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!


- 3 comments by 1 or more people Not publicly viewable

  1. Chris Keene

    Good to see it on biorxiv.

    I didn’t fully follow the second point about elife, your criticism seems to be that it has the same policy as Science (declining to publish response). the difference they fanfare is they are publicly available open access. Put another way, there is nothing implicit in being Open Access that

    They also make all their review decisions publicly available, according to their website, something I believe Science does not do.

    The may also address what was your first point, a suggest (‘may or may not’) that sponsorship may compromise the editorial/peer review process, which i do find quite a strong suggestion.

    So I don’t really understand:
    “However, in addition to problems with the substance of the arguments, there have been problems in the way in which they have been made.”
    I may have missed the point, all (credible) journals reject papers, including surely responses. Is there something unique about elife, different to the majority of journals, which is at fault?

    18 Nov 2015, 20:46

  2. Mark Pallen

    Hi Chris,
    You are right that there is nothing implicit in being Open Access that guarantees a right to reply and it is good that eLife makes peer reviews and decisions publicly available. However, it is disappointing that eLife did not give us an automatic right to reply to the Weiss et al paper, because that paper is clearly an attack on our previous work published in Science and without a right to reply many people have assumed that our work was in some way flawed, which is not true. Debate in science is fine, but it has to be a two-way process and, as in a court of law, the accussed should be given the chance to defend themsleves. The problem was compounded by the Weiss et al paper benefitting from the full force of the eLife/Max Planck media machinery.

    But we have now had an apology of sorts from eLife editor Andy Collings:
    “We reviewed the Burbano paper as a Short Report, but we should have provided some warning to you about its upcoming publication, so I apologise for that. Though it’s no consolation in this case, we are currently devising a distinct process for future submissions of this type, which would likely involve a response from the original authors being considered within the review process.”

    It also a little disappointing that Science did not let us respond on their pages to the eLife paper, but this is more understandable, as the Weiss et al paper was published in another journal. Science did give us right to reply to a previous critique.

    My suggestion that sponsorship might compromise the review process stands as a general point, although I am not certain in this case whether this really is a Max Planck journal gving an easy ride to Max Planck research. I am not the first to make these points about eLife:
    http://scholarlykitchen.sspnet.org/2012/10/17/recuse-refuse-or-excuse-the-conflicts-of-interest-at-the-heart-of-funder-backed-journals/
    http://www.usnews.com/news/articles/2013/02/21/can-some-of-the-largest-backers-of-scientific-research-alter-the-peer-review-process?page=3
    http://scholarlykitchen.sspnet.org/2013/02/28/the-elife-story-continues-no-pmc-application-was-made-and-evasions-seem-the-best-we-can-expect/

    Anyhow, we have found a way to get our message out and in the fullness of time our manuscript will appear in a peer-reviewed journal, so I don’t think we should dwell on these issues, but on the science. Right now we invite the readers to do their own peer review and make a judgment on who is right here: please read all three manuscripts. And it would be good if the authors of Weiss et al and those who supported them were to make a public comment on our manuscript and whether they still wish to maintain the claims that they have made. And if they are not prepared to speak up, the scientific community should draw a conclusion from their silence.

    19 Nov 2015, 07:13

  3. Mark Pallen

    I have just seen this paper on the ~7-thousand-year auroochs genome:
    http://www.genomebiology.com/2015/16/1/234

    and note the comment:
    “The absence of significant post-mortem cytosine deamination [in aurochs aDNA] may be attributable to the Phusion High-Fidelity DNA polymerase used during library preparation. This polymerase has been shown to inefficiently amplify DNA fragments containing uracil residues that have been generated via the deamination of cytosine”

    23 Nov 2015, 07:16


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  • I have just seen this paper on the ~7–thousand–year auroochs genome: http://www.genomebiology.com/20… by Mark Pallen on this entry
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