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November 18, 2015

Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

Writing about web page http://biorxiv.org/content/early/2015/11/17/032060

You may recall these two earlier blog posts:

Well, this story has taken an unfortunate turn recently, in that a group from the Max Planck Institutes in Tübingen has contested our finding of wheat in the British Isles 8kya, essentially arguing that the results are too good to be true!

At the heart of their argument is the assumption (almost dogma) that DNA ages in a certain predictable way (through cytosine deamination) and these changes can be used to determine the age of DNA. As they could not detect the signatures of DNA damage in our wheat sequences, they have jumped to the conclusion that the wheat sequences must represent modern contamination.

However,this doesn't take into account the environment in which the DNA has been stored: the submerged sediments have effectively been stored in a refrigerator for the last 8000 years, because the ambient temperature for such sediments is only ~4 ° C. The argument here is a bit like saying that if you bought two loaves of bread and put one at room temperature in the bread bin and the other in the fridge or freezer and then came back a couple of weeks later to find only the loaf in the breadbin was mouldy it was safe to conclude that they couldn't possibly have been bought on the same day!

However, in addition to problems with the substance of the arguments, there have been problems in the way in which they have been made. They have been published in eLife, a fairly new open-access peer-reviewed journal, sponsored by the Max Planck Society:

The fact that the journal is sponsored by the Max Planck Society may or may not mean that authors from Max Planck Centres get an easier ride through peer review: judge for yourself as eLife publishes the reviews and decision letter.

But more problematic is that eLife, despite all its fanfare about being a revolutionary new open-access journal has not given us any right to reply to this publication, even though it is clearly a polemical piece aimed at discrediting our work. Oddly, Science, the journal we published in, also declined to let us publish a response. Luckily, given the old Internet addage that "information wants to be free", we have alternatives!

So, I am pleased to announce the appearance of this manuscript on bioRxiv, the preprint server for biology, and would ask you to read it, comment on it, Tweet it and Like it!

The manuscript goes far beyond a simple rebuttal to encompass an analysisof 148 palaeogenomic data sets to show that the rate of cytosine deamination is a thermally correlated process and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. In addition, we argue that the PCR enzyme used in our sedaDNA study would not have had the capability to report 5-prime cytosine deamination, so absence of this feature is to be expected.

Robin Allaby has worked extremely hard to prepare this manuscript and get it up there on bioRxiv. However, I have suggested to him that the work merits eventual publication in a peer-reviewed journal. Who knows, eLife might even take it! Watch this space!! And read and Tweet the manuscript!


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