In a feat at the limit of our scientific capabilities, an international team of geneticists has recovered and sequenced the oldest DNA to date.
From the teeth of three ancient mammoths that roamed Siberia between 700,000 and 1.2 million years ago, researchers extracted extremely degraded DNA and reconstructed it to reveal a previously unknown mammoth genetic lineage.
Previously, the oldest recovered DNA sample was from a horse bone found in the Yukon permafrost, dating to between 560,000 and 780,000 years ago.
“This DNA is incredibly old,” said evolutionary geneticist Love Dalén of the Center for Paleogenetics in Sweden. “The samples are a thousand times older than Viking remains, and even predate the existence of humans and Neanderthals.”
About a million years ago, even woolly mammoths (Mammuthus primigenius) did not exist yet. Known and beloved beasts did not begin to emerge until about 800,000 years ago, living in the icy climates of Earth until they finally became extinct about 4,000 years ago.
Because this is relatively recent, in geologic time, and because they preferred cold habitats (which best preserve the remains), we know quite a bit about these ancient creatures.
Woolly mammoths existed alongside Colombian mammoths (M. columbi), which inhabited North America and became extinct about 11,500 years ago.
Their predecessors, the mammoths from which woolly mammoths evolved, are less well known. We know that woolly mammoths are descended from steppe mammoths (M. trogontherii), which roamed most of Eurasia until about 200,000 years ago. We also think that Columbian mammoths were descended from steppe mammoths that had crossed into North America around 1.5 million years ago.
In an attempt to learn more about this ancestor, scientists turned the gigantic genealogy upside down.
The three mammoth teeth from which they extracted DNA were excavated decades ago and carefully kept in a museum collection. The youngest, at 700,000 years old, belonged to a woolly mammoth, one of the first known. The two oldest, 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 DNA that had been preserved within the hard enamel of the animals’ teeth. The second oldest of the three specimens, found at Adycha, confirmed this: it was very close to the steppe mammoth in morphology and DNA.
The oldest specimen, found at Krestovka and dating to 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 was a complete surprise to us,” said geneticist Tom van der Valk of Uppsala University in Sweden.
“All previous studies have indicated that there was only one species of mammoth in Siberia at that time, called the steppe mammoth. But our DNA analyzes 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 they may represent two different species. “
It gets even more interesting. By comparing the DNA of these ancient mammoths with those that came later, the researchers found that it could have been the Krestovka mammoth that crossed the Bering land bridge into North America 1.5 million years ago, not the mammoth of the steppe.
The Columbian mammoth DNA has a mix of Krestovka and woolly mammoth, suggesting that the two were bred when woolly mammoths migrated to North America, producing a hybrid.
“This is an important discovery,” said paleogeneticist Patrícia Pečnerová of the University of Copenhagen in Denmark. “It appears that the Columbian mammoth, one of North America’s most iconic ice age species, evolved through hybridization that took place approximately 420,000 years ago.”
The mammoth Adycha, while more in line with expectations, also had some secrets to reveal. By comparing its genome with that of woolly mammoths from 700,000 to a few thousand years ago, the team sought to understand how the woolly mammoth adapted to an icy 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, long before the woolly mammoth emerged. But the animals also continued to evolve; the gene involved in temperature sensing, for example, had more variants in later woolly mammoths.
Team techniques won’t work for all remains. The cold temperature of the permafrost slows down the degradation of DNA, so remnants of a similar age from elsewhere would probably degrade too much; and, within permafrost, there is a limit to how old DNA is recovered.
“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 Center for Paleogenetics.
“An educated guess would be that we could recover DNA that is 2 million years old, and possibly go back as far as 2.6 million. Before that, there was no permafrost where ancient DNA could have been preserved.”
Many preserved creatures have been excavated from Earth’s permafrost. The research shows what remarkable discoveries may be lurking in bones that were previously considered too old to attempt to study.
The research has been published in Nature.