Million-year-old DNA data from molars reveals unexpected mammoth origins

February 17, 2021

A woolly mammoth tusk emerges from permafrost on central Wrangel Island, located in northeastern Siberia.(Love Dalén)

A study published in Nature on Wednesday reports that the oldest DNA information ever recorded, from up to 1.65 million years ago, was extracted from the molars of mammoth specimens, one of which belonged to a previously unknown lineage.

The study offers new insights into the evolution of mammoths, from their origins to extinction. It also advances the use of mammoth evolution as a model to study a wide range of species origins. 

The international team of researchers leveraged DNA sequencing and reported the recovery of DNA from the molars of three mammoth specimens from the Early and Middle Pleistocene subepochs in northeast Siberia. The first, and potentially oldest, sample was linked to a previously unrecognized lineage, dubbed the Krestovka mammoth. The second specimen in the study was the Adycha mammoth, at approximately 1.34 million years old, followed by the Chukochya mammoth at about 870,000 years old.

Love Dalén, a professor in evolutionary genetics at the Centre for Palaeogenetics in Stockholm, and Tom van der Valk, a postdoctoral researcher also at the center, which is a joint venture between Stockholm University and the Swedish Museum of Natural History, spoke to reporters Tuesday about their findings. 

“This is, with a wide margin, the oldest DNA ever recovered," Dalén said.

The precise age of the Krestovka sample is not clear, however. Researchers said that because of their wide confidence interval, the specimen could be between 1.2 million and 1.65 million years old.

Dalén said there are "at least two reasonable explanations" for the difference.

“One is that the Krestovka specimen actually is 1.6 million years old, but it had been reworked," he said. That means that at some point, the specimen fell out of the permafrost where it was buried, only to be smothered again by sediment that does not date back that far.

“We do think this is quite unlikely because there are no other mammoths that we know of that have been found at that age," Dalén acknowledged. "The alternative explanation is that we have slightly underestimated the molecular clock rate." That would mean that the sample is younger.

With the aim of the study being to recover genomes from before and after the woolly mammoth originated, researchers expected the two oldest specimens to be from the steppe mammoth, a direct ancestor of the woolly. 

“This ancestral relationship is indeed what we found for one of the million-year-old specimens,” Dalén said. But the team was surprised to find that the other specimen belonged to Krestovka, which diverged from the woolly mammoth more than 2 million years ago.

“Our hypothesis now is that we believe that it was the Krestovka mammoth that first migrated to North America about 1.5 million years ago," Valk said. 

The study also dates a later migration of the woolly mammoth to around 4,000 to 5,000 years ago. 

“These two lineages hybridized and formed what we now call the Colombian mammoth,” Valk said.

The discoveries reported in the study raise the prospect of bridging a gap in DNA research. With theoretical models suggesting that ancient DNA can be reconstructed, researchers explored evolutionary processes that further deepen their understanding of prehistoric populations. Such evolutionary processes include speciation, the process by which new and distinct species form. 

A leg bone of a horse dating from 780,000 to 560,000 years ago is among the oldest previously sequenced DNA, as a 2013 study published in Nature reported. In 2019, another study from Nature described the tooth enamel of a rhinoceros living 1.7 million years ago.

Yet both of those studies sequenced proteins, rather than the DNA itself. Dalén, who also coauthored the 2019 study, maintained confidence that the newly recovered DNA in the mammoth specimens is the oldest ever recorded, thanks to the process of DNA sequencing. 

The process wasn't without its challenges, Dalén said. 

The DNA “was extremely degraded into very small pieces, and so we had to sequence many billions of ultra-short DNA sequences in order to puzzle these genomes together,” he said. “It has taken quite a lot of effort to do this.”

But the extraction of billions of markers in the study will allow the researchers to further study other species. This includes lemmings and a small rodent, among others, they said.

The paper, “Million-year-old DNA sheds light on the genomic history of mammoths,” was published in Nature on Feb. 17. The authors of the study are Love Dalén, Tom van der Valk, David Díez-del-Molino, Marianne Dehasque and Anders Götherström, Centre for Palaeogenetics; Patrícia Pečnerová, Swedish Museum of Natural History; Anders Bergström and Pontus Skoglund, The Francis Crick Institute; Jonas Oppenheimer and Beth Shapiro, University of California Santa Cruz; Stefanie Hartmann, Georgios Xenikoudakis, Jessica A. Thomas and Michael Hofreiter, University of Potsdam; Ekin Sağlıcan, Fatma Rabia Fidan and Mehmet Somel, Middle East Technical University; Ian Barnes and Adrian M. Lister, Natural History Museum, London; Shanlin Liu, China Agricultural University; Peter D. Heintzman, The Arctic University of Norway; and Pavel Nikolskiy, Russian Academy of Sciences.

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