In science, we tend to share our successes and ignore the less glamorous mishaps. We decided to take a different approach. This is the story of how several generations of scientists worked together to decipher the genome of the mammoth formerly known as Lonely Boy, often called the last mammoth on Earth.
The woolly mammoth was one of the most charismatic species of the last Ice Age, about 120,000 to 12,000 years ago. Yet the cause of its extinction remains a mystery. Mammoths roamed much of the Northern Hemisphere during their heyday, but by the end of the Ice Age they had disappeared from most of their former range. The last population of mammoths lived on Wrangel Island, a small island off the coast of Siberia, until its final demise about 4,000 years ago.
In our new study, published in Cell, we investigated whether the mammoth population on Wrangel Island was genetically destined for extinction. And despite many mistakes along the way, we eventually discovered that this was not the case.
Mammoths became isolated on Wrangel Island about 10,000 years ago due to rising sea levels and survived as a small population for thousands of years. Inbreeding is a common problem in small populations and its negative effects can accumulate over time, eventually leading to a non-viable population and extinction.
Inbreeding can cause many problems. Portraits of Charles II of Spain, the last monarch of the Habsburg house, show his deformed chin due to generations of inbreeding. Scientists have long wondered whether genomic processes led to the extinction of Wrangel Island’s mammoths.
To address this, we generated a dataset of 21 mammoth genomes covering the last 50,000 years of the species’ existence. This dataset allowed us to travel back in time and study the genetic effects of their isolation over time.
Lonely Boy was the most valuable individual in our data set, the key to understanding why mammoths became extinct. However, sequencing Lonely Boy’s DNA proved to be a challenge.
The Adventures of Lonely Boy
Generating a genome for Lonely Boy took multiple attempts over nearly a decade. Our first attempt to extract DNA found our sample to be plagued by human contamination. Our second attempt used bleach to remove as much contamination as possible.
While this is common in the field of ancient DNA, it also has the disadvantage that some of the mammoth DNA will be inadvertently destroyed. In our case, this meant that not enough mammoth material remained in the sample to generate a high-quality genome.
In a final attempt, we combined the data from the different DNA extracts of Lonely Boy. Although the DNA from our different extracts was similar, it seemed to be from different individuals. We came up with the wildest theories to explain these new results.
One of our leading theories at the time was that Lonely Boy had a condition called “vanishing twin syndrome.” Apparently, in some rare cases, a mammalian fetus can absorb the genetic material of an affected twin during pregnancy. This would explain why the DNA extracts looked the same, but were not completely identical.
In the end, the explanation wasn’t nearly as exciting and it all came down to the sheer amount of effort we put into this sample. This resulted in strange lab artifacts (anything that causes problems when interpreting a sample) – normally not even noticeable – that introduced spurious genetic variation into the sample. So we created a simple filter to remove these artifacts.
But even after all these steps, Lonely Boy still seemed like an outlier. At this point we decided to re-date the sample. Lonely Boy was long dated and its methods have improved significantly since then.
The result came as a big surprise. Lonely Boy was not 4,000 years old as initially thought, but closer to 5,500 years – making him a completely average mammoth in our data set, and not the last of this species on Earth.
Causes of extinction
To answer the original question of this project: no, the Wrangel Island population probably did not become extinct due to inbreeding. By comparing our genomic data with the results of computer simulations, we now know that the mammoth population decline following isolation on Wrangel Island around 10,000 years ago must have been dramatic, with only eight breeding individuals left.
Nevertheless, our results show that the population quickly recovered to a population size of 300 within twenty generations and remained stable until the mammoth’s eventual demise. We can see that it remained stable as there was virtually no change in inbreeding levels during this period.
However, our results on deleterious mutations tell a different story. While the most damaging mutations were gradually removed from the population by natural selection, mildly damaging mutations accumulated over time. This indicates that the initial population decline – despite the rapid recovery – had long-lasting genetic effects.
Predicting the exact effect of deleterious mutations is challenging, especially in an extinct species. Comparison with known human diseases suggests that some of the most damaging purified mutations likely disrupted genes that may have been important for the development of several senses, such as hearing and vision.
However, it seems unlikely that this caused the mammoth’s eventual demise. Based on our results, the extinction must have occurred quickly. Humans did not coexist with mammoths on the island, but a sudden event, such as a disease outbreak or a weather event, could have caused the population to suddenly die out.
As with most things in science, more research will hopefully yield new insights. Possibly even with a new Lonely Boy or Girl.
Although we finally succeeded in analyzing mammoth inbreeding, it was a long journey with many detours. Yet as a lab group we have learned a lot from this project. We devised a new bioinformatic method to tackle human contamination and discovered a new type of laboratory artifact. This new information could be crucial to uncovering the exact reasons why the woolly mammoth became extinct.
This article is republished from The Conversation under a Creative Commons license. Read the original article.
Marianne Dehasque receives funding from the Carl Tryggers Foundation.
Love Dalén receives funding from the Swedish Research Council, the Knut and Alice Wallenberg Foundation and the European Research Council.