World’s oldest DNA reveals how mammoths evolved and adapted to different climates

The ability to sequence increasingly ancient DNA samples could open door to further evolutionary discoveries, writes Harry Cockburn

Reconstruction of the steppe mammoths that preceded the woolly mammoth, based on new genetic knowledge from the Adycha mammoth (Beth Zaiken/CPG)

Scientists have sequenced what is thought to be the world’s oldest DNA samples, taken from the ancient steppe mammoth, revealing new information about how later species of mammoth evolved and adapted to different climates.

An international team led by researchers at the Centre for Palaeogenetics in Stockholm sequenced DNA recovered from mammoth remains up to 1.2 million years old.

The analyses found the Columbian mammoth species, which inhabited North America during the last ice age, was a hybrid between the woolly mammoth and a previously unknown genetic lineage of mammoth.

The study also provides clues as to when and how quickly mammoths adapted to colder climates.

The DNA samples, from remains which were in some cases over a million years old, are from a period before either the woolly or Columbian mammoths had evolved.

This was the era of their predecessor, the steppe mammoth. Researchers have now managed to analyse the genomes of three of these ancient mammoths, using DNA recovered from their teeth that had been buried for 0.7-1.2 million years in the Siberian permafrost.

The study marks the first time DNA has been sequenced and authenticated from million-year-old specimens.

Unsurprisingly, extracting the DNA from the samples was challenging. Scientists working on the project said only minuscule amounts of DNA remained in the samples - and even that had degraded into very small fragments.

“This DNA is incredibly old. The samples are a thousand times older than Viking remains, and even pre-date the existence of humans and Neanderthals,” said senior author Love Dalén, a professor of evolutionary genetics at the Centre for Palaeogenetics.

The team worked out the age of the specimens using both local geological data and the molecular clock.

Both of these methods revealed two of the three mammoth specimens are more than one million years old, whereas the third is roughly 700 thousand years old and represents one of the earliest known woolly mammoths.

The steppe mammoth was the largest of all mammoth species to walk the earth, and survived until around 33,000 years ago.

Woolly mammoths emerged later and were roughly the same size as modern African elephants, though with thick coats to maintain warmth in cold regions. The last remaining populations died out around 4,000 years ago.

The analysis of the genomes showed the oldest specimen, which was approximately 1.2 million years old, belonged to a previously unknown genetic lineage of mammoth.

Researchers refer to this as the Krestovka mammoth, based on where it was found. The results show that the Krestovka mammoth diverged from other Siberian mammoths more than two million years ago.

"This came as a complete surprise to us. All previous studies have indicated that there was only one species of mammoth in Siberia at that point in time, called the steppe mammoth,” said the study’s lead author Tom van der Valk.

“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.”

The researchers also suggest it was the mammoths which belonged to the Krestovka lineage that colonised North America some 1.5 million years ago.

In addition, their analysis showed the Columbian mammoth that inhabited North America during the last ice age was a hybrid: roughly half of its genome came from the Krestovka lineage and the other half from the woolly mammoth.

“This is an important discovery,” said co-lead author Patrícia Pečnerová.

“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 420,000 years ago.”

The second million-year-old genome, which the team sequenced from the Adycha mammoth, appears to have been an ancestor to the woolly mammoth.

This has allowed researchers to compare its genome with the genome from one of the earliest known woolly mammoths which lived 700,000 years ago, as well as with mammoth genomes that are just a few thousand years old.

As a result it was possible to investigate how mammoths adapted to a life in cold environments and to what extent these adaptations evolved during speciation - the process under which organisms diverge into new, distinct species.

Their research revealed that specific genetic adaptations associated with life in the Arctic, such as hair growth, thermoregulation, fat deposits, cold tolerance and circadian rhythms, were already present in the million-year-old mammoth, long before the first woolly mammoths emerged.

They said the results indicate that most adaptations in the mammoth lineage happened slowly and gradually over time.

"To be able to trace genetic changes across a speciation event is unique,” said co-lead author David Díez-del-Molino.

“Our analyses show that most cold adaptations were present already in the ancestor of the woolly mammoth, and we find no evidence that natural selection was faster during the speciation process.”

The scientists said the study will “open the door for a broad array of future studies on other species”.

Around a million years ago many species expanded across the globe. This was also a time period of major changes in climate and sea levels, as well as being the last time that Earth’s magnetic poles switched.

The ability to conduct genetic analyses on this time scale could have significant potential to explore a wide range of scientific questions.

“One of the big questions now is how far back in time we can go,” said Anders Götherström, a professor in molecular archaeology and joint research leader at the Centre for Palaeogenetics.

“We haven’t reached the limit yet. An educated guess would be that we could recover DNA that is two 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.”

The research is published in the journal Nature.