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

Ancient DNA revolutionized the way we understand human evolution, revealing how populations moved and interacted and introduced us to relatives like the Denisovans, a “ghost line” that we would not realize existed without the discovery of their DNA. But humans aren’t the only ones who have left DNA in their bones, and the same analyzes that worked for humans can work for any other group of species.

Today, mammoths take their turn in the spotlight, aided by what appears to be the oldest DNA ever to be sequenced. DNA from three ancient molars, one of which is probably over a million years old, has revealed that there is a ghost line of mammoths that have crossed with distant relatives to produce the mammoth population of North America.

Mammoth Dating and Family Tree

Mammoths share something with humans: Like us, they started out as an African population but have spread over much of the planet. Having dispersed much earlier, the mammoth populations spent enough time separated from each other to form different species. After separating from the elephants, the mammoths first split into the so-called southern and steppe species. Still later, adaptations to Ice Age climates produced the Woolly Mammoth and its close relative, the North American Mammoth, called the Colombian Mammoth. All of these species, however, are extinct, and the only living relatives are the elephants.

We obtained the DNA of two of these species, the woolly and Colombian mammoths. These revealed both a number of adaptations to cold climates and a small degree of interbreeding, as woolly mammoths made their way to 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 favored both the preservation of the 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 Ice Age, when the ancestors of the woolly mammoth population should have been present in the area.

We do not have specific dates for any of the teeth, as they appear to be too old for carbon dating. Instead, the dates were inferred using a combination of the species present in the deposits and the known time of reversals in the orientation of the Earth’s magnetic field. In addition, the shape of the teeth gives some indication of the species with which they cluster and provides an additional indication of when they were deposited. In all, one tooth is likely to be at least half a million years old, another about a million years old, and a third a little older.

Very old, almost genomes

Previously, the oldest DNA obtained from animal remains roughly matched the age of the youngest of these samples. But the researchers were able to recover some elephant-like DNA from each of the molars, despite it being severely fragmented and many individual bases damaged. The researchers were able to isolate the complete mitochondrial genome for each of the three teeth, because each cell contains many copies of this genome in each of its mitochondria. However, only fragments of the nuclear genome could be obtained – at most about 10 percent of a genome and at worst less than 2 percent. (Although less than two percent still represents tens of millions of individual bases.)

Using the differences between mammoth and elephant DNA and assuming a constant rate of mutation, the research team were able to obtain independent dates for which 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 genomes to analyze, the dates were 1.3 million and 600,000 years ago. The dates based on the DNA of these two people aligned well with each other and the date of the material in which they were found. The oldest sample could be older than the deposit it is in, and therefore it could have been moved after death.

While these dates are quite uncertain, they quite clearly place two of the samples as the oldest DNA ever obtained from animals. And that would mean these mammoths were living in Siberia shortly after Ice Age conditions prevailed, albeit before there was a clear woolly mammoth lineage. They would also predate the known appearance of mammoths in North America.

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

A phantom line and adaptations

And they do. The two youngest samples clearly belong to the same line that ultimately produced the Woolly Mammoth, although they clearly predate the more recent samples that yielded more complete genomes. But the oldest, from a site called Krestovka, appears to belong entirely to a separate lineage. Although it is related to the branch of the woolly mammoth, it clearly diverged from it, and analysis suggests the split occurred at least 1.8 million years ago.

Krestovka also does not have direct modern descendants, indicating that she may have died as a separate population. But much of its DNA continued as part of the Columbia mammoth genome. Apparently, at some point after the Krestovka, the lineage he was on crossed with the ancestors of the woolly mammoths. The result was an almost 50/50 mixture of the genomes of the two branches, whose descendants migrated to North America and formed the Columbia mammoth population. It was not until much later that he encountered the descendants, now a distinct population of woolly mammoths, when they came to North America.

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

In other words, these things probably looked a lot like woolly mammoths, although they belonged to a population that was still part of a larger group of mammoth ancestors living in Siberia at the time.

Mammoths may be a relatively rare case, as we have a lot of their remains, and they lived in a part of the world where conditions are great to preserve DNA. But they probably also had a long generation, so they underwent population changes at a much more gradual rate than many other species.

Even though obtaining such ancient DNA is rare, we may not need ancient DNA to gain valuable insight into how the species around us came to be. And based on us and the mammoths, digging into these stories can offer a lot of surprises.

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