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Million-year-old mammoth DNA rewrites animal’s evolutionary tree

Image of a fractured, white post partially embedded in the soil.
Enlarge / A mammoth tusk thaws out of the ground in Siberia.

Ancient DNA has revolutionized how we understand human evolution, revealing how populations moved and interacted and introducing us to relatives like the Denisovans, a “ghost lineage” that we wouldn’t realize existed if it weren’t for discovering their DNA. But humans aren’t the only ones who have left DNA behind in their bones, and the same analyses that worked for humans can work for any other group of species.

Today, the mammoths take their turn in the spotlight, helped by what appears to be the oldest DNA ever sequenced. DNA from three ancient molars, one likely to be over a million years old, has revealed that there is a ghost lineage of mammoths that interbred with distant relatives to produce the North American mammoth population.

Dating and the mammoth family tree

Mammoths share something with humans: like us, they started as an African population but spread across much of the planet. Having spread out much earlier, mammoth populations spent enough time separated from each other to form different species. After branching off from elephants, the mammoths first split into what are called southern and steppe species. Later still, adaptations to ice age climates produced the woolly mammoth and its close relative, the North American mammoth, called the Columbian mammoth. All of those species, however, are extinct, and the only living relatives are the elephants.

We have obtained DNA from two of these species, the woolly and Columbian mammoths. These revealed both a number of adaptations to cold climates, and a small degree of interbreeding, as woolly mammoths made their way into North America and contributed a small amount (about 10 percent) to the genome of the Columbia population.

The new work focused on mammoth teeth found in Siberia, where conditions have favored both the preservation of remains and the preservation of the DNA they contain. The teeth come from layers of material that appear to have been deposited at the start of the most recent glacial period, which is when the ancestors of the woolly mammoth population should have been present in the area.

We don’t have precise dates for any of the teeth, as they appear to be too old for carbon dating. Instead, dates have been inferred using a combination of the species present in the deposits and the known timing of flips in the orientation of Earth’s magnetic field. In addition, the shape of the teeth provide some hints about what species they group with and provide some further indication of when they were deposited. In all, one tooth is likely to be at least a half-million years old, another about a million years old, and a third somewhat older still.

Very old, almost genomes

Previously, the oldest DNA obtained from animal remains is roughly the age of the youngest of these samples. But the researchers were able to recover some elephant-like DNA from each of the molars, although it was badly fragmented, and many individual bases were damaged. Researchers were able to isolate the full mitochondrial genome for each of the three teeth, as each cell contains many copies of this genome in each of its mitochondria. Only fragments of the nuclear genome could be obtained, however—at most, about 10 percent of one genome, and at worst under two percent. (Although less than two percent is still tens of millions of individual bases.)

Using the differences between the mammoth and elephant DNA and assuming a constant rate of mutation, the research team was able to derive independent dates for when each of the animals that left a tooth must have lived. Based on the mitochondria genome, the dates were 1.6 million, 1.3 million, and 900,000 years ago. For the two that had enough nuclear genome to analyze, the dates were 1.3 million and 600,000 years ago. The DNA-based dates for these two lined up nicely with each other and the date of the material they were found in. The oldest sample might be older than the deposit it’s in, and thus it might have been moved after death.

While these dates are fairly uncertain, they pretty clearly place two of the samples as the oldest DNA ever obtained from animals. And it would mean that these mammoths were living in Siberia shortly after ice-age conditions prevailed, although before there was a clear woolly mammoth lineage. They’d also predate the known appearance of mammoths in North America.

For all these reasons, the genomes potentially have a lot to say about the history of mammoths.

A ghost lineage and adaptations

And they do. The two younger samples are clearly on the same lineage that eventually produced the woolly mammoth, although they obviously predate the more recent samples that have yielded more complete genomes. But the oldest, from a site called Krestovka, looks like it’s from a separate lineage entirely. While it’s related to the woolly mammoth branch, it clearly diverged from it, and the analysis suggests that the split occurred at least 1.8 million years ago.

Krestovka also doesn’t have any direct modern descendants, indicating that it may have died off as a distinct population. But a lot of its DNA carried on as part of the Columbia mammoth genome. Apparently, at some point after the Krestovka, the lineage it was on interbred with the ancestors of the woolly mammoths. The result was a nearly 50/50 mix of the genomes of the two branches, the descendants of which migrated into North America and formed the Columbia mammoth population. Only much later did it meet the descendants, now a distinct woolly mammoth population, when they crossed into North America.

These animals were also already nearly as well adapted to the cold as their descendants, the woolly mammoths. The researchers identified 5,600 cases where the proteins of the mammoth genome differed from those in elephants. The ancient mammoths had already picked up over 85 percent of these changes, including ones involved in hair growth, fat deposits, temperature sensing, and handling of day/night cycles.

In other words, these things probably looked a lot like woolly mammoths, even if they were from a population that was still part of a larger cluster of mammoth ancestors living in Siberia at the time.

Mammoths may provide a relatively rare case, as we have a lot of their remains, and they lived in a part of the world where conditions are excellent for preserving DNA. But they also likely had a long generation time, so they underwent population changes at a far more gradual pace than many other species.

Even though getting DNA this old is rare, we might not need ancient DNA to get valuable information on how the species around us came into existence. And based on us and the mammoths, digging into these histories may provide lots of surprises.

Nature, 2021. DOI: 10.1038/s41586-021-03224-9  (About DOIs).

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