Transcript Taxonomic Value Chain (in rough sequence)

Consortium for the
Barcode of Life (CBOL):
Linking Molecules to the
Catalogue 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
Catalogue of Life, Reading, UK, 29 March 2007
Species Identification Matters
Basic research on evolution, ecology
 Endangered/protected species
 Agricultural pests/beneficial species
 Invasive species
 Disease vectors/pathogens
 Hazards (e.g., bird strikes on airplanes)
 Environmental quality indicators
 Managing for sustainable harvesting
 Fidelity of cell lines/culture collections
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Catalogue of Life, Reading, UK, 29 March 2007
Infrastructure of Taxonomy:
Fragmented, Disconnected
Collections and databases of specimens
 Seedbanks, culture/cell line collections
 Compilations of taxonomic names
 Floristic and faunistic surveys/inventories
 Monographs, Taxonomic revisions
 Data repositories (gene sequences,
characters, images, trees)
 The (undigitized) Taxonomic Literature
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Catalogue of Life, Reading, UK, 29 March 2007
Biodiversity Informatics:
Fragmented, Unconnected
Voucher
Specimen
Type specimens
Varied species concepts:
- BSC (hard to apply)
- Typology
- Genetic lineages
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Journal
Publication
Species
Name
Catalogue of Life, Reading, UK, 29 March 2007
Growth of Biodiversity Databases
Voucher
Specimen
Journal
Publication
Museum
databases of
associated data
Species
Name
Authority files
of taxonomic
names
Catalogue of Life, Reading, UK, 29 March 2007
Catalogue of Life, Reading, UK, 29 March 2007
Catalogue of Life, Reading, UK, 29 March 2007
Catalogue of Life, Reading, UK, 29 March 2007
Databases of Species Distributions
Voucher
Specimen
Museum
databases of
associated data
Databases of species
occurrences and
distribution
Journal
Publication
Species
Name
Authority files
of taxonomic
names
Catalogue of Life, Reading, UK, 29 March 2007
Catalogue of Life, Reading, UK, 29 March 2007
DNA Barcodes:
A Key Variable for Biodiversity
Informatics
Voucher
Specimen
Museum
databases of
associated data
Databases of species
occurrences and
distribution (OBIS)
Barcode
Sequence
Journal
Publication
Species
Name
Authority files
of taxonomic
names
Catalogue of Life, Reading, UK, 29 March 2007
A DNA barcode is a
short gene sequence
taken from
standardized portions
of the genome,
used to identify species
Catalogue of Life, Reading, UK, 29 March 2007
Uses of DNA Barcodes
Research tool for improving species-level taxonomy:
 Associating all life history stages, genders
 Testing species boundaries, finding new variants
Applied tool for identifying regulated species:
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Disease vectors, agricultural pests, invasives
Environmental indicators, protected species
Using minimal samples, damaged specimens, gut
contents, droppings
“Triage” tool for flagging potential new species:
 Undescribed and cryptic species
Catalogue of Life, Reading, UK, 29 March 2007
Uses of DNA Barcodes
Research tool for improving species-level taxonomy:
 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
 Using minimal samples, damaged specimens, gut
contents, droppings
“Triage” tool for flagging potential new species:
 Undescribed and cryptic species
Catalogue of Life, Reading, UK, 29 March 2007
Uses of DNA Barcodes
Research tool for improving species-level taxonomy:
 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
 Using minimal samples, damaged specimens, gut
contents, droppings
“Triage” tool for flagging potential new species:
 Undescribed and cryptic species
Catalogue of Life, Reading, UK, 29 March 2007
CBOL Member Organizations: 2007
• 150+ Member organizations, 45 countries
• 30+ Member organizations from 20+ developing countries
Catalogue of Life, Reading, UK, 29 March 2007
CBOL’s Strategy
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Collaborate with existing biodiversity initiatives
Work to connect existing systems with new data
standards; avoid creating new databases
Rely on GenBank, EMBL and DDBJ as stable data
repositories
Global participation
Engage taxonomists and applied user
communities
Set tangible, realistic goals, near-term results
Catalogue of Life, Reading, UK, 29 March 2007
Taxonomy in GenBank
Species names provided by submitters
 Names added to Taxonomy Browser
 Only recently checked against
compilations
 Submitters informed of errors but not
forced to make corrections
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Catalogue of Life, Reading, UK, 29 March 2007
Barcode Data Standards
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Consensus results of Front Royal meeting
– GBIF
– NBII
– ICZN
 ITIS
 Species2000
 ZooRecord
 GRIN
 IPNI
 OBIS
Structured link to voucher specimen
 Species name selected from authority
 Online access to metadata
 Trace files and quality scores
 Minimum sequence length
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Catalogue of Life, Reading, UK, 29 March 2007
BARCODE Records in INSDC
Specimen
Metadata
Georeference
Habitat
Character sets
Images
Behavior
Other genes
Other
Databases
Phylogenetic
Pop’n Genetics
Ecological
Voucher
Specimen
Species
Name
Indices
- Catalogue of Life
- GBIF/ECAT
Barcode
Sequence
Trace files
Primers
Nomenclators
- Zoo Record
- IPNI
- NameBank
Publication links
- New species
Literature
(link to content or
citation)
Databases
- Provisional sp.
Catalogue of Life, Reading, UK, 29 March 2007
CBOL-Initiated Projects
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Fish Barcode of Life (FISH-BOL)
– 30,000 marine/freshwater species by 2010
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All Birds Barcoding Initiative (ABBI)
– 10,000 species by 2010
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Tephritid fruit flies
– 2,000 pest/beneficial species and relatives by 2008
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Mosquitoes
– 3,300 species by 2008
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African scale insects, lake fish, stem-borers
Catalogue of Life, Reading, UK, 29 March 2007
Taipei Barcode Conference
Second International Barcode Conference
 Academia Sinica, week of 17 September
 Regional Barcode Meeting for South/SE Asia
 CBOL Working Groups
 FISH-BOL/Marine Fisheries workshop
 Short course on biodiversity informatics
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Catalogue of Life, Reading, UK, 29 March 2007