[Taxacom] inapplicability of mtDNA barcoding to insects

Schindel, David schindeld at si.edu
Fri Sep 28 07:20:50 CDT 2007


Dear Colleagues,

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.  Genitalia
aren't reliable for species-level diagnosis in vertebrates, so are they
unreliable for insects?  Organellar DNA have some limitations relative
to nuclear DNA for taxonomy and phylogenetic research, but isn't the
opposite also true?  Arguments such as these reinforce the saying that
the perfect is the enemy of the good.
 
Ours is a comparative, historical science in which there are no magic
bullets.  The strength of our assertions comes from the corroboration
provided by different, independent, converging lines of evidence.  If
COI gives a pattern in conflict with morphology or geography or ecology,
there is no simple and automatic explanation for the underlying cause.
The Consortium for the Barcode of Life (CBOL; www.barcoding.si.edu) and
most barcoders make no claim of infallibility for barcode data.  We
claim only their utility in (1) assigning specimens to well-established
species (in most cases), and (2) testing our taxonomic (but not
phylogenetic) hypotheses.  That is the core mission for barcoding, and
we recognize its limitations while developing its strengths.
 
When taxonomists find discrepancies among types of data, we usually find
an interesting phenomenon, like lateral gene transfer or speciation
through hybridization.  If we dismissed mitochondrial data as locally
flawed and therefore universally useless, we blind ourselves to these
revealing, discrepant patterns.  "The exception probes the rule" and we
should take pleasure in (and seek funding for) probing these exceptions.

 
Regards to all,
 
David
 

David E. Schindel, Executive Secretary

Consortium for the Barcode of Life

202/633-0812; fax 202/633-2938; portable 202/557-1149

Email: SchindelD at si.edu <mailto:SchindelD at si.edu>  

CBOL WEBSITE: http://www.barcoding.si.edu <http://www.barcoding.si.edu/>


 

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National Museum of Natural History

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-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Ken Kinman
Sent: Thursday, September 27, 2007 11:51 PM
To: lammers at uwosh.edu; dyanega at ucr.edu; entomo-l at listserv.uoguelph.ca;
TAXACOM at MAILMAN.NHM.KU.EDU
Subject: Re: [Taxacom] inapplicability of mtDNA barcoding to insects

Dear All,
    Every particular genetic sequence has its strengths and weaknesses,
so it is not surprising this one does as well (including various plant
and insect taxa).  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.

      Not that nuclear sequences don't have their own problems, as an
over-reliance on rDNA sequences has caused problems as well (from
"Domain"
level on down).  So we must not put all our eggs in one basket, or to
quote a stock market mantra, we need to diversify our portfolios.  Each
line of evidence is different, so we always need to seek congruence from
several lines of evidence to feel we have something we can even consider
"betting the farm on".  The COI sequence that barcoding has started with
is pretty solid for some taxa, but very "sandy" for others.  By the time
"barcoding devices" are widely available, they will hopefully
incorporate several different sequences that will leave very few "sandy"
problem areas.  And when future barcoders can look at complete genomes,
these problems will even be uncommon at the population level (although
still enough to spark debates).  And even genetic data has its
limitations when it comes to higher taxa, especially those with a high
percentage of fossil taxa.
    -----Ken
*********************************
>From: "Thomas G. Lammers" <lammers at uwosh.edu>
>To: Doug Yanega <dyanega at ucr.edu>,
>entomo-l at listserv.uoguelph.ca,TAXACOM at MAILMAN.NHM.KU.EDU
>Subject: Re: [Taxacom] inapplicability of mtDNA barcoding to insects
>Date: Thu, 27 Sep 2007 12:47:49 -0500
>
>As far as I'm concerned, any study utilizing organelle DNA is a house
>built on sand.  Those genomes had very little to do with the species'
>evolution; at most they were along for the ride and might by chance
>reflect the true phylogeny.  I wouldn't bet the farm on it.
>
>At 12:07 PM 9/27/2007, Doug Yanega wrote:
> >This may be old news to many, but I just came across this paper
today:
> >
> >T.L. Whitworth, R.D. Dawson, H. Magalon, E. Baudry (2007) DNA
> >barcoding cannot reliably identify species of the blowfly genus
> >Protocalliphora (Diptera: Calliphoridae). Proceedings of the Royal
> >Society B: 274: 1731-1739
> >[http://www.journals.royalsoc.ac.uk/content/tu21831k825kv655]
> >
> >This excerpt from the abstract is pretty remarkable:
> >
> >Here, we investigated the performance of barcoding in a sample
> >comprising 12 species of the blow fly genus Protocalliphora, known to
> >be infected with the endosymbiotic bacteria Wolbachia. We found that
> >the barcoding approach showed very limited success: assignment of
> >unknown individuals to species is impossible for 60% of the species,
> >while using the technique to identify new species would underestimate
> >the species number in the genus by 75%. This very low success of the
> >barcoding approach is due to the non-monophyly of many of the species
> >at the mitochondrial level. We even observed individuals from four
> >different species with identical barcodes, which is, to our
> >knowledge, the most extensive case of mtDNA haplotype sharing yet
> >described. The pattern of Wolbachia infection strongly suggests that
> >the lack of within-species monophyly results from introgressive
> >hybridization associated with Wolbachia infection. Given that
> >Wolbachia is known to infect between 15 and 75% of insect species, we
> >conclude that identification at the species level based on
> >mitochondrial sequence might not be possible for many insects.
> >
> >I'm curious to know how many other studies have come to similar
> >conclusions, and how the barcoding community is responding to this
> >EXTREMELY serious issue - it could potentially invalidate almost
> >every barcoding study ever performed with insects (a brief glance at
> >a few such studies indicates that screening for Wolbachia is not part
> >of barcoding protocol).
> >
> >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
> >_______________________________________________
> >Taxacom mailing list
> >Taxacom at mailman.nhm.ku.edu
> >http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
>Thomas G. Lammers, Ph.D.
>
>Associate Professor and Curator of the Herbarium (OSH) Department of
>Biology and Microbiology University of Wisconsin Oshkosh Oshkosh,
>Wisconsin 54901-8640 USA
>
>e-mail:       lammers at uwosh.edu
>phone:      920-424-1002
>fax:           920-424-1101
>
>Plant systematics; classification, nomenclature, evolution, and
>biogeography of the Campanulaceae s. lat.
>
>Webpages:
>http://www.uwosh.edu/departments/biology/Lammers.htm
>http://www.uwosh.edu/departments/biology/herbarium/herbarium.html
>http://www.geocities.com/TheTropics/Resort/7156/lammers.html
>-----------------------------------------------------------
>"Today's mighty oak is yesterday's nut that stood his ground."
>                                                                --
>Anonymous

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