Man’s best molecular friend?

[Jacques Cinq-Mars]

All,

The following is certainly worthy of attention. Not to overdramatise, but could this mean what I think it may mean?

Malmström, Helena, Jan Storå, Love Dalén, Gunilla Holmlund,, and Anders Götherström. 2005. Extensive human DNA contamination in extracts from ancient dog bones and teeth. Molecular Biology and Evolution. [MBE Advance Access published June 15, 2005]

Abstract:

Ancient DNA (aDNA) sequences, especially those of human origin, are notoriously difficult to analyze due to molecular damage and exogenous DNA contamination. Relatively few systematic studies have focused on this problem. Here we investigate the extent and origin of human DNA contamination in the most frequently used sources for aDNA studies, that is, bones and teeth from museum collections. To distinguish contaminant DNA from authentic DNA we extracted DNA from dog (Canis familiaris) specimens. We monitored the presence of a 148 bp human specific and a 152 bp dog specific mitochondrial DNA (mtDNA) fragment in DNA extracts as well as in negative controls. The total number of human and dog template molecules were quantified using real-time PCR and the sequences were characterized by amplicon cloning and sequencing. Although standard precautions to avoid contamination were taken, we found that all samples from the 29 dog specimens contained human DNA, often at levels exceeding the amount of authentic ancient dog DNA. The level of contaminating human DNA was also significantly higher in the dog extracts than in the negative controls, and an experimental setup indicated that this was not caused by the carrier effect. This suggests that the contaminating human DNA mainly originated from the dog bones rather than from laboratory procedures. When cloned, fragments within a contaminated PCR product generally displayed several different sequences, although one haplotype was often found in majority. This leads us to believe that recognized criteria for authenticating ancient DNA cannot separate contamination from ancient human DNA the way they are presently used.

Click HERE for the full article.

Jacques Cinq-Mars

[Jason Eshleman]

First, an apology for posting before introducing myself.

All,

The following is certainly worthy of attention. Not to overdramatise, but could this mean what I think it may mean?

<link removed>

Jacques Cinq-Mars

That depends on what you think it means.  The authors state that they used "standard precautions" though, unfortunately, it seems like everyone and their brother's cousin's best friend now seems to want to do ancient DNA work.  There's far less "standard" than there should be. 

While much of their methodology seems fine, their decontamination protocol for the bone surface is not the most rigorous.  I recommend:

(Kemp, B. M. and D. G. Smith. 2005.  Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int Forthcoming.)

[sorry, I'm a newbie and can't seem to figure out how to link to the journal site]

I have found in my own work that extensive decontamination does not completely assure that results will not contain contaminant sequences, but it can cut down on the incidence greatly. 

-Jason

[Jacques Cinq-Mars]

First, an apology for posting before introducing myself.



That depends on what you think it means.  The authors state that they used "standard precautions" though, unfortunately, it seems like everyone and their brother's cousin's best friend now seems to want to do ancient DNA work.  There's far less "standard" than there should be. 

While much of their methodology seems fine, their decontamination protocol for the bone surface is not the most rigorous.  I recommend:

(Kemp, B. M. and D. G. Smith. 2005.  Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int Forthcoming.)

[sorry, I'm a newbie and can't seem to figure out how to link to the journal site]

I have found in my own work that extensive decontamination does not completely assure that results will not contain contaminant sequences, but it can cut down on the incidence greatly. 

-Jason

Dear Jason,

What I meant was that the paper definitely gave the ominous impression -- to someone like me who may feel inclined, at times, to make use/refer to “molecular” data -- that the accuracy of such studies may well be inversely proportional to the “bravado” they frequently exhibit in their published forms. In this regard, you might be interested in reading the following note (HERE) from Maciej Henneberg.

But anyway, welcome to the Forum and thanks for the qualified reassuring words.

Jacques

PS   To provide a link in a post, use the following html code:

url=http://*]CLICK HERE[/url

The asterisk marks the position of the actual URL, and make sure that the whole string begins and ends with [ ].

[Jason Eshleman]

Ah, if only there were an easy way to present what *hasn't* worked in the ancient DNA world...

[Jacques Cinq-Mars]

Ah, if only there were an easy way to present what *hasn't* worked in the ancient DNA world...

Do not despair, there are ways. For starters, people should read the following paper that is clearly telling of some sort of a “molecular malaise” and that points to a few corrective measures. I would also add to these, the need, on the part of researchers to develop a better appreciation of what true interdisciplinarity is all about. After all, there is more to human history than just "molecules".

Gilbert, M. Thomas P., Hans-Jürgen Bandelt, Michael Hofreiter, and Ian Barnes. 2005. Assessing ancient DNA studies. TRENDS in Ecology and Evolution (in press).

Abstract:

The study of ancient DNA has the potential to make significant and unique contributions to ecology and evolution. However, the techniques used contain inherent problems, particularly with regards to the generation of authentic and useful data. The solution currently advocated to reduce contamination and artefactual results is to adopt criteria for authentication. Nevertheless, these criteria are not foolproof, and we believe that they have, in practice, replaced the use of thought and prudence when designing and executing ancient DNA studies. We argue here that researchers in this field must take a more cognitive and self-critical approach. Specifically, in place of checking criteria off lists, researchers must explain, in sufficient enough detail to dispel doubt, how the data were obtained, and why they should be believed to be authentic.

Click HERE for the article.

Jacques Cinq-Mars

[Jason Eshleman]

i just saw that one on Friday.  Thanks!

-Jason