From the teeth of three ancient mammoths that roamed Siberia between 700,000 and 1.2 million years ago, the researchers extracted extremely degraded DNA and pieced it back together to reveal a previously unknown genetic mammoth lineage.
Previously, the oldest recovered DNA sample was from a horse bone found in the Yukon permafrost, dating back to between 560,000 and 780,000 years ago.
"This DNA is incredibly old," said evolutionary geneticist Love Dalén of the Centre for Palaeogenetics in Sweden. "The samples are a thousand times older than Viking remains, and even pre-date the existence of humans and Neanderthals."
Around a million years ago, even woolly mammoths (Mammuthus primigenius) didn't exist yet. The well-known and beloved beasts didn't start to emerge until around 800,000 years ago, living in Earth's frozen climates until they finally went extinct around 4,000 years ago.
Because this is relatively recent, in geological time, and because they preferred cold habitats (which better preserve remains), we know a fair bit about these ancient creatures.
Woolly mammoths existed alongside Columbian mammoths (M. columbi), which inhabited North America and died out around 11,500 years ago.
Their predecessors, the mammoths that woolly mammoths evolved from, are less well known. We know that woolly mammoths are descended from steppe mammoths (M. trogontherii), which roamed over most of Eurasia up until about 200,000 years ago. We also thought that Columbian mammoths were descended from steppe mammoths that had crossed over into North America around 1.5 million years ago.
In an attempt to learn more about this ancestor, the scientists turned mammoth genealogy on its head.
The three mammoth teeth from which they extracted DNA were excavated decades ago and had been carefully kept in a museum collection. The youngest, at 700,000 years old, belonged to a woolly mammoth - one of the earliest known. The older two, at over 1 million years old, were expected to belong to the steppe mammoth.
Through painstaking restoration and comparative efforts, the researchers were able to piece together and sequence the DNA that had been preserved inside the hard enamel of the animals' teeth. The second-oldest of the three specimens, found in Adycha, bore this out: it was very close to steppe mammoth in morphology and DNA.
The oldest specimen, found in Krestovka and dating from around 1.6 million years ago, was more surprising. It turned out to belong to a previously unknown genetic mammoth lineage that diverged from a common ancestor more than 2 million years ago.
"This came as a complete surprise to us," said geneticist Tom van der Valk of Uppsala University in Sweden.
"All previous studies have indicated that there were only one species of mammoth in Siberia at that point in time, called the steppe mammoth. But our DNA analyses now show that there were two different genetic lineages, which we here refer to as the Adycha mammoth and the Krestovka mammoth. We can't say for sure yet, but we think these may represent two different species."
It gets even more interesting. By comparing the DNA of these ancient mammoths to those that came later, the researchers found it could have been the Krestovka mammoth that crossed the Bering Land Bridge into North America 1.5 million years ago, not the steppe mammoth.
The Columbian mammoth's DNA has a mixture of Krestovka and woolly mammoth, suggesting that the two bred when woolly mammoths migrated to North America, producing a hybrid.
"This is an important discovery," said palaeogeneticist Patrícia Pečnerová of the University of Copenhagen in Denmark. "It appears that the Columbian mammoth, one of the most iconic ice age species of North America, evolved through a hybridisation that took place approximately 420 thousand years ago."
The Adycha mammoth, although more in line with expectations, also had some secrets to reveal. By comparing its genome to that of woolly mammoths from 700,000 to a few thousand years ago, the team sought to understand how the woolly mammoth became adapted to a frozen Arctic environment.
The traits associated with that adaptation - genes associated with thermoregulation, hair growth, circadian rhythm, and white and brown fat deposits - were already present in the Adycha genome, well before the woolly mammoth emerged. But the animals continued to evolve, too; the gene involved in sensing temperature, for example, had more variants in later woolly mammoths.
The team's techniques won't work for all remains. The cold temperature of the permafrost slows the degradation of DNA, so remains of a similar age from other locations would likely be too degraded; and, within the permafrost, there is a limit to how far back that DNA is recoverable.
"One of the big questions now is how far back in time we can go. We haven't reached the limit yet," said molecular archaeologist Anders Götherström of the Centre for Palaeogenetics.
"An educated guess would be that we could recover DNA that is 2 million years old, and possibly go even as far back as 2.6 million. Before that, there was no permafrost where ancient DNA could have been preserved."
A lot of preserved creatures have been excavated from Earth's permafrost. The research demonstrates what remarkable discoveries may be lurking in bones previously considered too ancient to try to study.
The research has been published in Nature.