Million-year-old mammoth DNA sequenced

Scientists have extracted and sequenced DNA from mammoth specimens that are more than a million years old, the oldest genetic material analyzed to date.

Why it matters: The study pushes back how far researchers can trace genetic changes, allowing them to capture the variations in DNA that occur as new species emerge.

It's "quite close to the limit of what is possible," Love Dalén, an evolutionary geneticist at the Centre for Palaeogenetics in Stockholm and an author of the paper, said in a press briefing Tuesday.

• "We’re confident it is possible to go beyond 1.2 million years — we see that in our data. How much longer is a pure guess. There is no permafrost in the northern hemisphere older than 2.5 million years."

Details: The researchers extracted DNA from mammoth molars discovered in the Siberian permafrost in the 1970s and combed mammoth DNA from microbe DNA in the highly degraded samples.

• They then used algorithms to compare the billions of short mammoth genetic sequences to genomes of African and Asian elephants and other mammoths, and then reassemble the mammoth sequences.
• The researchers dated two of the specimens at around 1.2 million and 1 million years old and a third between 500,000 and 8o0,000 years old, using those DNA sequences and mitochondrial DNA sequences, along with dating of rodents found in the same sediment layers as the mammoth molars.
• Just about 49 million base pairs could be sequenced from the oldest genome, which was found in Krestovka, Siberia. That's "a relatively small fraction of the genome but more than enough to confidently place the genome on the phylogenetic tree," said study co-author Tom van der Valk, also of the Centre for Palaeogenetics.

Background: The first mammoth species were in Africa about five million years ago. During the Pleistocene epoch (which lasted from 2.6 million years ago to 11,7000 years ago and was punctuated by glacial periods), southern and steppe mammoth species emerged and in turn led to the woolly and Columbian mammoths.

The intrigue: The specimens in the new study suggest two different, isolated mammoth populations were in eastern Siberia during the Early Pleistocene, the researchers report today in the journal Nature.

• "We can’t say for sure yet, but we think these may represent two different species," van der Valk said in a press release.
• The authors report one population of steppe mammoths may have led to the evolution of the woolly mammoth and the other — a newly discovered lineage seen in the Krestovka sample — was an ancestor to the first mammoths in North America, known as Columbian mammoths. The researchers suggest mammoths from this lineage crossed into North America about 1.5 million years ago.
• Roughly half of the genome of Columbian mammoths could be traced to the woolly mammoth and half to the Krestovka lineage, the result of two different species meeting and hybridizing about 420,000 years ago.

• Other species hybridize — polar and brown bears, humans and Neanderthals — but the Columbian mammoth interestingly maintained a roughly equal split in its genome for hundreds of thousands of year, the researchers said. (For comparison, just a few percent of the genome of modern humans is Neanderthal.)

The big picture: Researchers want to understand the genetic changes that occur as animals adapt to their environments and new species arise.

• The study found hints in the two younger DNA sequences of when woolly mammoths adapted to their cold environments. The genetic variants associated with thermoregulation, altered circadian clocks and a lot of thick hair were already present in the one-million-year-old genome from the woolly mammoth's ancestor.
• "We don’t think there was one shot rapid burst of adaptation that led to woolly mammoth but a gradual process," says Valk.
• Dalen said the group is "working on other mammoth genomes from closer to the extinction date to investigate exactly what happened at the very end."

What's next: The researchers said they plan to also look at other species of mammals — for example, small rodents, horses, and musk ox — that emerged more than a million years ago to understand "the origins of the species we see today," Dalen said.