Transcript Taxonomic Value Chain (in rough sequence)

Linking Barcode
Data to
Multiple Users
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
A DNA barcode is a
short gene sequence
taken from
standardized portions
of the genome,
used to identify species
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
The Barcode Assembly Line
Freshly collected
specimens
Frozen tissue
Young museum
specimens
BOLD
GenBank
BARCODE
Records
Taxonomic
Identifications and
BARCODE Data
Standards
Users with
unidentified
specimens
Projects, Networks, Organizations
• Promote barcoding
as a global standard
• Build participation
• Working Groups
• BARCODE standard
• International
Conferences
• Increase production
of public BARCODE
records
Uses of DNA Barcodes
Research tool for species-level taxonomy, ecology:
 Associating all life history stages, genders
 Testing species boundaries, finding new variants
Applied tool for identifying regulated species:
Disease vectors, agricultural pests, invasives
 Environmental indicators, protected species
“Triage” tool for flagging potential new species:
 Undescribed and cryptic species
 Taxonomic groups with few morphological features

New Sources of
Taxonomic/Ecological Data
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Immature stages, damaged specimens
Trophic webs from gut contents
Fecal droppings
Non-invasive sampling (catch/release, shed
feathers, moults, fin clips)
Rapid ecological sampling and ecosystem
assessment
Ecogenomic mixtures
Uses of DNA Barcodes
Research tool for species-level taxonomy, ecology:
 Associating all life history stages, genders
 Testing species boundaries, finding new variants
Applied tool for identifying regulated species:
Disease vectors, agricultural pests, invasives
 Environmental indicators, protected species
“Triage” tool for flagging potential new species:
 Undescribed and cryptic species
 Taxonomic groups with few morphological features

Uses of DNA Barcodes
Research tool for species-level taxonomy, ecology:
 Associating all life history stages, genders
 Testing species boundaries, finding new variants
Applied tool for identifying regulated species:
Disease vectors, agricultural pests, invasives
 Environmental indicators, protected species
“Triage” tool for flagging potential new species:
 Undescribed and cryptic species
 Taxonomic groups with few morphological features

# gene
regions
Total
sequence
length per
species
Species
sampled
Specimens
per species
Total #
specimens
sequenced
DNA
barcoding
105
5-50
106-107
1-3
102-103
Tree of
Life
102-103
1
102-103
5-15
103-104
Genomics
102
1
102
105
109
NA - no
vouchers
NA - no
vouchers
?
NA
Eco105-106 (?)
genomics
What DNA Barcoding is NOT

Barcoding is not DNA taxonomy; no
single gene (or character) is adequate
 Barcoding is not Tree of Life; barcode
clusters are not phylogenetic trees
 Barcoding is not just COI; standardizing on
one region has benefits and limits
 Molecules in taxonomy is not new; but
large-scale and standardization are new
What DNA Barcoding is NOT

Barcoding is not DNA taxonomy; no
single gene (or character) is adequate
 Barcoding is not Tree of Life; barcode
clusters are not phylogenetic trees
 Barcoding is not just COI; standardizing on
one region has benefits and limits
 Molecules in taxonomy is not new; but
large-scale and standardization are new
CBOL’s History
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Sloan Foundation support for two Banbury
planning workshops in 2003
Sloan 2-year inaugural CBOL grant, May 2004
Secretariat opens at Smithsonian, September 2004
International conference London, February 2005
$1.55 million 2-year renewal in April 2006
Now an international affiliation of:
Natural history museums, biodiversity organizations
 Users: e.g., government agencies
 Private sector biotech companies, database providers

CBOL Member Organizations: 2007
• 160+ Member organizations, 50 countries
• 54 Member organizations from 23 developing countries
CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Acceptance by taxonomic community
Adoption by regulatory agencies
Excitement in other fields of science
Product development by private companies
BARCODE Records in INSDC
Specimen
Metadata
Georeference
Habitat
Character sets
Images
Behavior
Other genes
Other
Databases
Phylogenetic
Pop’n Genetics
Ecological
Voucher
Specimen
Barcode
Sequence
Trace files
Primers
Literature
(link to content or
citation)
Species
Name
Indices
- Catalogue of Life
- GBIF/ECAT
Nomenclators
- Zoo Record
- IPNI
- NameBank
Publication links
- New species
Databases
- Provisional sp.
CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Acceptance by taxonomic community
Adoption by regulatory agencies
Excitement in other fields of science
Product development by private companies
CBOL-Initiated Projects
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Tephritid fruit flies (USDA)
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2,000 pest/beneficial species and relatives by 2008
Mosquitoes 3,300 species by 2008
 Fish Barcode of Life, FISH-BOL
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30,000 marine/freshwater species by 2010
All Birds Barcoding Initiative (aviation agencies)
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10,000 species by 2010
Water quality assessment (USEPA)
 Scale insects, commercial fish, hardwood
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CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Acceptance by taxonomic community
Adoption by regulatory agencies
Excitement in other fields of science
Product development by private companies
Geographic Outreach Activities
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Regional meetings in:
Cape Town, South Africa, 7-8 April 2006, SANBI
 Nairobi, Kenya, 18-19 October 2006
 Brazil, February 2007
 Taiwan, September 2007
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Assess technical/scientific capacity
Identify high-priority barcoding projects
Initiate regional networks, partnerships
Partnership with BioNET-INTERNATIONAL
Leading Lab Network
Taipei Short Course, September 2007
STRI
SI-LAB
BOLD
CCDB
GenBank
BioCode
New CBOL Activities, 2008-2009
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Leading Lab Network
“Phase 2” support for regional networks
Offer to promote Fungal Barcoding Initiative
Outreach to west/central Africa, India, China
More direct communication with Member
Organizations
Promote acceptance by CBD, developing countries
Expand partnerships with GBIF, Encyclopedia of
Life, Census of Marine Life, Catalog of Life
CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Acceptance by taxonomic community
Adoption by regulatory agencies
Excitement in other fields of science
Product development by private companies
Adoption by Regulators
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US Federal Aviation Administration – All Birds
US Environmental Protection Agency
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US Food and Drug Administration
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CBOL workshop in Taipei, September 2007
FAO International Plant Protection Commission
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Reference barcodes for commercial fish
FISH-BOL and fish regulatory agencies
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$250K pilot test, water quality bioassessment
Proposal for Diagnostic Protocols for fruit flies
CITES, National Agencies, Conservation NGOs
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International Steering Committee, identifying pilot projects
CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Acceptance by taxonomic community
Adoption by regulatory agencies
Excitement in other fields of science
Product development by private companies
Intellectual Outreach Activities

BOLI/Assembling the Tree of Life meeting
Building operational collaborations
 Seeking database interoperability
 Identifying research opportunities
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EMBO Workshop on Molecular Biodiversity and
DNA Barcodes
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Behavior of molecular markers across taxa
Banbury 3 workshop on molecular evolution
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Barcode data in research on speciation,
phylogeography, DNA dynamics