, Berkeley, compare the complete genome of a mainland mammoth (Mammuthus primigenius) that lived about 45,000 years ago with that of a Wrangel Island mammoth from just 4,300 years ago, when a mere 300 woolly mammoths were left. The sequences were made available by Love Dalén at the Swedish Museum of Natural History in Stockholm.
“As I looked at the sequence data,” says Rogers, “it became very clear that the Wrangel mammoth had an excess of what looked like bad mutations.”Some of these changes are only visible to a geneticist’s eye. Compared with the mainland mammoth, in the Wrangel Island specimen some parts of the genome had been deleted and there were too many instances of sequences called stop codons — which tell the body when to stop making proteins — among other changes to the DNA. But some of the changes would also have been visible in the mammoth’s behaviour and appearance.Rogers and Slatkin found that genes related to smell and urinary proteins, which in modern elphants are important for eliciting behaviours like mate choice or signalling social status [chk] were shut down by the mutations. These might be related, the researchers hypothesize, because a duller sense of smell was hitched in a feedback loop to the loss of proteins related to mammoth social status and mate selection. Changes to the Wrangel mammoths’ coats would have been even more obvious. Rogers and Slatkin propose that a mutation in a part of the genome called FOXQ1 would have given the mammoths a ‘satin’ coat, marked by fur that is the same colour as normal but is shiny and translucent.
What happened on Wrangel wasn’t a matter of inbreeding, Rogers says — the genetic signal is different.
“What did happen was that the population was simply small,” she says, and “under these circumstances any mammoth was better than no mammoth at all”, so natural selection did not operate in the usual way. This allowed unhelpful mutations to rack up, following a previously identified phenomenon called nearly neutral genome evolution. “Bad mutations that would normally be weeded out weren’t removed from the population because of reduced competition,” says Rogers.
“Isolation and reducing population size have long been recognized as important factors causing endangerment,” says palaeontologist Ross MacPhee of the American Museum of Natural History in New York City, but the recognition of the mammoth’s “genetic meltdown” is a sign of how far studies of ancient DNA have come, and the work that still lies ahead.
The changes on Wrangel Island took place after mammoths had already been wiped out on the mainland. Tracking the downfall of the larger population is an ongoing effort, says MacPhee. “With additional specimens, drawn from other times and parts of the woolly mammoths’ enormous range, we may get a better picture of the genetic load that this species was labouring under at the end of its tenure.”
Still, MacPhee adds, the study “is maybe telling us something very important about what happens in populations already under severe threat because of diminished range and numbers”.
Further genetic research will provide more details. Although he points out that no single animal or genome can tell the entire story, MacPhee notes that “it is not unreasonable to think that maybe human hunting, climate change or any other external factor on the table was insufficient to cause complete losses at the end of the Pleistocene unless there was some powerful cofactor operating within the animals themselves”.
As dramatic as genetic meltdown sounds, Rogers says that it’s difficult to tell whether the increase in bad mutations contributed directly to the final extinction of the woolly mammoth. Yet the findings have implications for the survival of the mammoths’ elephant cousins and other endangered mammals. Rogers notes that it’s better to prevent a species from becoming endangered in the first place than to try to recover its genetic diversity after a sharp plummet.
“Even though we can improve the number of individuals in endangered populations,” she says, “their genomes may still bear the hallmarks of genomic meltdown, which will be difficult to undo.”
Rogers, R. L. & Slatkin, M. PLoS Genet. 13, e1006601 (2017).
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Center for Theoretical Evolutionary Genomics, University of California Berkeley
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Switek, B. Dying woolly mammoths were in ‘genetic meltdown’. Nature (2017). https://doi.org/10.1038/nature.2017.21575