Publication of aDNA

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Greg Adcock writes: "what are the minimum requirements for publication? I
would be interested in what the new Ancient Biomolecules editorial policy
(written and unwritten) is on this matter"

and Jere Lipps: "As I read their policy on there flyer, it states only "All
articles are professionally refereed and are accepted for publication only
if the results are fully substantiated."  I'd sure like to know how they
will do
the latter."

So I guess I had better try to respond.

First, the sentence before the one Jere quotes is "The Editors are
committed to improving the standard of the published research archive on
ancient biomolecules". That was the reason I agreed to set up the new
journal and I agree with just about everything that has been said in the
previous contributions to this discussion. Mark Marshall, who started the
discussion, is not the only mainstream molecular biologist who finds it
hard to believe some of the ancient DNA reports in the literature. This
situation will stay with us, even get worse, if we do not raise our
standards and address the issues of verification and authentication.

In the long run I think there is only one answer. We must understand how
DNA decays in fossil material and demonstrate how and why DNA can evade the
standard processes of decay as described by Lindahl. If we can demonstrate
that DNA in amber, fossil bone, burnt seeds or whatever decays in a
different way, with different rates, to DNA in aqueous solution then we
will begin to counter the main argument against our work, that with many of
our specimens there shouldn't be any DNA. In my opinion the statement
'ancient DNA exists' is our grand hypothesis, equivalent to killer
asteroids, cold fusion or whatever. No-one can say that the hypothesis has
been stifled, we have had widespread opportunities to publicise it. Now we
have to get the fully substantiated, scientifically-valid data to support
the hypothesis.

That was the build up, now the let down - I don't yet know what the
'requirements for publication' are, or even if you can devise a consistent
set of criteria for every aDNA project. Should the criteria for a
100-year-old museum skin be the same as for a 10,000-year-old human bone,
or a 20-million-year-old amber specimen? Is it counter-productive to insist
on requirements which many labs might have difficulty in meeting for
financial reasons - in the end it will be the weight of evidence which gets
our hypothesis accepted so it would be wrong to say that only the
highly-grant-supported few can contribute the data.

At adna3 Matthias Krings of Paabo's lab gave an excellent talk in which he
described his own criteria for an acceptable aDNA result from human
material. My own ideas for authentication are based on his talk. Here they
are with comments in brackets (I want to state very clearly that these are
not currently 'requirements for publication' in Ancient Biomolecules):

1. The standard PCR controls (water and extract blanks) must be run for
each extraction/amplification from ancient material. [This has to be an
absolute requirement.]

2. It must be shown that smaller sized molecules predominate in the ancient
extract. This could be done by attempting PCRs with two, three or more
primer pairs for different sized targets. [We all agree that ancient DNA is
fragmented. This would cause a bit more expense as you would need a few
more primers. For human DNA it should be possible to agree on sets of
primers that we all use for this purpose. Problems: contaminating DNA could
also be fragmented; the presence of inhibitors could result in the more
widely spaced primers giving lower amounts of products with a contaminating
template.]

3. It must be shown that the PCR product derives entirely from a single
source. In other words, the product must be cloned and a dozen or so
sequences obtained, all of which should be identical. ['Identical' has to
take account of Taq error rate, which would have to be assayed with
products from a modern template, using precisely the same PCR conditions as
the ancient extract - would inhibitors in the ancient extract influence the
error rate?]

4. The results must be replicated with a second sample from the same
specimen. [Again, an essential one unless you have very good arguments for
not being able to do this.]

5. The results must be duplicated by a second lab. [Several groups are
setting up collaborations to duplicate results but there are practical
reasons for not insisting on this - e.g. material cannot always be moved
out of the country of origin - as well as financial issues, the people who
pay for my research have certainly not given me money for this.]

6. A non DNA technique such as amino acid racemisation should be used to
get a more general picture of biomolecular preservation in the ancient
material. [Not keen to make this an absolute requirement as it requires new
skills, and who is to say that amino acid racemisation parallels DNA decay
in all specimens?]

7. 'Phylogenetic inference', in other words 'the sequences must make
sense'. [But the most interesting results might be the ones that don't make
sense.]

Those are few ideas, but I'm fairly certain that the definition of 'fully
substantiated' has to be redefined for each individual research project. I
hope this does not sound like a climb down. Presumably you believe that
your results are fully substantiated otherwise you would not be submitting
them for publication. So describe your criteria and say why they are
convincing. The difference between Ancient Biomolecules and some other
journals is that the referees and editors that you must convince will all
have direct expertise in aDNA research and will know the problems and
pitfalls with this type of work.

This is a good discussion, let's hear some more.

Terry Brown
Dept of Biochemistry and Applied Molecular Biology,
UMIST, Manchester M60 1QD, UK