[Taxacom] inapplicability of mtDNA barcoding to insects

[Doug Yanega]

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