Transcript Taxonomic Value Chain (in rough sequence)

DNA Barcoding and
the Consortium for
the Barcode of Life
David E. Schindel, Executive Secretary
National Museum of Natural History
Smithsonian Institution
[email protected]; http://www.barcoding.si.edu
202/633-0812; fax 202/633-2938
Data Analysis Working Group, DIMACS, 26 Sept 2005
Species Identification Matters
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Endangered/protected species
Agricultural pests
Invasive species
Disease vectors/pathogens
Hazards (e.g., bird strikes on airplanes)
Environmental quality indicators
Unsustainable harvesting
Fidelity of cell lines/culture collections
Data Analysis Working Group, DIMACS, 26 Sept 2005
The Practice of
Taxonomy
Distributions of
Character
Variation
Characters
Taxonomists
Taxonomic DecisionMaking
The Uses of
Taxonomy
Socioeconomic
Decisions
Concerns/
Regulations
Specimens
Specimens
Data Analysis Working Group, DIMACS, 26 Sept 2005
The Problem…
• Taxonomists are a limited resource
• Taxonomic infrastructure is not widely
available
• Taxonomic decisions are difficult for nonspecialists
• Therefore, the practice of taxonomy does
not scale up to meet the needs of society
(or ecology, ecosystem studies, etc.)
Data Analysis Working Group, DIMACS, 26 Sept 2005
A DNA barcode is a
short gene sequence
taken from
standardized portions
of the genome,
used to identify species
Data Analysis Working Group, DIMACS, 26 Sept 2005
Uses of DNA Barcodes
“Triage” tool for flagging potential new species:
• Undescribed and cryptic species
Research tool for assigning specimens to known
species, including:
• Life history stages, damaged specimens, gut
contents, droppings
Applied tool for identifying regulated species:
• Disease vectors, agricultural pests, invasives
• Protected species, CITES listed, trade-sensitive
Data Analysis Working Group, DIMACS, 26 Sept 2005
The Mitochondrial Genome
D-Loop
Small ribosomal RNA
Large
ribosomal RNA
Cyt b
ND1
ND6
ND5
L-strand
COI
COI
ND2
H-strand
ND4
COI
ND4L
ND3
COIII
COII
ATPase subunit 8
ATPase subunit 6
Data Analysis Working Group, DIMACS, 26 Sept 2005
How much information is there
in a DNA Barcode?
• Human genome:
– Contains 3 billion base-pairs
– Identified by 648 bp COI barcode sequence
– Content-to-label ratio: 5 X 106
• Oxford English Dictionary, 2nd Ed.,1989:
– 20 volumes, 21,730 pages, 500,000 entries, 59
million words, 350 million print characters
– Identified by 10-character ISBN
– Content-to-label ratio: 4 X 107
Data Analysis Working Group, DIMACS, 26 Sept 2005
Current Norm: High throughput
Large capacity PCR and
sequencing reactions
ABI 3100 capillary
automated sequencer
Data Analysis Working Group, DIMACS, 26 Sept 2005
Future Norm?
• A taxonomic GPS
• Link to reference
database
• Usable by nonspecialists.
Data Analysis Working Group, DIMACS, 26 Sept 2005
Data Analysis Working Group, DIMACS, 26 Sept 2005
Consortium for the
Barcode of Life (CBOL)
• An international affiliation of:
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80+ Members Org’s, 35+ countries, 6 continents
Natural history museums, biodiversity organizations
Users: e.g., government agencies
Private sector biotech companies, database providers
First barcoding publications in 2002
Cold Spring Harbor planning workshops in 2003
Sloan Foundation grant, launch in May 2004
Secretariat opens at Smithsonian, September 2004
First international conference February 2005
Data Analysis Working Group, DIMACS, 26 Sept 2005
CBOL Member Organizations
(as of May 2005)
Data Analysis Working Group, DIMACS, 26 Sept 2005
CBOL’s Working Groups
• Database: Designing/constructing the
Barcode Section of GenBank
• DNA: Protocols for formalin-fixed and old
museum specimens; Producing LIMS for
dissemination
• Data Analysis: Beyond phenetic methods;
population genetics perspective
• Plants: Identify gene region(s) for
barcoding
Data Analysis Working Group, DIMACS, 26 Sept 2005
CBOL’s Goals
• Create a reference barcode database
• Identify high-priority taxa and societal needs
• Promote/facilitate barcoding projects and
‘CBOL campaigns’
• Improve methods, address shared obstacles
through WGs
• Populate database from collections
• More portability, less time/expense
• Improve taxonomic research environment
Data Analysis Working Group, DIMACS, 26 Sept 2005
Recent and Planned Activities
• Data standards, Barcode records in
GenBank
• Launch of FishBOL, All Birds Initiatives
• International Network for Barcoding
Invasive and Pest Species (INBIPS)
• APEC Workshop on Invasives, Beijing
• Mosquitoes and disease vectors
• Plans for CITES species, endangered
Vertebrates, Bushmeat
Data Analysis Working Group, DIMACS, 26 Sept 2005
Barcode Section of GenBank
Specimen
Metadata
Georeference
Habitat
Character sets
Images
Behavior
Other genes
Other
Databases
Phylogenetic
Pop’n Genetics
Ecological
Voucher
Specimen
Barcode
Sequence
Trace files
Species
Name
Indices
- Catalog of Life
- GBIF/ECAT
Nomenclators
- Zoo Record
- IPNI
NameBank
Literature
Publication links
- New species
(link to content or
citation)
Data Analysis Working Group, DIMACS, 26 Sept 2005