Using Ancient DNA to Reconstruct Past Ecosystems

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The student of ancient DNA has increasingly become better at not only deriving information about various fauna and flora that lived in the past but we can now begin to reconstruct large parts of ancient ecosystems.

In fact, one great benefit is we can push deeper now into the past than only a few years ago. This has the benefit of telling us how the Earth has changed as well as providing insights into long lost species that once roamed in unexpected places. 

The oldest sequence of DNA

Two-million-year-old DNA sequences, the oldest certifiable sequence of DNA so far made, have been found in the northeastern tip of Greenland.

Today, this is a very remote, cold area looking largely devoid of a lot of life; however, DNA found and sequenced from permafrost sediment has showed a vast thriving ecosystem once existed in this remote land.

How ancient DNA gets preserved

Typically, sediments can contain biological material, and thus DNA, but usually that DNA breaks down rapidly and does not preserve well. In frozen, cold places, that DNA degradation is dramatically slowed down.

If the right conditions are found, it seems particularly in frozen permafrost sediment, then it is possible to extract organic content that has DNA.

A team from the University of Copenhagen collected such sediment from the Kap København Formation in Greenland. The team collected these samples in 2006 but DNA extraction at that point had not been good enough to sequence such fragile DNA.

Over time, however, methods for extracting even very small amount of DNA improved, which has led to a recent study that highlights not only individual species’ DNA but also provides a picture of an ecosystem from two million years ago.

In fact, this is about one million years older than the previous record of DNA extraction, which was from a mastodon tooth.

A drawing of a mastodon with large tusks walking through a lush green forest.
Mastodon. Image: Tiere der Urwelt (Animals of the Prehistoric World), Heinrich Harder, public domain.

Evidence of mastodon populations in Greenland

Large herbivores such as reindeer and mastodons were found, but also small animals including rodents, geese, and rabbits. For the mastodons, they had never been found in Greenland and the finding there is not only surprising but the fact they lived so far north suggests Greenland may have had a once thriving mastodon population.

DNA reveals more accurate records than analyzing fossils

This opens up an important point, which is we cannot entirely depend on the fossil record to indicate to us what any regions’ ecosystem may have looked like. Fossils for mastodons and other large mammals have not been found in Greenland, but now DNA shows they were present even if they migrated in such places.

A black and white photo of two men standing on either side of a collection of mastodon rib bones stack agains a log wall.
Ancient bones of mastodons. Photo: ca. 1900-1930, Loc.gov via U.S. Forest Service, public domain.

The results demonstrate the importance of ancient sedimentary DNA in helping us to understand past ecosystems and even better techniques at extracting more fragmentary DNA could yield even more surprising results in the near future. Furthermore, this type of work highlights the importance of understanding how animals adapt to climate change.

The evidence shows that Greenland was much warmer two million years ago, perhaps more similar to what has been forecasted in future climate change for our own future, allowing these large mammals and others to thrive in far northern latitudes. Such animals demonstrate their ability to adapt and change to climate and as ecosystems change.

By collecting this type of evidence, we might be better able to see how ecosystems respond under different conditions of climate change, helping us to gain insight into how our own ecosystems may respond in the near future.[1]

Sequencing DNA from the Age of Dinosaurs

While the DNA sequenced from Greenland is the oldest known, scientists do believe it is possible to go even deeper in time, perhaps back tens of millions of years ago and into the Age of Dinosaurs. Recent data from cell nuclei that have been recovered from plants and dinosaurs between 30-80 million years ago suggests it might be theoretically possible to sequence DNA comparable to what has been done in the Greenland study.

In some instances, base pairs of DNA strands could survive fossilization. New microscopy-based DNA sequencing techniques might be able to recover small parts or areas of preserved DNA. While no results demonstrate that this is definitive as of yet, biological cellular remains found does suggest this is possible.

More research is, however, needed to understand how DNA fossilizes and if there is a theoretical limit as to how old DNA could preserve to, that is if there is a limit as to when DNA molecules breakdown even if preserved in ideal conditions.[2]

Reconstructing paleoecoystems

The recent results from northern Greenland highlight how unexpected past ecosystems may have been and how DNA could help us understand them. There are many limitations to DNA, particularly as they are sensitive to temperature and chemical conditions, which makes them easily breakdown.

In some, limited conditions, we are now better able to reconstruct paleoecoystems, but we will need better ways to extract more poorly preserved DNA if we are to push our understanding of Earth’s deep history from a genetic perspective.

The recent results highlight also the effects of climate change, where animals were able to exploit very northerly locations under conditions of a much warmer Earth.

The prospect of reconstructing ecosystems from sedimentary DNA is also an exciting research area for understanding the relationship between different plant and animal species.

References

[1]    A Nature press release about the oldest ever DNA sequencing can be found here:  Callaway E (2022) Oldest-ever DNA shows mastodons roamed Greenland 2 million years ago. Nature: d41586-022-04377–x. DOI: 10.1038/d41586-022-04377-x.  For more from the scientific article about this work, see:  Kjær KH, Winther Pedersen M, De Sanctis B, et al. (2022) A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 612(7939): 283–291. DOI: 10.1038/s41586-022-05453-y.

[2]    For more on possible limits and new innovations to extracting DNA older than two million years, see:  Bailleul AM and Li Z (2021) DNA staining in fossil cells beyond the Quaternary: Reassessment of the evidence and prospects for an improved understanding of DNA preservation in deep time. Earth-Science Reviews 216: 103600. DOI: 10.1016/j.earscirev.2021.103600.

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