[Taxacom] inapplicability of mtDNA barcoding to insects

Schindel, David schindeld at si.edu
Fri Sep 28 12:57:48 CDT 2007


Doug,

In answer to your first question, CBOL has never argued that barcoding
is restricted to COI.  Please refer to CBOL's protocols for proposing
non-COI barcode regions, posted at
http://www.barcoding.si.edu/PDF/Guidelines%20for%20non-CO1%20selection%2
0-%204%20June.pdf.  CBOL is working with representatives of several
taxonomic communities who are developing proposals to give non-COI
regions "barcode status" as recorded in GenBank, EMBL and DDBJ.  

I hope this lays one myth to rest.

David


-----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 1:42 PM
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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