Transcript Taxonomic Value Chain (in rough sequence)

Overview of
Consortium for the
Barcode of Life (CBOL)
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
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Species Identification Matters
Endangered/protected species
 Agricultural pests/beneficial species
 Invasive species
 Disease vectors/pathogens
 Hazards (e.g., bird strikes on airplanes)
 Environmental quality indicators
 Unsustainable harvesting
 Fidelity of cell lines/culture collections
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Global Taxonomy Initiative
Established by Convention on Biological
Diversity in 2002 (COP6)
 Purpose is to remove or reduce the
”taxonomic impediment”
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
The taxonomic impediment
Knowledge gaps in our taxonomic system
 Shortage of trained taxonomists and
curators
 Impact of these deficiencies on our ability
to conserve, use and share the benefits of
biological diversity
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Operational objectives of GTI
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Assess taxonomic needs and capacities
Build and maintain human resources,
systems and infrastructure
Facilitate improved and effective
infrastructure for access to taxonomic
information
Include taxonomic objectives in CBD
work programmes and cross-cutting
issues
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
What is an effective
infrastructure for taxonomy?
Taxonomists
 Training
 Access to information
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Literature
Primary data
Research tools
Bandwidth
Other computing resources
Links to other biological web-based resources
(e-biology/e-biodiversity)
South/Central America Regional Meeting, Campinas, Brazil, 19 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 (characters, gene
sequences, images, trees)
 The (undigitized) Taxonomic Literature
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
What do we mean by
primary biodiversity data?
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Label data on ~ 1.5 - 3.0 billion specimens in
natural history collections, herbaria, botanical
gardens, etc.
 Associated notes,
recordings, publications,
etc.
 Observational data (e.g.
bird banding data)
These data have been
amassed over ~ 300
years; most not digital
 Big legacy data problem
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Biodiversity Informatics:
Fragmented, Unconnected
Voucher
Specimen
Journal
Publication
Species
Name
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Growth of Biodiversity Databases
Voucher
Specimen
Journal
Publication
Museum
databases of
associated data
Species
Name
Authority files
of taxonomic
names
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
South/Central America Regional Meeting, Campinas, Brazil, 19 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
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
South/Central America Regional Meeting, Campinas, Brazil, 19 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
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Some existing e-biodiversity
resources
DNA sequence databases (GenBank et al.)
(www.ncbi.nlm.nih.gov/Genbank)
 Protein Data Bank (www.rcsb.org/pdb)
 BOLD (www.barcodinglife.org)
 Catalogue of Life (spice.sp2000.org)
 Zoological Record
(http://scientific.thomson.com/products/zr)
 GBIF (www.gbif.net)
 Cyber Infrastructure for Phylogenetic Research (CIPRES)
(www.phylo.org)
 Long-Term Ecological Research (LTER) Network
(www.lternet.edu)
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Emerging e-biodiversity
resources
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European Distributed Institute for Taxonomy
(EDIT)
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Biodiversity Heritage Library: Digitizing
Taxonomic Literature (www.bhl.si.edu)
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Encyclopedia of Life: Web pages for every
species
South/Central America Regional Meeting, Campinas, Brazil, 19 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
South/Central America Regional Meeting, Campinas, Brazil, 19 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
South/Central America Regional Meeting, Campinas, Brazil, 19 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
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Using a Million Barcodes
A critical mass of standardized data for:
 Biogeographic patterns, habitat dynamics
 Phylogeography
 Niche modelling
 Ecological relationships
 Dynamics of molecular evolution
 Complementing Tree of Life
 Long-term biodiversity monitoring
 Understanding and preserving biodiversity
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Consortium for the Barcode of
Life: Major Points
Mission: Promoting DNA barcoding as a global
standard for species identification
 History of development
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– Recent origin, rapid growth
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Mode of operation as an international initiative
– Compromise between bottom-up, democratic (slow) and
top-down, centrally-managed (nimble) organization
– Distributed activity that seeks global participation
– Minimal bureaucracy, highly user-driven
– Focused on projects with near- and mid-term results
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
CBOL Structure
Member Organizations
Secretariat
Office
Working
Groups
Executive
Committee
Scientific Advisory
Board
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
CBOL Member Organizations: 2007
• 150+ Member organizations, 45 countries
• 30+ Member organizations from 20+ developing countries
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Consortium for the
Barcode of Life (CBOL)
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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
Now an international affiliation of:
– Natural history museums, biodiversity organizations
– Users: e.g., government agencies
– Private sector biotech companies, database providers
South/Central America Regional Meeting, Campinas, Brazil, 19 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
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Logistical Issues
The Organization: By taxonomy?
Geography? Application?
2. The Taxonomic Framework: Consensus list
of species
3. The Sampling Strategy
4. The Supply Chain
5. The Data: Assembling and comparing data
6. The Funding
7. The Resulting Publications
1.
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Projects initiated by others
 Marine
zooplankton (CMarZ):
Marine habitat, multiple taxa
 All-Leps: Multiple regions/habitats, single
taxon
 BioCode, Moorea: Single location, multiple
habitats, multiple taxa
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Major Challenges
Lack of funding to acquire, identify, curate
specimens
 Assembling, managing, editing, QA for
BARCODE-compliant data are labor-intensive
 Technical problems with data transfer to
BOLD, barcoding workbench at Guelph
 GenBank’s BarSTool is new
 Aversion to sharing data pre-publication
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Support from CBOL
ABBI, FISH-BOL, TBI, MBI get $50K per year
 Internships for data management
 Travel/consulting by taxonomists for
specimen identification
 Assistance in proposal writing
 Interactions with Working Groups
 “Leading Lab” initiative to improve lab and
data management protocols
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
CBOL’s Working Groups
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Database: Data standards and
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DNA: Lab protocols
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Data Analysis: New analytical methods;
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Plants: Identify gene region(s) for
interoperability
population genetics perspective
barcoding
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Taipei Barcode Conference
Second International Barcode Conference
 Academia Sinica, week of 17 September
 Regional Barcode Meeting for South/East Asia
 CBOL Working Groups
 FISH-BOL/Marine Fisheries workshop
 Short course on lab and data protocols
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007