Feb 01 2022

DNA Microfossils and the Woolly Mammoth

About 12 thousand years ago the late Pleistocene was transitioning to the current Holocene. This transition was marked by the end of the last glacial period, and turnover of entire ecosystems to a new homeostasis. Specifically in the Arctic North America, the mammoth-steppe biome was transitioning to the boreal forest we know today. As the name suggests, the most famous of the megafauna of the late Pleistocene was the woolly mammoth, and a lot of research has focused on nailing down the exact date when the woolly mammoth went extinct.

Dating the lifespan of a species is always a matter of finding the earliest and latest evidence for its existence. Such date ranges are always an underestimation, because it’s unlikely that we have discovered the very first or very last specimen, so it is very common for new fossil discoveries to expand the known date range. This is why headlines such as, “Woolly Mammoths Survived Longer than Previously Thought” are extremely common. Of course they did – most extinct species survived longer than we currently think.

However, it is not common that scientists hit upon an entirely new method for exploring the past and dating species, but that is what is happening now. Researchers from the McMaster Ancient DNA Centre are pioneering a technique to explore ancient environmental DNA. This is made possible by the extreme advances in genetics technology over the last few decades. Already environmental DNA is giving us a new powerful tool to explore ecosystems. We no longer have to track and tag representatives of all the species in an environment to get a sense of what plants and animals live there. We can just take a few scoops of soil and water and sequence the environmental DNA that we find. Every living things sheds DNA into the environment, and as their remains decay into the soil and water it spills their DNA for scientists to find later. My favorite application of environmental DNA technology is a survey of Loch Ness showing the complete absence of DNA from a plesiosaur or any similar creature.

What the McMaster researchers are now doing is looking at permafrost sediments to survey ancient environmental DNA. The half-life of DNA is 521 years, which means for practical purposes you can still find pieces of DNA that can be sequenced from tens of thousands of years ago, but not millions (so no Jurassic Park). They surveyed the last 30,000 years of the mammoth-steppe region for ancient environmental DNA. Unsurprisingly, and like modern samples, they found: “Bacterial, fungal and unidentifiable DNA make up over 99.99 percent of an environmental sample.” Most living stuff out there is bacteria. If you were ground up and your DNA catalogued, most would be from bacteria. In any case, they were able to find the 0.01% of interesting DNA from ancient species.

Unsurprisingly, they found woolly mammoth DNA survived later that the fossil record indicates. This makes sense as fossilization is a rare event. Further, as a population diminishes there are fewer and fewer individuals and less opportunity for a fossil to be made and found. So lingering survivors would likely to be missed, but a thorough survey of an entire ecosystem by environmental DNA sampling has a much greater chance of finding those few survivors. And that’s exactly what happened.

They found evidence of environmental woolly mammoth DNA as much as 7,000 years later than the fossil record, as late as 5,700 years ago in this region. We already have fossil evidence for the late survival of woolly mammoths in Siberia, at 3,900 years, so this is not implausible. The researchers surveyed multiple regions, and most of the changes in the ecosystem they were seeing were consistent across samples, which means the transition was happening all over the ecosystem. But they also found that late survivors of woolly mammoths and other species, such as horses and steppe bison. They found that in later samples the range of these animals tended to decrease, and they survived in “refugia” – isolated locations. This is the “land that time forgot” scenario.

Ancient environmental DNA is a powerful new technique that will likely contribute significantly to our understanding of ancient ecosystems, and a more complete assessment of the lifespan of extinct species. The technique, however, is dependent on permafrost, which is an effective means of preserving ancient DNA. The worry here is that a warming Arctic may spell the rapid end of the permafrost, before we have a chance to survey it all. This makes this research somewhat urgent. Sure, we likely have decades, but research like this takes time, meanwhile information is constantly being lost.

The researchers also report that they were able to find enough bits of DNA from individual species that they could assemble them into an entire genome. You assemble DNA fragments by looking for overlapping sequences. It’s a giant puzzle, but now, of course, we have computers to assist in the process. This, then, leads to the question – can we clone ancient extinct species from their DNA? The short answer is yes, well, probably. Several groups are working on this technology, and we may see success in the coming decades. Woolly mammoths are on the short list, and the fact that they lived in a frozen environment is a boon.

In any case, if environmental DNA was not on your radar, it should be, and now we can add ancient environmental DNA to that. This is a powerful window into surveying ecosystems – data we did not know existed a hundred years ago is just sitting in the environment for us to discover.

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