Ancient DNA revolutionized the way we understand human evolution, revealed how populations moved and interacted, and introduced us to family members like the Denisovans, a ‘ghost generation’ we would not realize existed if have not discovered their DNA. But humans are not the only ones who have left DNA in their bones, and the same analyzes that have worked for humans can work for any other group of species.
Today, the mammoths are taking their turn in the spotlight, aided by what appears to be the oldest DNA ever. DNA from three ancient molars, one of which is probably more than a million years old, has revealed that there is a ghost generation of mammoths that have been linked to distant relatives to produce the North American mammoth population.
Dating and the mammoth family tree
Mammoths share something with humans: like us, they started out as an African population but spread across a large part of the planet. After spreading much earlier, mammoth populations separated enough time to form different species. After the mammoths branched off from elephants, they first split into what are called southern and steppe species. Later, adaptations to the ice age climate yielded the woolly mammoth and the relative, the North American mammoth, called the Columbia mammoth. However, all these species are extinct, and the only living relatives are the elephants.
We obtained DNA from two of these species, the woolly and Columbian mammoths. This revealed both a number of adaptations to cold climate systems and a small degree of mutual breeding, as woolly mammoths moved to North America and a small amount (about 10 percent) to the genome of the Columbia population. contributed.
The new work focused on giant teeth found in Siberia, where the preservation of remains and the preservation of the DNA it contains are favored. The teeth are derived from layers of material that were apparently deposited at the beginning of the most recent ice age, that is, when the ancestors of the woolly population must have been in the area.
We do not have exact dates for any of the teeth as it seems to be too old for dating carbon. Instead, dates were derived using a combination of the species found in the deposits and the known timing of sheets in the direction of the Earth’s magnetic field. In addition, the shape of the teeth gives some hints as to which species they group, and gives a further indication of when they were laid down. In total, one tooth will probably be at least half a million years old, another about a million years old and a third even slightly older.
Very old, almost taken
Previously, the oldest DNA obtained from animal remains was approximately the age of the youngest of these samples. However, the researchers were able to recover some elephant-like DNA from each of the molars, although it was severely fragmented and many individual bases were damaged. Researchers were able to isolate the full mitochondrial genome for each of the three teeth, since each cell contains many copies of this genome in each of the mitochondria. However, only fragments of the nuclear genome could be obtained – at most about 10 percent from one genome, and in the worst case under two percent. (Although less than two percent are still millions of individual bases.)
Using the differences between the mammoth and elephant DNA and the assumption of a constant rate of mutation, the research team was able to deduce independent dates for when all 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 who had enough core genomes to analyze, the dates were 1.3 million and 600,000 years ago. The DNA-based dates for these two arranged nicely on top of each other and the date of the material in which they were found. The oldest sample may be older than the deposit it is in, so it may have been moved to death.
Although these dates are fairly uncertain, they place two distinct samples as the oldest DNA ever obtained from animals. And that would mean that these mammoths lived in Siberia shortly after the ice age conditions prevailed, although there had previously been a distinct woolly mammoth lineage. They also preceded the known appearance of mammoths in North America.
For all these reasons, the genome may have a lot to say about the history of mammoths.
A ghost line and adjustments
And they do. The two younger specimens are clearly of the same sex that eventually produced the woolly mammoth, although this naturally precedes the more recent specimens that yielded more complete genomes. But the oldest, from a site called Krestovka, seems to come entirely from a separate generation. Although related to the woolly mammoth branch, it has clearly deviated from it, and the analysis suggests that the split occurred at least 1.8 million years ago.
Krestovka also has no direct modern descendants, indicating that it died out as a distinct population. But much of its DNA continues as part of the Columbia mammoth genome. Apparently, at some point after the Krestovka, the lineage on which it was was inbred with the ancestors of the woolly mammoths. The result was an almost 50/50 mixture of the genomes of the two branches, the descendants of which migrated to North America and formed the mammoth population of Columbia. Only much later did it meet the descendants, now a distinctly woolly population, as they migrated to North America.
These animals were also almost as well adapted to the cold as their offspring, the woolly mammoths. The researchers identified 5,600 cases where the proteins of the mammoth genome differ from those of elephants. The ancient mammoths have already picked up more than 85 percent of these changes, including those involved in hair growth, fat deposits, temperature sensing and dealing with day / night cycles.
In other words, these things probably looked a lot like woolly mammoths, even if they came from a population that was still part of a larger group of mammoth ancestors living in Siberia at the time.
Mammoths can be a relatively rare case, as we have many of their remains, and they have lived in a part of the world where the conditions are excellent for conserving DNA. But they probably also had a long generation time, and therefore they underwent population change at a much slower pace than many other species.
Although it is rare to get DNA so old, we may not need old DNA to get valuable information about how the species around us came into being. And based on us and the mammoths, exploring this history can offer many surprises.
Nature, 2021. DOI: 10.1038 / s41586-021-03224-9 (About DOIs).