[Taxacom] Dark taxa: GenBank in a post-taxonomic world

[Jason Mate]

Really what you are describing is the rise of the wrong kind of lab-based taxonomy, i.e. the sequence becomes the organism and is solely defined by it. I agree that names have no value in themselves, that they are just tags to get to the actual knowledge. But if somebody, anybody, wants to offer an alternative to our current admitedly flawed system, then you have to offer a better argument than "cause everybody is doing it". Off the top of my head some of the problems I forsee with the brave new world you envisage:
Practicality. Even when the day comes that sequencing is instantaneous, cheap and portable (Star Trek, GATTACA, your choice), it is just not very practical to sample every organism to know what it is. Imagine you are taking a census, in a reef for example, and you had to chase down every fish for a bit of tissue to identify. So DNA field work is out.
Existing collections. Like it or not the grand majority of the biogeographical and ecological information currently exists in museums. Even if we avoid a major extinction event in the next 50 years we have lost much of the "information". How would you tie your barcode to a pinned specimen? Bioinformatists dislike names because they like neat and clean (synonyms are the bane of all) but they will just have to get used to it.

Which tag? In spite of the hype that it can be done with a couple of markers (i.e. COI, rbcL, matK) more and more examples are showing that this is just not true. i.e. in the current issue of Cladistics (Pang et al): ''...from 893 species in 96 diverse genera, ITS2 successfully identified 78 and 100% of them...". This was the best performing gene (and not even the first choice of the barcoding initiative) out of 4 and the authors were enthusiastic about the results. But I guess 78% is better than 0 if you can´t tell one organism from another.

Contamination. Your Carabus auratus just had a meal of Nebria. You sequence and voilá, you record your specimen as Nebria. This happens a lot but if you know what you are sequencing is Carabus, probably auratus, and not Nebria then you repeat the PCR or reextract from an area that will minimise the problem.

Failure to amplify. We´ve all been there. But now you are stuck because the farmer is waiting to know which treatment to carry out and you can´t tell him/her if it is a Thrips tabaci or Frankliniella occidentalis.
Fossils. Same problem as existing collections.

Randomness. You can get a false hit if you run a sequence against hundreds of thousands. Again, if you are ignorant of the organism you won´t be able to tell.
I actually like the idea of barcodes as an aid, something that allows the identification of previously intractable problems (fragments, gut contents, microorganisms, nematodes, etc) or when you come across something novel. But for most day-to-day work, identifying macroorganisms via barcoding is ludicrously impractical.

Best

Jason


> From: r.page at bio.gla.ac.uk
> Date: Tue, 12 Apr 2011 14:53:00 +0100
> To: taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] Dark taxa: GenBank in a post-taxonomic world
> 
> This post may be of interest to TAXACOM readers. "Dark taxa: GenBank in a post-taxonomic world"
> 
> http://iphylo.blogspot.com/2011/04/dark-taxa-genbank-in-post-taxonomic.html
> 
> Regards
> 
> Rod
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
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