[Taxacom] inapplicability of mtDNA barcoding to insects

Nieukerken, E.J. van Nieukerken at naturalis.nnm.nl
Fri Sep 28 03:32:57 CDT 2007


A comparable paper - in the same journal - was published recently:

M. Elias et al, 2007 (4 September), Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proceedings of the Royal
Society B: 2881-2889. doi:10.1098/rspb.2007.1035

DNA 'barcoding' relies on a short fragment of mitochondrial DNA to infer identification of specimens.
The method depends on genetic diversity being markedly lower within than between species. Closely
related species are most likely to share genetic variation in communities where speciation rates are rapid
and effective population sizes are large, such that coalescence times are long. We assessed the applicability
of DNA barcoding (here the 50 half of the cytochrome c oxidase I ) to a diverse community of butterflies from
the upper Amazon, using a group with a well-established morphological taxonomy to serve as a reference.
Only 77% of species could be accurately identified using the barcode data, a figure that dropped to 68% in
species represented in the analyses by more than one geographical race and at least one congener. The use
of additional mitochondrial sequence data hardly improved species identification, while a fragment of a
nuclear gene resolved issues in some of the problematic species. We acknowledge the utility of barcodes
when morphological characters are ambiguous or unknown, but we also recommend the addition of
nuclear sequence data, and caution that species-level identification rates might be lower in the most diverse
habitats of our planet.

End of abstract

Despite this, CO1 works quite well in many groups of Lepidoptera and other insects, we have been successfully identifying larvae and linking sexes in most Nepticulidae (leafmining Lepidoptera). Elias et al suggestion to use EF1alpha in addition (or in stead) is a good one: a much used and easily amplified gene, often with similar or better results than  in CO1.

Erik


Erik J. van Nieukerken
curator of Entomology (Microlepidoptera + Arachnida et al.)/ 
editor Tijdschrift voor Entomologie
National Museum of Natural History Naturalis
dep. of Entomology
PO Box 9517, 2300 RA Leiden, Netherlands
direct phone: +31-71-56 87 682 (secretary ..622)
fax:      +31-71-5687666
e-mail:  nieukerken at naturalis.nl
http://www.naturalis.nl/nieukerken
Tijdschrift voor Entomologie: http://www.nev.nl/tve



-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu]On Behalf Of Doug Yanega
Sent: Thursday, September 27, 2007 7:07 PM
To: entomo-l at listserv.uoguelph.ca; TAXACOM at MAILMAN.NHM.KU.EDU
Subject: [Taxacom] inapplicability of mtDNA barcoding to insects

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
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