Scientists Extract DNA Over a Million Years Old From Frozen Mammoths

First shock from genetic analysis of three ancient mammoths: Siberia had two lineages of steppe mammoth. Second surprise: The North American mammoth was a hybrid

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Reconstruction of the steppe mammoths that preceded the woolly mammoth, based on the genetic knowledge we now have from the Adycha mammoth.
Reconstruction of the steppe mammoths that preceded the woolly mammoth, based on the genetic knowledge we now have from the Adycha mammoth.Credit: Illustration: Beth Zaiken/Centre for Parthenogenesis

Scientists have retrieved DNA from mammoths that had lain in the Siberian permafrost for over a million years, in an elephantine leap forward for the study of ancient DNA.

The previous record was held by a horse who lived three-quarters to half a million years ago, whose genome was retrieved and analyzed in 2013.

Analysis of the whole genomes from two mammoths dating to more than 1.2 million years, and one that died “only” 900,000 years ago, showed there had been two distinct mammoth lineages in northern Siberia over a million years ago, Tom van der Valk and Love Dalén of the Swedish Center for Paleogenetics with colleagues reported in Nature on Wednesday. The two mammoth lineages may not even have been the same species.

That was a shock. Science had thought there was only one lineage of steppe mammoth in Siberia at that time, van der Valk explains.

The mammoths’ ages were estimated using geological data and the genetic “molecular clock.” Some data indicates that the mammoth dubbed Krestovka lived as long as 1.65 million years ago, but the more reliable date seems to be around 1.2 million years, the scientists say.

A woolly mammoth tusk emerging from permafrost on central Wrangel Island, located in northeastern Siberia.Credit: Love Dalén

Krestovka’s body may have moved in the sediment during its eons in the ice, during which time ice ages came and went. That could be the reason underlying discrepancy between the geological and molecular clock results, the scientists suggest. 

The mammoth lineage dubbed Adycha also lived over a million years ago, and the Chukochya line walked the planet about 900,000 to 700,000 years ago.

The oldest one, Krestovka, was a previously unknown lineage of steppe mammoth, which diverged from other mammoths more than 2 million years ago. The Krestovka line was not ancestral to woolly mammoths.

No. 2, Adycha, was also a type of steppe mammoth – albeit a different one – and was ancestral to woolly mammoths.

No. 3, Chukochya, was either a woolly precursor or was an actual early woolly mammoth. We note that the long-furred proboscids began to appear in the fossil record about 700,000 years ago.

Young mammoth (cast) discovered in Siberian permafrost, Royal Belgian Institute of Natural Sciences, Brussels.Credit: Ben2

Were Krestovka and Adycha/Chukochya not only different lineages but different species? They aren’t sure, van der Valk says. But it is now clearer that the steppe mammoth – not the Krestovka lineage but the Adycha lineage – begat the woolly mammoth.

These are not the first mammoth genomes to be published, but they are by far the oldest. It bears adding that the achievement is an extraordinary one. The mammals had to have remained frozen throughout, and even so, their DNA had become degraded. The ice slows decay, but doesn’t stop it entirely.

One question the new study resolved is when the mammoth species adapted to the arctic conditions, and the answer is: early. “We wanted to pinpoint when the adaptations occurredUp to now it was speculative,” van der Valk says: Did it happen in the ancestral steppe mammoth, or the later woolly mammoth?

Now we know. “We found many of the adaptations were present in the million-year-old steppe mammoth,” he says. “We don’t think there was one short rapid burst of adaptations, but rather, there had been a gradual process of adapting to the cold arctic environment.”

Another big surprise was that the mammoth who colonized North America about 1.5 million years ago, the Columbian mammoth (Mammuthus columbi), was a hybrid.

Size comparison of mammoth species. M. primigenius (3.4 meters), M. exilis (1.8 meters), M. columbi, M. trogontherii, and M. meridionalis (4 meters).Credit: Lister, A.; Bahn, P. (2007). Mam

Its main lineage was Krestovkan. But its genome has the signatures of not one but two admixtures with the Adycha lineage – one a very late event, only after the woolly mammoth itself also made the trip to America over the Beringia land bridge about 100,000 years ago.

It begs noting that when these mammoths lived, modern humans hadn’t even begun to evolve. It also bears noting that in the hominin line, Neanderthals, Denisovans and modern humans all interbred too, leading to arguments over the definition of “species.” (If belonging to different species means that offspring would be infertile, then we and the Neaderthals and Denisovans were the same species.)

Out of Africa, through Bethlehem

The story of the elephant group begins in Africa. That is where all elephants, like all humans, originated, starting around 7 million years ago. The ancestral African savannah elephant line and ancestral mammoth line are believed to have diverged around 5.3 million years ago.

Both elephants and mammoths spread northward out of Africa to Eurasia. And they did so via the Levant. Along this migration of primitive elephants out of Africa, two sites have been found in Israel so far.

Love Dalén and co-lead author Patrícia Pečnerová with a mammoth tusk on Wrangel Island.Credit: Gleb Danilov

Decades ago, the earliest known remains of proboscideans outside Africa were found in Bethlehem, of all places. The discovery was excavated in 1934 by the geologist Elinor Gardner and the paleontologist Dorothea Bate. The Bethlehem remains are between 3.4 to 3.5 million years old, says paleontologist Prof. Rivka Rabinovich of Hebrew University, who researches elephant evolution, among other things.

Interestingly, it’s hard to tell whether the primitive proboscideans of Bethlehem were mammoths or elephants, she tells Haaretz. Some teeth look more mammoth-like, and one looks more like an ancient elephant. Or the teeth in Bethlehem could have come from some precursor to both – even if elephants and mammoths diverged over 5 million years ago, that doesn’t mean the ancestral species didn’t survive too for a while. Again, note that multiple hominin species coexisted, some in the same place. Also, the fossil record is extremely spotty.

The second Israeli site bearing ancient proboscideans is Erq el Ahmar, right by Kibbutz Gesher in the Jordan Valley, which Rabinovich and colleagues described in 2019.

It has been reported, by Eitan Tchernov and colleagues, that the earliest evidence of hominin exits from Africa were also found in Erq el Ahmar (also spelled Erk): stone tools estimated to date to 2 million years ago, the early Paleolithic. That would theoretically suit the timeline of Homo erectus’ exit from Africa, and separate research has shown that the climate in Israel would have been suitable for the great migration.

However, Rabinovich says that during orderly excavations at Erq el Ahmar, they found no such tools. “There could be, but we are still searching,” she says.

A mammoth tusk discovered on Wrankel Island in 2017. Credit: Love Dalén

Indeed, crude stone tools can be hard to identify, unlike later, more sophisticated efforts. Sometimes a rock is just a rock.

“Israel is on the route for dispersal out of Africa,” Rabinovich points out – for both animals (including we) and plants. And the key value in the latest research is the genetic analysis of the Siberian mammoths. “Through the DNA we understand there was interbreeding, which [we] can’t necessarily identify morphologically,” she explains.

So, to be clear, it seems the primitive proboscideans who passed through Israel about 3.5 million years ago begat the southern mammoth (Mammuthus meridionalis) and the steppe mammoth (Mammuthus trogontherii), which diverged from other mammoths 2.6 million to 1.7 million years ago.

The steppe mammoth begat the woolly mammoth. The steppe and ancestral woolly mammoth commingled, resulting in the Columbian mammoth that colonized North America 1.5 million years ago.

Aficionados would note that there was also a dwarf mammoth, a mere 1.7 meters (5 feet, 7 inches) tall at the shoulder. It lived on the Channel Islands of California and descended from the Columbian mammoth. It isn’t included in this genetic study.

It is frustrating for fans of elephant lines to know that we almost got to know them. Mammoths were still widely found from Spain to Alaska until 15,000 years ago, then disappeared from most areas – apparently due to predation and warming. One group on St. Paul Island in Alaska hung on until 5,600 years ago, and the last population of all, cut off from the mainland by rising sea levels on Wrangel Island in the Arctic Ocean, died out just 4,000 years ago.

Yes, the scientists are working on other ancient species that have been lying peacefully in their permafrost graves. And yes, climate change baking the Arctic has been thawing the permafrost, exposing some of these bodies for the first time in thousands of years. But another reason they’re coming to light is Russians “mining” the permafrost for mammoth tusks, which they sell, the scientists point out. And yes, they dearly, dearly hope to one day find an ancient hominin frozen in ice: an erectus, cross fingers. Homo erectus reached that part of the world almost two million years ago.

That is what the picture looks like at this stage of the game. We add that hominins liked to eat mammoths and did so until the giant animals went extinct.