[Taxacom] inapplicability of mtDNA barcoding to insects

Ken Kinman kinman at hotmail.com
Thu Sep 27 22:51:28 CDT 2007


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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