Transcript DNA Barcoding - Columbia University

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Director James Hanken
Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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DNA barcoding: a new diagnostic
tool for rapid species recognition,
identification, and discovery
James Hanken
Museum of Comparative Zoology
Harvard University, USA
What is DNA barcoding?
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Definition: Derivation of a short DNA sequence(s)
that enables species identification or recognition in
a particular domain of life (eucaryotes).
Focus to date—in animals—has been on a 658
base-pair (bp) fragment of the mitochondrial gene,
cytochrome oxidase subunit I (COI).
The Barcode of Life Initiative (BOLI) would resolve
barcodes for named species and use a barcoding
approach to assess undescribed biological diversity.
Very controversial!
What isn’t DNA barcoding?
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It is not intended to, in any way, supplant
or invalidate existing taxonomic practice.
It is not DNA-taxonomy; it does not equate
species identity, formally or informally, with
a particular DNA sequence.
It is not intended to duplicate or compete
with efforts to resolve deep phylogeny,
e.g., Assembling the Tree of Life (ATOL).
“the role of any molecular diagnostic is to aid research,
not to serve as an end in itself. Barcoding … is
independent of questions as to whether individual taxa
are species, what species are (or should be), and
where they fit in a unified tree of life…. Barcoding is
not an end in itself, but will boost the rate of discovery.
The unique contribution of DNA barcoding to …
taxonomy and systematics is a compressed timeline
for the exploration and analysis of biodiversity.”
Recent chronology (2003)
January
February
March
May
June
September
December
Hebert et al., in Proc. Roy. Soc. Lond.
Tautz et al., in TREE, and related letters
and commentary.
Banbury I at CSHL, Taxonomy and DNA.
Hebert et al., in Proc. Roy. Soc. Lond.
More letters and commentary in TREE.
Pennisi, in “Tree of Life” issue of Science;
“It’s not research” (J. Rodman, NSF).
Stoeckle, in BioScience.
Banbury II at CSHL, Taxonomy, DNA and
the Barcode of Life.
Besansky et al., in Trends in Parasitology.
Potential applications
1) Facilitating identification and recognition of
named (described) species:
 linking life history stages, genders;
 differentiating cryptic species;
 identifying gut contents;
 human disease vectors;
 agricultural pests;
 biosecurity (?).
2) Surveying and inventorying biodiversity; e.g.,
flagging potentially new (undescribed) species.
Linking life history
stages, genders
female C. fenyesi
(parasitic in cricket)
male C. fenyesi
(parasitic in ant)
Differentiating cryptic species
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D. Janzen, et al., submitted
Astraptes fulgerator, skipper
butterfly.
Wide-ranging; southern U.S.
to northern Argentina.
In northwestern Costa Rica,
comprises complex of 10
sympatric species that are
distinct in DNA sequence
(COI), larval coloration, food
plants, and subtle
morphological traits.
Sympatric larvae of
Astraptes fulgerator
Food plant:
Trigonia
(2 species);
larvae will
starve if
reared on
plants used
by other
larval types.
Food plant:
Celtis
iguanaea
Strengths
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Offers alternative taxonomic identification tool for
situations in which morphology is inconclusive.
Focus on one or a small number of genes
provides greater efficiency of effort.
Cost of DNA sequencing is dropping rapidly due
to technical advances.
Potential capacity for high throughput and
processing large numbers of samples.
Once reference database is established, can be
applied by non-specialist.
Weaknesses
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Assumes intraspecific variation is negligible, or
at least lower than interspecific values.
No single gene will work for all taxa (e.g., COI is
not appropriate for vascular plants, or even for
some animals).
Single-gene approach is less precise than using
multiple genes; may introduce unacceptable
error.
Some of the most attractive aspects rely on
future technology, e.g., handheld sequencer.
Proportion of species pairs
Between-species sequence
divergence in COI (%)
1.0
n = 13,320
1.0
0.8
0.8
0.6
0.6
0.4
0.4
0.2
0.2
0
0
2 4 8 16 32 64%
Annelida, Arthropoda, Chordata, Mollusca,
Echinodermata, Nematoda, Platyhelminthes
n = 17
2 4 8 16 32 64%
Cnidaria (corals, anemones,
jellyfish, sea pens, etc.)
COI sequence divergence
among North American birds
K2P (%)
Barcoding must adhere to standards
for specimen and data management
Sequence data
Voucher specimens
and electronic
databases
Digital images
Pilot projects
1) Goals and objectives:
 Validate barcoding approach, in general, and the use of
COI, in particular (for animals); i.e., proof of principle.
 Assess feasibility of large-scale effort, e.g., identify
bottlenecks, cost, logistic issues.
2) Possible targets:
 “All taxa”—primates, turtles, mosquitoes, tephritid
fruitflies, birds, sphinx moths, salamanders, etc.
 Regional faunas, e.g., Gulf of Maine megafauna.
 Existing inventories, e.g., INBio and ACG (Costa Rica).
3) Would rely principally on museum specimens.
Role of museums (and impact)
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Barcoding must validate existing taxonomy
before it can be offered as an identification tool,
and especially before it can be used to discover
new species.
Pilot projects will utilize museum specimens.
New inventory efforts will yield large numbers of
vouchers, which must be properly accessioned,
databased, and stored.
Results will flag many new species requiring
formal description.
 Additional burden on museums, herbaria,
etc., but may also offer new sources of support.
DNA barcoding is under way…
See also Nature 426: 514 (4 Dec 2003)
and appeals to the biotech sector
Anticipated next steps (2004)
January: Working group submits a
grant proposal to found a coordinating
Secretariat to develop a Barcode of Life
Initiative (BOLI) based in Washington,
DC; decision expected late March.
 May: Founding meeting of the BOLI
Consortium (museums and herbaria) at
U.S. Smithsonian Institution (NMNH).
 Late fall: First International Barcode of
Life Conference; venue TBD.
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The Barcode of Life Initiative needs
broad international participation
Please consider joining the consortium
as an institutional member.
 Plan to attend the BOL conference in
late 2004.
 For further information, please contact
Scott Miller <[email protected]>.
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