DNA from mammoth remains reveals history of last remaining population

A small group of woolly mammoths became stranded on Wrangel Island about 10,000 years ago when rising sea levels separated the island from mainland Siberia. Small, isolated populations of animals lead to inbreeding and genetic defects, and it was long thought that the Wrangel Island mammoths eventually succumbed to this problem about 4,000 years ago.

However, a paper in Cell on Thursday compared 50,000 years of genomes from mammoths from the mainland and isolated Wrangel Island and found that this was not the case. What the paper’s authors discovered not only challenges our understanding of this isolated group of mammoths and the evolution of small populations, it also has important implications for conservation efforts today.

A serious bottleneck

It is the result of years of genetic sequencing by members of the international team behind this new paper. They studied 21 mammoth genomes, 13 of which were re-sequenced by lead author Marianne Dehasque; others had been sequenced years earlier by co-authors Patrícia Pečnerová, Foteini Kanellidou and Héloïse Muller. The genomes were obtained from Siberian woolly mammoths (Mammuthus primigenius), both from the mainland and from the island before and after it became isolated. The oldest genome came from a female Siberian mammoth that died about 52,300 years ago. The youngest came from male mammoths from Wrangel Island that died around the same time as the last of these mammoths (one of them died only 4,333 years ago).

It’s a remarkable and telling time span: the sample included mammoths from a population that started out large and genetically healthy, became isolated and eventually became extinct.

Mammoths, the team noted in their paper, experienced a “climatically turbulent period,” specifically during a period of rapid warming called the Bølling-Allerød interstadial (about 14,700 to 12,900 years ago) — a time that others have suggested may have led to local extinctions of woolly mammoths. However, the genomes of mammoths studied during this period do not indicate that the warming had any adverse effects.

Adverse consequences only occurred – and they were drastic – when the population on that island became isolated.

The team’s simulations indicate that, at its smallest, the total population of Wrangel Island mammoths was fewer than 10 individuals. This represents a serious population bottleneck. This was seen genetically due to increased runs of homozygosity within the genome, caused when both parents contribute nearly identical chromosomes, both coming from a recent ancestor. The runs of homozygosity within isolated Wrangel Island mammoths were four times greater than those before sea levels rose.

Despite the dangerously low numbers of mammoths, they recovered. Population size, as well as levels of inbreeding and genetic diversity, remained stable for the next 6,000 years until their extinction. In contrast to the initial population bottleneck, genomic signatures over time seem to indicate that inbreeding eventually shifted toward more distantly related pairs, suggesting either a larger mammoth population or a change in behavior.

Their simulations indicate that within twenty generations the population size would have increased to about 200 to 300 mammoths. This is consistent with the slower decline in heterozygosity they found in the genome.

Long-term negative effects

It is possible that the Wrangel Island mammoths survived despite all odds, and that harmful genetic defects were not the reason for their extinction. Still, the research suggests that their story is complicated.

At about 7,608 square kilometers today, slightly larger than the island of Crete, Wrangel Island would have offered a fair amount of space and resources, although these were large animals. For example, for 6,000 years after their isolation, they suffered from inbreeding depression, which refers to increased mortality due to inbreeding and the resulting defects.

This inbreeding has also helped to purge harmful mutations. This may sound like a good thing, and it can be, but it usually happens because individuals carrying two copies of harmful mutations die or do not reproduce. So it is only good if the population survives.

The team’s results show that clearing genetic mutations can be a lengthy evolutionary process. Lead author Marianne Dehasque is a paleogeneticist and obtained her PhD from the Center for Paleogenetics. She explained to Ars: “The clearing of harmful mutations for more than 6,000 years actually indicates long-term negative effects caused by these extremely damaging mutations. Because the purge of the Wrangel Island population took so long, this indicates that the population was negatively impacted by these mutations until its extinction.”