Ancient DNA: a story of a (R)evolution

As you know, ancient DNA (aDNA) is a big part of our COMMIOS project! 
And we now count legions of studies in aDNA! But how did this story start?

aDNA: a recent development at the archaeological scale

Well, everything began in 1984 with Hichugi and his team, when they recovered a fragment of DNA from a stuffed quagga, a species who disappeared at the end of the 19th century. This discovery was rapidly followed by the first human aDNA! Indeed, in 1985, Svante Pääbo and his team published DNA data from an Egyptian mummy, who died more than 2000 years ago… To be fair, people later realized that this result was due to a modern contamination. But the excitement was there, and palaeogenetics was born.

During the following years, the race to publish the ‘most ancient DNA’ was on, and unfortunately, many results were due to contamination. But this was really instructive and allowed for the development of methods and rules.

aDNA: how to do it and do it well

So, you’re probably bursting with interest now: how do we do?

Firstable, let me tell you more about the characteristics of ancient DNA. When DNA is still available in samples, it’s fragmented (short segments of nucleotides), degraded (chemical alteration) and in low quantity. 

One of the major developments (which is not only used in aDNA) is the PCR (yes, I know, this acronym is well known since the beginning of the Co*** crisis). But what does it stand for? Polymerase Chain Reaction. Three words that make the difference. The PCR is the key to amplify fragments of DNA, which is absolutely needed when DNA is in low quantity. And we are lucky because it works well on short fragments!

And how do we extract fragments of DNA? As you may have noticed, in 1984 and 1985, results were obtained from a stuffed animal and a mummy, meaning that teams worked with soft tissues. But how often do we find a mummy in archaeology? Well, this is the second major development: the ability to extract DNA from bones and teeth, in other words, from mineralized tissues. I won’t go into details, but it’s like cooking, we just follow a recipe.

This, dear readers, was an amazing step forward.

Someone (me!) working in a clean lab

As I told you before, during the race to find the most ancient DNA, palaeogeneticists learned a lot and published rules to do it right. 
Those rules include working in a clean lab (yeah, you probably can’t tell but that’s me in the picture!), getting a clean sample and if not possible, decontaminating the sample… And then, 16 years after the first publication, Cooper and Poinard published a paper in Science summarizing the key criteria and titled ‘Ancient DNA: Do It Right or Not at All’.

From palaeogenetics to palaeogenomics

It took almost 20 years to develop a fully reproducible method in ancient DNA (which, at the archaeologic scale might be a second). Because the ‘Sky is the limit,’ as our American colleagues say, developments continued. Less than 5 years after Cooper and Poinard’s paper, and 20 years after Pääbo’s paper, the first genome – or at least parts of the genome – from a cave bear dated back to 40,000 years ago was published (Noonan et al., 2005). I know! It’s absolutely amazing. But you’re probably wondering: what’s the difference between palaeogenetics and palaeogenomics? I promise I will tell you more about that in my next post, but in a few words: in palaeogenetics, we work a priori, meaning that we target a specific spot in the DNA, and we amplify this fragment only by PCR. A contrario, in palaeogenomics, we amplify everything and choose the sequence of interest a posteriori

It took five additional years to obtain the first human genome (Rasmussen et al., 2010), and another 10 years to obtain the oldest ancient DNA – a mammoth genome dated back to more than a million years (van der Valk et al., 2021).

Yes, 1.2 million. That’s it.

Think about the timeline: first ancient DNA fragment in 1984 and oldest genome in 2021. Thirty-seven years – that’s how long it took to accomplish something that incredible. 

Palaeogenomics: a boom since 2015

Something else is quite amazing: the number of published human genomes. However, in 2018, among the 1372 ancient human genomes, 1144 were from Europe (400 dated back to the Neolithic and the Bronze Age) revealing strong disparities across the studied regions and periods, which can be explained, at least partially, by issues regarding the conservation of DNA (I will tell you about it in the next blog post, don’t worry!)

When I finished my PhD, at the end of 2019, only 26 data were available for the Iron Age in Western Europe. Yep, 26 (and the data that I produced during my PhD, of course!) Now, thanks to a joint effort from different teams, including COMMIOS, more than 500 data are available for the Iron Age.

By the way, I truly encourage you to read this awesome paper: ‘Large-scale migration into Britain during the Middle to Late Bronze Age’!

The DNA Boom (https://reich.hms.harvard.edu/research)

Well, that’s it for today. I hope you enjoyed this story about the rise of ancient DNA, and that you are as impressed as I am with how quickly this method was developed!

We’ll talk soon about characteristics of ancient DNA and go deeper into the methods in palaeogenetics VS. palaeogenetics!

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