DNA Barcoding: Promise and Pitfalls
Craig Moritz* , Carla Cicero

Academic Editor: Charles Godfray, Imperial College

Craig Moritz and Carla Cicero are at the Museum of Vertebrate Zoology,
University of California, Berkeley, California, United States of America.

Published September 28, 2004

DOI: 10.1371/journal.pbio.0020354

Copyright: © 2004 Craig Moritz and Carla Cicero. This is an open-access
article distributed under the terms of the Creative Commons Attribution
License, which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.

Citation: Moritz C, Cicero C (2004) DNA Barcoding: Promise and Pitfalls.
PLoS Biol 2(10): e354.

In this issue of PLoS Biology, Hebert et al. (2004) have set out to test the
resolution and performance of "DNA barcoding," using a single mtDNA gene,
cytochrome c oxidase I (COI), for a sample of North American birds. Before
turning to details of this study, it is useful as context to consider the
following questions: What is DNA barcoding, and what does it promise? What
is new about it? Why is it controversial? What are the potential pitfalls?

Put simply, the intent of DNA barcoding is to use large-scale screening of
one or a few reference genes in order to (i) assign unknown individuals to
species, and (ii) enhance discovery of new species (Hebert et al. 2003;
Stoeckle 2003). Proponents envisage development of a comprehensive database
of sequences, preferably associated with voucher specimens representing
described species, against which sequences from sampled individuals can be
compared. Given the long history of use of molecular markers (e.g.,
allozymes, rDNA, and mtDNA) for these purposes (Avise 2004), there is
nothing fundamentally new in the DNA barcoding concept, except increased
scale and proposed standardization. The former is inevitable.
Standardization, i.e., the selection of one or more reference genes, is of
proven value in the microbial community and in stimulating large-scale
phylogenetic analyses, but whether "one gene fits all" is open to debate.

Full Text at PLoS Biology
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0020354

A Molecular Model of Blood Cell Renewal
DOI: 10.1371/journal.pbio.0020349

Published September 28, 2004

Copyright: © 2004 Public Library of Science. This is an open-access article
distributed under the terms of the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited.

Citation: (2004) A Molecular Model of Blood Cell Renewal. PLoS Biol 2(10):
e349.

A developing organism captured on time-lapse video is a wonder to behold. If
you're watching a chick embryo, by day 3, you'll see millions of cells
engaged in a frenzy of activity, as rapidly dividing cells migrate to new
positions, acquire the characteristics of specialized cells, and craft
well-defined tissues, organs, and limbs in just under two weeks. In addition
to the cells destined for specialization is another important group, stem
cells, whose progeny have two very different fates. They can either "self
renew"-that is, make identical copies of themselves-or generate intermediate
progenitor cells that give rise to mature, differentiated cells.

Both differentiation and self renewal are guided by an elaborately regulated
genetic program, which transforms embryonic stem cells into the many
different cell types that make up the body. Adult stem cells share the
hallmark trait of self renewal, but are relatively rare: in bone marrow, the
source of hematopoietic, or blood-forming, only an estimated one in
10,000-15,000 cells is an adult hematopoietic stem cell (HSC).

Studies that have compared the gene expression profiles of different types
of stem cells to identify genetic signatures of "stemness" have
found only a
limited number of signature genes. And the molecular mechanisms that
regulate this so-called potency and the self renewal process have remained
obscure. Now, focusing on HSCs, Margaret Goodell and colleagues have
undertaken a systematic evaluation of HSC renewal. The study identifies
molecular signatures associated with discrete stages of the HSC self renewal
cycle and proposes a molecular model of the process.

Full Text at PLoS Biology
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0020349

A Test Case for DNA Barcodes to Identify Species
DOI: 10.1371/journal.pbio.0020357

Published September 28, 2004

Copyright: © 2004 Public Library of Science. This is an open-access article
distributed under the terms of the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited.

Citation: (2004) A Test Case for DNA Barcodes to Identify Species. PLoS Biol
2(10): e357.

One hundred years before Darwin returned from his voyage on the H. M. S.
Beagle "struck with certain facts" that "seemed to throw
some light on the
origin of species," Linnaeus published the first systematic taxonomy of
life. In Systema Naturae, the Swedish botanist divided organisms into
plants, animals, and minerals, eventually assigning scientific names to
7,700 plant and 4,400 animal species, and popularizing the binomial
system-as in Homo sapiens-of naming species.

In the 1700s and 1800s, naturalists classified organisms based on
morphology, devoting their careers to naming newfound plants and animals.
Today biologists still use Linnaean taxonomy as the foundation of scientific
classification. But with just a fraction of the estimated 5-30 million
species on the planet already named and too few specialists to do the job,
biologists are looking for high-throughput tools that can rapidly and
accurately identify both individuals of a species and entirely new species.
That's what some scientists say the DNA barcode will do. The DNA barcode, as
the name implies, uses genes to identify species much like supermarket barco
des identify products. The idea is that a short stretch of genetic code from
a reference gene is unique enough to one species to distinguish it from
every other species, and that comparisons of sequence variations in that
stretch of gene can reveal evolutionary relationships among species.

Full Text at PLoS Biology
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0020357

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