[Annelida] marine polychaete survey
(by kfitzhugh from nhm.org)
Wed Apr 4 22:22:05 EST 2007
I addressed the problem of the naive barcoding mentality in the following article:
Fitzhugh, K. 2006. DNA Barcoding: An Instance of Technology-driven Science? BioScience 56(6): 462-463.
From: annelida-bounces from oat.bio.indiana.edu on behalf of Elena Kupriyanova
Sent: Wed 4/4/2007 5:46 PM
To: Annelida from magpie.bio.indiana.edu
Subject: Re: [Annelida] marine polychaete survey
Helmut Zibrowius wrote:
>> I would recommend to try to id them using morphology first
> that's old-fashioned, you are of another age (like me, I even
> have some advance on you: I am now a retired person, no longer good
> for science in France, but not yet totally moved out of SME, old
> people become slowand unefficient).
> Didn't you hear about the bar-codings fantasm? That's it, the radiant
> future of science!
I am thankful to Helmut for his sarcastic remarks because they made me
about bar-coding applications to any type of faunistic surveys. I may be
really old-fashioned, but to save my life I cannot figure out how
sequencing several genes mentioned in the original message can help to
id 5 species of polychaetes. No, I do understand what it is supposed to
look like in an ideal world.
In this ideal world all species have been properly described and named
(yeap, it does sound like an introduction to a science fiction book
already), their population genetic structure has been studied, the best
"car-coding" genes have been chosen, the appropriate gene fragments have
been sequenced from the type material that has been carefully preserved
and deposited in a museum, and the bar-codes are easily available on
some kind of Gene Bank of the Type Material. In this glorious ideal
world one collects a tiny worm and goes through down the
extraction-amplification-sequencing road without even bothering to look
the worm. The sequence is submitted to the Gene Bank, it matches exactly
one of the "type sequences" and bingo - the answer is (not 42, mind you)
clear and simple: it is Owenia fusiformis!
But what do we have now? One collects a tiny worm and goes through down
the extraction-amplification-sequencing road without even bothering to
look the worms. It is unclear what genes one has to sequence, therefore,
s/he sequences several most commonly used bar-coding genes. The
sequences are submitted to Genbank and the answer is that the sequence
does not match exactly any of existing sequences, but most closely
resembles existing sequences of several terebellids. Ok, it is a
terebellid, fine. But would not it be cheaper and faster to arrive to
this exciting answer using a taxonomic key and a dissecting microscope?
I would appreciate if anybody points out where I get it wrong.
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