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June 24, 2009
Source:
American Journal of Botany
The goal of DNA barcoding is to
find a simple, cheap, and rapid DNA assay that can be converted
to a readily accessible technical skill that bypasses the need
to rely on highly trained taxonomic specialists for
identifications of the world's biota. This is driven by a desire
to open taxonomic identifications to all user groups and by the
short supply of taxonomists that do not even exist in many
groups. Although DNA barcoding is being rapidly accepted in the
scientific literature and popular press, some scientists warn
that we are being too hasty in wholeheartedly embracing this
technique. Dr. David Spooner, a researcher with the USDA and an
expert in the potato and tomato family (Solanaceae), offers just
such a cautionary note against accepting this technique without
closer examination in his recent article, "DNA Barcoding will
Frequently Fail in Complicated Groups: An example in Wild
Potatoes" in the June 2009 issue of the
American Journal of Botany.
One of the critical issues surrounding the DNA barcoding debate
is that using a section of DNA may not adequately distinguish
among closely related species or complex groups. Moreover, in
plants, there is still much debate over which gene sequence
region should be used and its reliability. In animals, the 5'
segment of mitochondrial cytochrome oxidase subunit I (COI) is
relatively established as a barcoding marker, but Spooner
highlights many groups where COI fails to distinguish species.
The COI region fails completely for plants because it evolves at
a slower rate in plants and has a much more variable sequence.
The search for alternative barcoding regions in plants is
especially problematic. Although several gene sequences have
been proposed for plants, none of them serves as a universal
barcode marker. Regions that have been proposed for plants
include a section of the nuclear ribosomal DNA: the internal
non-transcribed spacer region (ITS); and various plastid regions
to include the trnH-psbA intergenic spacer and the plastid genes
rpoC1, rpoB, and matK.
Spooner tested the utility of barcoding in a well-studied but
complex plant group, wild and cultivated potatoes (Solanum
section Petota). Section Petota includes over 200 species and is
widespread throughout the Americas. In his study, 63 ingroup
species and 9 outgroup species (in the genera Solanum, Capsicum,
and Datura) were used. DNA was extracted from young leaves of
single plants. Spooner tested the most frequently suggested DNA
barcoding regions for plants: ITS, trnH-psbA, and matK. He found
that none of these regions were very accurate at distinguishing
or serving as markers for species boundaries in the section
Petota. There was too much intraspecific variation in the
nuclear ITS region, and the plastid markers did not have enough
variation and thus failed to group together some well-supported
species. Section Petota is a complex group because, among other
things, there is much hybridization among species; some of the
species have multiple divergent copies of their DNA arising from
past hybridization (allopolyploidy); there is a mixture of
sexual and asexual reproduction; and there is possible recent
species divergence. Such complications are not uncommon in many
plant groups. Spooner concludes that a variety of morphological
and molecular approaches are needed, and we cannot rely on a DNA
barcode alone to distinguish among species in complex groups
such as section Petota.
Spooner extrapolates from the taxonomic difficulties of section
Petota to many other groups possessing similar biological
traits, and points out that DNA barcoding needs to be accepted
with great caution as these groups have not been tested with the
technique. He also urges caution against limiting the
identification, or in some cases even the definition of a
species to a small sequence of DNA. He suggests that the search
for a DNA barcoding marker or limited set of such markers that
reliably identify the majority of life forms will be a
continuously elusive goal. |
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