[Taxacom] inapplicability of mtDNA barcoding to insects

Richard Pyle deepreef at bishopmuseum.org
Fri Sep 28 14:43:52 CDT 2007


I've been keeping an eye on the barcoding thing pretty-much since its
inception, but I must have missed a lot of popular press surrounding it,
and/or have not been talking to the same barcoders that some others on this
list have.

My impression has been that, in the early life of barcoding (which I'll
define here as roughly 2002-2004), there was a lot of bold predictions about
how barcoding will re-define taxonomy, etc., etc. (e.g., the following quote
from a prominent barcode proponent: "Let's face it, the morphological
approach has had 250 years to advance the task, and we're only 10% of the
way towards the goalposts..."). However, most of the conversations I've had
with active barcoders since then (including the author of the aforementioned
quote) have characterized it much less as a replacement to other forms of
taxonomic practice, and more as a supplement to them (i.e., very much in
line with David Schindel's recent Taxacom post).

There was a debate held at the September 2004 PEET conference, which I was
unable to attend, but for which I submitted the following question:

"Would taxonomists use barcodes to make decisions about species boundaries,
or would the technique only be used as an aid to identification of
specimens?"

I don't know what the specific answer to that question was from the debate,
but I'm generally comfortable with the answer I get from active barcoders in
recent years:  I.e., most see it as a tool that can be very valuable for
identification purposes in some cases (or at least an effective means to
narrow down the scope of likely taxa) -- particularly for linking larval
forms to adult forms, etc.  And also as a tool that can inform taxonomists
about the possibility of (yes) cryptic species complexes and other
interesting taxonomic phenomena in some cases.  I've yet to meet anyone who
actually sees it as a full-blown replacement to more traditional taxonomic
practices.

As a non-molecular alpha-level taxonomist myself, I am planning to have the
holotype specimens of our next batch of new species barcoded -- not as a
means to *define* the species, but as yet another piece of information that,
like the morphological characters that distinguish the species, offer one
more line of information that may or may not be of use to future
researchers.

Overall, I do see value in the barcoding process, and I'm interested to see
what we end up learning from it.  Whether or not it is worth the financial
investment it has/will receive/d is a question for the funders to answer for
themselves.

But I would suggest to David Schindel and other leaders in the barcoding
community that there clearly remains a problem of perception from the
perspective of active (non-barcoding) taxonomists, as evidenced by this
taxacom thread.  I imagine I would have the same perception had I not had
specific opportunities to had long and thoughtful conversations with active
barcoding folks over the past few years. And there is a real risk of
perception among new/young taxonomists that molecules are the best way to
*define* species (but this problem is not specific to barcoding per se).

Aloha,
Rich

P.S. To be clear, I'm not shaking the pom-poms for barcoding the way I have
for other biodiversity informatics initiatives -- but I still find it less
threatening, and more potentially useful than many of my morphology-oriented
alpha-level taxonomist brethren might.


> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Doug Yanega
> Sent: Friday, September 28, 2007 7:42 AM
> To: TAXACOM at MAILMAN.NHM.KU.EDU; entomo-l at listserv.uoguelph.ca
> Subject: Re: [Taxacom] inapplicability of mtDNA barcoding to insects
> 
> Some of the things being said now are NOT the things that I 
> have heard from Paul Hebert and others in the not-too-distant 
> past. For example, Ken Kinman wrote:
> 
> >Barcoding in the long run obviously cannot rely on a single 
> sequence, 
> >and organelle sequences alone are probably going to be (on
> >average) more problematic than nuclear sequences.
> 
> The entire CONCEPT of barcoding, by definition at its 
> inception, was to examine a single standardized sequence for 
> all organisms on earth
> - that was the secret to its speed and ease of application:
> 
> "One gene to rule them all,
> One gene to find them,
> One gene to bring them all
> and with their barcodes bind them"
> 
> >And when future barcoders can look at complete genomes
> 
> ...then it will no longer be a "barcode", by definition! Or 
> am I missing something?
> 
> Then, in a similar vein, David Schindel said:
> 
> >This and previous exchanges about barcoding on Taxacom 
> started on what 
> >I consider a false premise - that a gene region or any taxonomic 
> >character is flawed if it doesn't work for all purposes on 
> all groups. 
> >(snip) The strength of our assertions comes from the corroboration 
> >provided by different, independent, converging lines of evidence.
> 
> Which, again, does not match the definition of barcoding most 
> of us are familiar with. You accuse others of using "straw 
> man" arguments, but it could be turned around and interpreted 
> as "bait-and-switch".
> 
> and Peter Kevan added:
> 
> >Why imply through nay-saying that barcoding should be dismissed 
> >outright because it is not 100% accurate 100% of the time?
> 
> Because if we rely exclusively on COI to make species IDs, 
> and are sinking huge amounts of funding into it (whether or 
> not it is to the exclusion of morphological taxonomy), then 
> ~70% accuracy is certainly not much of a selling point for 
> that MASSIVE investment. I don't think anyone here is saying 
> it should be *dismissed*, but it certainly doesn't look like 
> it deserves *any greater attention than any other gene*, or 
> *any other data set*. It is this specific point that prompted 
> my original question: if we now know that COI cannot be used 
> for recognizing all organisms, then why are there people 
> still acting as if it can do just that?
> 
> For instance, contrast Ken's, David's, Peter's, and others' 
> claims with what Karl Magnacca wrote:
> 
> >one major
> >disappointment was seeing how many people doing barcoding 
> studies are 
> >rather ignorant of basic principles of genetics, phylogenetics, and 
> >taxonomy.  That, I think, is a far greater problem than the 
> existence 
> >of taxa where barcoding fails.
> 
> The failure of COI barcoding *is* a problem if COI is being 
> treated as the only viable source of taxonomic data, and - if 
> what Karl says is true - there are apparently a number of 
> barcoders who are NOT using COI as an adjunct to traditional 
> taxonomy, but as a replacement for it (or treating taxonomy 
> as an adjunct to COI). At least several MAJOR papers on the 
> topic I have read concluded that the discrepancies between 
> what the taxonomists called species versus what COI grouped 
> as species meant that the taxonomy was wrong (i.e., there 
> were cryptic species the morphological taxonomists had 
> completely overlooked).
> 
> That is directly in conflict with the statement by David Schindel:
> 
> >If COI gives a pattern in conflict with morphology or geography or 
> >ecology, there is no simple and automatic explanation for the 
> >underlying cause.
> 
> To me, repeatedly invoking "cryptic species" seems like a 
> simple and automatic explanation. Or am I missing something?
> 
> It leaves us with a dilemma as far as any debate here: if 
> everyone here claims to be a "good" barcoder, for whom COI is 
> just one of an array of character sets used to determine 
> species, but if those folks acknowledge that there are "bad" 
> barcoders that believe in using (or
> trusting) COI alone, then we may actually be condemning a 
> common enemy, and should be acting as allies rather than adversaries.
> 
> So, let's sit back one second, take a breather, and ask two questions:
> 
> (1) Can we agree upon a definition of "barcoding"? As far as 
> I knew, it meant using COI, and ONLY COI in order to make 
> species assignments.
> (2) Can we agree that there ARE researchers who use COI only, 
> or give COI results *greater weight* than taxonomy?
> 
> If so, can we then treat the debate here as a matter of 
> whether THAT approach is worthy of support, or should be put 
> aside in favor of genuinely *integrated* studies?
> 
> Sincerely,
> -- 
> 
> Doug Yanega        Dept. of Entomology         Entomology 
> Research Museum
> Univ. of California, Riverside, CA 92521-0314        skype: dyanega
> phone: (951) 827-4315 (standard disclaimer: opinions are 
> mine, not UCR's)
>               http://cache.ucr.edu/~heraty/yanega.html
>    "There are some enterprises in which a careful disorderliness
>          is the true method" - Herman Melville, Moby Dick, 
> Chap. 82 _______________________________________________
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