Vieraskynä: Ancient DNA

Hei! Before I write about the super interesting topic of ancient DNA, I would first like to introduce myself a little. My name is Sven, you can call me Svenni though, and I’m a biochemistry student from Germany, currently working on my master thesis at the University of Leipzig. In the past semester I visited the University of Oulu as an exchange student. Best. Decision. Ever.
During my stay in Oulu I learned lots of new things in the field of biochemistry, especially protein biochemistry, as I was working in a research group focusing in protein science. The exchange was also a great way to improve my English skills in both science and everyday situations. But by far the best part about Oulu was the people I met. Or better, the friends I made. They made this already great experience an unforgettable, super awesome one. Kiitti! I would like to encourage everyone, if given the opportunity, to take part in exchange programs. It’s super useful when working in science to have experience in international communication, and vice versa is working in science a great way to meet people from all over the world.

Ok, but now let’s get straight to the topic: Ancient DNA! (short: aDNA). As the name suggests, it’s about old DNA. Not old in a way where a DNA sample was left on the windowsill over the weekend by accident, but rather it’s about DNA from thousands and hundreds of thousands of years ago – which still can be analyzed today. Let’s start slowly. There should be of course the very basic understanding that DNA encodes the information for every living individual in a sequence of base pairs. Having the DNA sequence of an individual gives not only a lot of information about that individual, but also can give us clues about how related it is to other individuals and species. As for extinct species, there is no other way than comparing the fossil structure of these to other skeletons to make conclusions about their relations. Or is there? Here is where ancient DNA comes into play. Using advanced next generation sequencing methods, researchers are able to reconstruct DNA sequences from fossils of individuals that died a long time ago. Some examples are mammoths (10,000 years), Neanderthals (40,000 years) and a Pleistocene horse (700,000 years).[1]

Examples of extinct organisms from which the genomes were sequenced.
The rapid development of sequencing technologies helps to analyze more and more genomes every year.[2]

Seeing how it is possible to sequence genomes from individuals that died nearly one million years ago, should we be expecting sequenced dinosaur genomes soon? Unfortunately, sequencing of ancient DNA has its limitations. Over the decades, centuries and millennia, the DNA is exposed to various environmental conditions such as UV-light, heat and microorganisms that destroy a lot of the DNA. Therefore, ancient DNA is highly degraded into small DNA fragments. These small fragments (in the range of about 100 base pairs) are sequenced and put together, like in a super scientific puzzle game. Even under very good conditions, studies have shown that recovering a sequence from a DNA sample is not possible if the DNA sample is older than about a million years.[3]

Estimated DNA survival rate after 10,000 years.
In warmer areas DNA degrades faster, while in colder areas DNA can be well preserved even after thousands of years.[3]

Another challenge to face when it comes to sequencing of ancient DNA is that there is a high amount of contamination. Most of the DNA that is found from ancient bone samples often times comes from millions of generations of microorganisms that inhabited the bone during the past. However, it is possible to distinguish ancient DNA from not-so-ancient DNA using a simple trick: The older the DNA fragment is, the higher is also the rate of modifications of the bases, as over time chemical reactions occur (cytosine deamination). Only DNA fragments with a high amount of these chemical modifications are taken into account when it comes to the reconstruction of ancient genomes.[3]

Given the possibilities of sequencing DNA from fossils, a lot about the past can be revealed. A famous example is the sequenced genome of the Neanderthal that was published in 2009. From studies of the Neanderthal genome, it was concluded that interbreeding between Neanderthals and modern humans happened outside of Africa about 50,000 years ago.[4] Generally can be said that sequencing of ancient DNA enables us to reconstruct the past quite accurately and helps us to better understand evolutionary relationships within and between different species.

Sources:

[1] Rizzi, Ermanno, et al. "Ancient DNA studies: new perspectives on old samples." Genet Sel Evol 44.1 (2012): 21.

[2] Hofreiter, Michael, et al. "Ancient DNA." Nature Reviews Genetics 2.5 (2001): 353-359.

[3] Hofreiter, Michael, et al. "The future of ancient DNA: Technical advances and conceptual shifts." BioEssays 37.3 (2015): 284-293.

[4] Sankararaman, Sriram, et al. "The genomic landscape of Neanderthal ancestry in present-day humans." Nature 507.7492 (2014): 354-357.

Best wishes, Svenni