Marianne Dehasque and Love Dalen: In science, we tend to share our successes and ignore the less spectacular failures. We decided to take a different approach.
This is the story of how multiple 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, which occurred some 120,000–12,000 years ago. But the cause of its extinction remains a mystery.
Mammoths roamed gigantic areas 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 miniature island off the coast of Siberia, until its final extinction about 4,000 years ago.
In our fresh study published in Cell, we investigated whether the Wrangel Island mammoth population was genetically destined for extinction. And despite many missteps along the way, we ultimately found 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 miniature population for thousands of years. Inbreeding is a common problem in miniature populations, and its negative effects can accumulate over time, eventually leading to a non-viable population and extinction.
Inbreeding can cause a lot of problems. Portraits of Charles II of Spain, the last Habsburg monarch, show his beard deformed due to generations of inbreeding. Scientists have long wondered whether genomic processes led to the extinction of the mammoths on Wrangel Island.
To address this, we generated a dataset of 21 mammoth genomes spanning the last 50,000 years of the species' existence. This dataset allowed us to go back in time and examine the genetic consequences of their isolation over time.
Lonely Boy was the most valuable individual in our data set, key to understanding why mammoths went extinct. Sequencing Lonely Boy’s DNA, however, proved challenging.
Adventures of a Lonely Boy
Generating the genome for Lonely Boy took many attempts over nearly a decade. The first attempt at DNA extraction turned out to be contaminated with human contamination. In the second attempt, we used bleach to remove as much of the contamination as possible.
While this is common practice in the historic DNA field, it also comes with the trade-off that some of the mammoth DNA will also be accidentally destroyed. In our case, this meant that there was not enough mammoth material left in the sample to generate a high-quality genome.
In a final attempt, we combined data from different DNA extracts from Lonely Boy. However, the DNA from our different extracts, although similar, looked like they belonged to different people. We came up with the wildest theories to explain these fresh results.
One of our leading theories at the time was that Lonely Boy had a condition called “vanishing twin syndrome.” Apparently, in some uncommon cases, a mammalian fetus can absorb genetic material from its affected twin during pregnancy. That would explain why the DNA extracts looked similar but not identical.
Ultimately, the explanation wasn’t that electrifying, and it could all be traced back to the glaring amount of effort we put into the sample. The result was weird lab artifacts (anything that makes it challenging to interpret a sample)—usually not even noticeable—that introduced spurious genetic variability into the sample. So we created a basic filter to remove these artifacts.
But even after all these steps, Lonely Boy still looked like an exception. At this point, we decided to re-date the sample. Lonely Boy had been dated a long time ago, and the methods had improved considerably since then.
The result was a substantial surprise. Lonely Boy was not 4,000 years venerable, as initially thought, but closer to 5,500 years venerable—making him a completely average mammoth in our data set, and not the last such individual on Earth.
Causes of extinction
To answer the original project question, no, the Wrangel Island population likely did not become extinct due to inbreeding.
By comparing our genomic data with the results of computer simulations, we now know that the decline in the mammoth population following its isolation on Wrangel Island about 10,000 years ago must have been massive, as only eight reproductive individuals remained.
Nevertheless, our results show that the population quickly recovered to a size of 300 individuals within 20 generations and remained stable until the final extinction of the mammoth. We see that it remained stable because there was virtually no change in inbreeding levels during this period.
However, our results on deleterious mutations tell a different story. While the most deleterious mutations were gradually removed from the population by natural selection, mildly deleterious mutations accumulated over time. This suggests that the initial population decline – despite a rapid recovery – had long-lasting genetic consequences.
Predicting the exact impact of deleterious mutations is challenging, especially in an extinct species. Comparisons with known human diseases suggest that some of the most deleterious purified mutations likely disrupted genes that may have been vital for the development of various senses, such as hearing and vision.
However, it seems unlikely that this caused the mammoth's final demise. Based on our results, the extinction must have happened quickly. Humans did not coexist with mammoths on the island, but a sudden event, such as a disease outbreak or weather, could have caused the population to go extinct suddenly.
As with most things in science, hopefully more research will yield fresh insights. Potentially even a fresh Lonely Boy or Girl.
Although we were ultimately able to analyze inbreeding in mammoths, it was a long journey with many detours. Nevertheless, as a lab group, we learned a lot from this project.
We have invented a fresh bioinformatics method to deal with human contamination and discovered a fresh type of laboratory artifact. This fresh information could be crucial to determining the exact causes of the woolly mammoth's extinction.
Marianne Dehasque, Postdoctoral Researcher, Uppsala University and Love Dalen, Professor, Stockholm University
This article was reprinted from Conversation under Creative Commons license. Read original article.
Image Source: Pixabay.com
