south/central america regional meeting, campinas, brazil, 19 march 2007 overview of consortium for...
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South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Overview of Overview of Consortium for the Consortium for the
Barcode of Life Barcode of Life (CBOL)(CBOL)
David E. Schindel, Executive David E. Schindel, Executive SecretarySecretary
National Museum of Natural HistoryNational Museum of Natural HistorySmithsonian InstitutionSmithsonian Institution
[email protected]@si.edu;; http://www.barcoding.si.eduhttp://www.barcoding.si.edu202/633-0812; fax 202/633-2938202/633-0812; fax 202/633-2938
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Species Identification Species Identification MattersMatters
Endangered/protected species Endangered/protected species Agricultural pests/beneficial speciesAgricultural pests/beneficial species Invasive speciesInvasive species Disease vectors/pathogensDisease vectors/pathogens Hazards (e.g., bird strikes on airplanes)Hazards (e.g., bird strikes on airplanes) Environmental quality indicatorsEnvironmental quality indicators Unsustainable harvestingUnsustainable harvesting Fidelity of cell lines/culture collectionsFidelity of cell lines/culture collections
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Global Taxonomy Global Taxonomy InitiativeInitiative
Established by Convention on Established by Convention on Biological Diversity in 2002 (COP6)Biological Diversity in 2002 (COP6)
Purpose is to remove or reduce the Purpose is to remove or reduce the ”taxonomic impediment””taxonomic impediment”
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
The taxonomic The taxonomic impedimentimpediment
Knowledge gaps in our taxonomic Knowledge gaps in our taxonomic systemsystem
Shortage of trained taxonomists and Shortage of trained taxonomists and curatorscurators
Impact of these deficiencies on our Impact of these deficiencies on our ability to conserve, use and share the ability to conserve, use and share the benefits of biological diversity benefits of biological diversity
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Operational objectives of Operational objectives of GTIGTI
Assess taxonomic needs and Assess taxonomic needs and capacitiescapacities
Build and maintain human resources, Build and maintain human resources, systems and infrastructuresystems and infrastructure
Facilitate improved and Facilitate improved and effective effective infrastructureinfrastructure for access to taxonomic for access to taxonomic informationinformation
Include taxonomic objectives in CBD Include taxonomic objectives in CBD work programmes and cross-cutting work programmes and cross-cutting issuesissues
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
What is an effective What is an effective infrastructure for infrastructure for
taxonomy?taxonomy? TaxonomistsTaxonomists TrainingTraining Access to informationAccess to information
– LiteratureLiterature– Primary dataPrimary data– Research toolsResearch tools– BandwidthBandwidth– Other computing resourcesOther computing resources– Links to other biological web-based resources Links to other biological web-based resources
(e-biology/e-biodiversity)(e-biology/e-biodiversity)
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Infrastructure of Taxonomy:Infrastructure of Taxonomy:Fragmented, DisconnectedFragmented, Disconnected
Collections and databases of specimensCollections and databases of specimens Seedbanks, culture/cell line collectionsSeedbanks, culture/cell line collections Compilations of taxonomic namesCompilations of taxonomic names Floristic and faunistic Floristic and faunistic
surveys/inventoriessurveys/inventories Monographs, Taxonomic revisionsMonographs, Taxonomic revisions Data repositories (characters, gene Data repositories (characters, gene
sequences, images, trees)sequences, images, trees) The (undigitized) Taxonomic LiteratureThe (undigitized) Taxonomic Literature
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
What do we mean by What do we mean by primary biodiversity primary biodiversity
data?data?
Associated notes, recordings, Associated notes, recordings, publications, etc.publications, etc.
Observational dataObservational data (e.g. bird banding (e.g. bird banding data)data)
Label dataLabel data on ~ 1.5 - 3.0 billion specimens in natural on ~ 1.5 - 3.0 billion specimens in natural history collections, herbaria, botanical gardens, etc.history collections, herbaria, botanical gardens, etc.
These data have been These data have been amassed over ~ 300 years; amassed over ~ 300 years; most not digitalmost not digital
Big Big legacy datalegacy data problem problem
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Biodiversity Informatics:Biodiversity Informatics:Fragmented, UnconnectedFragmented, Unconnected
Journal Publication
Species Name
Voucher Specimen
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Growth of Biodiversity DatabasesGrowth of Biodiversity Databases
Journal Publication
Species Name
Voucher Specimen
Authority files of taxonomic
names
Museum databases of
associated data
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 Databases of Species DistributionsDistributions
Journal Publication
Species Name
Voucher Specimen
Authority files of taxonomic
names
Museum databases of
associated dataDatabases of species
occurrences and distribution
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
DNA Barcodes:DNA Barcodes:A Key Variable for Biodiversity A Key Variable for Biodiversity
InformaticsInformatics
Journal Publication
Species Name
Voucher Specimen
Barcode Sequence
Authority files of taxonomic
names
Museum databases of
associated dataDatabases of species
occurrences and distribution (OBIS)
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Some existing e-Some existing e-biodiversity resourcesbiodiversity resources
DNA sequence databases (GenBank et al.) (DNA sequence databases (GenBank et al.) (www.ncbi.nlm.nih.gov/Genbankwww.ncbi.nlm.nih.gov/Genbank) )
Protein Data Bank (Protein Data Bank (www.rcsb.org/pdbwww.rcsb.org/pdb) ) BOLD (BOLD (www.barcodinglife.orgwww.barcodinglife.org)) Catalogue of Life (Catalogue of Life (spice.sp2000.orgspice.sp2000.org) ) Zoological Record (Zoological Record (
http://scientific.thomson.com/products/zrhttp://scientific.thomson.com/products/zr) ) GBIF (GBIF (www.gbif.netwww.gbif.net) ) Cyber Infrastructure for Phylogenetic Research Cyber Infrastructure for Phylogenetic Research
(CIPRES) ((CIPRES) (www.phylo.orgwww.phylo.org) ) Long-Term Ecological Research (LTER) Network (Long-Term Ecological Research (LTER) Network (
www.lternet.eduwww.lternet.edu) )
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Emerging e-biodiversity Emerging e-biodiversity resourcesresources
European Distributed Institute for European Distributed Institute for Taxonomy (EDIT)Taxonomy (EDIT)
Biodiversity Heritage Library: Digitizing Biodiversity Heritage Library: Digitizing Taxonomic Literature (Taxonomic Literature (www.bhl.si.eduwww.bhl.si.edu))
Encyclopedia of Life: Web pages for every Encyclopedia of Life: Web pages for every speciesspecies
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Uses of DNA BarcodesUses of DNA BarcodesResearch tool for improving species-level Research tool for improving species-level
taxonomy:taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new Testing species boundaries, finding new
variantsvariants
Applied tool for identifying regulated species:Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasivesDisease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, Using minimal samples, damaged specimens,
gut contents, droppingsgut contents, droppings
““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Uses of DNA BarcodesUses of DNA BarcodesResearch tool for improving species-level Research tool for improving species-level
taxonomy:taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variantsTesting species boundaries, finding new variants
Applied tool for identifying regulated species:Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasivesDisease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, Using minimal samples, damaged specimens,
gut contents, droppingsgut contents, droppings
““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Uses of DNA BarcodesUses of DNA BarcodesResearch tool for improving species-level Research tool for improving species-level
taxonomy:taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variantsTesting species boundaries, finding new variants
Applied tool for identifying regulated species:Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasivesDisease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, Using minimal samples, damaged specimens,
gut contents, droppingsgut contents, droppings
““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Using a Million BarcodesUsing a Million BarcodesA critical mass of standardized data for:A critical mass of standardized data for: Biogeographic patterns, habitat dynamicsBiogeographic patterns, habitat dynamics PhylogeographyPhylogeography Niche modellingNiche modelling Ecological relationshipsEcological relationships Dynamics of molecular evolutionDynamics of molecular evolution Complementing Tree of LifeComplementing Tree of Life Long-term biodiversity monitoringLong-term biodiversity monitoring Understanding and preserving Understanding and preserving
biodiversitybiodiversity
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Mission: Promoting DNA barcoding as a global Mission: Promoting DNA barcoding as a global standard for species identificationstandard for species identification
History of developmentHistory of development– Recent origin, rapid growthRecent origin, rapid growth
Mode of operation as an international initiativeMode of operation as an international initiative– Compromise between bottom-up, democratic (slow) Compromise between bottom-up, democratic (slow)
and top-down, centrally-managed (nimble) and top-down, centrally-managed (nimble) organizationorganization
– Distributed activity that seeks global participationDistributed activity that seeks global participation– Minimal bureaucracy, highly user-drivenMinimal bureaucracy, highly user-driven– Focused on projects with near- and mid-term Focused on projects with near- and mid-term
resultsresults
Consortium for the Barcode Consortium for the Barcode of Life: Major Pointsof Life: Major Points
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
CBOL StructureCBOL Structure
Member Organizations
Executive Committee
Working Groups
Scientific Advisory Board
Secretariat Office
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 Consortium for the Barcode of Life (CBOL)Barcode of Life (CBOL)
First barcoding publications in 2002First barcoding publications in 2002 Cold Spring Harbor planning workshops in 2003Cold Spring Harbor planning workshops in 2003 Sloan Foundation grant, launch in May 2004Sloan Foundation grant, launch in May 2004 Secretariat opens at Smithsonian, September Secretariat opens at Smithsonian, September
20042004 First international conference February 2005First international conference February 2005 Now an international affiliation of:Now an international affiliation of:
– Natural history museums, biodiversity organizationsNatural history museums, biodiversity organizations– Users: e.g., government agenciesUsers: e.g., government agencies– Private sector biotech companies, database providersPrivate sector biotech companies, database providers
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
CBOL-Initiated ProjectsCBOL-Initiated Projects Fish Barcode of Life (FISH-BOL)Fish Barcode of Life (FISH-BOL)
– 30,000 marine/freshwater species by 201030,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI)All Birds Barcoding Initiative (ABBI)
– 10,000 species by 201010,000 species by 2010 Tephritid fruit fliesTephritid fruit flies
– 2,000 pest/beneficial species and relatives by 2,000 pest/beneficial species and relatives by 20082008
MosquitoesMosquitoes– 3,300 species by 20083,300 species by 2008
African scale insects, lake fish, stem-borersAfrican scale insects, lake fish, stem-borers
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Logistical IssuesLogistical Issues1.1. The Organization: By taxonomy? The Organization: By taxonomy?
Geography? Application?Geography? Application?2.2. The Taxonomic Framework: Consensus The Taxonomic Framework: Consensus
list of species list of species 3.3. The Sampling StrategyThe Sampling Strategy4.4. The Supply ChainThe Supply Chain5.5. The Data: Assembling and comparing The Data: Assembling and comparing
datadata6.6. The FundingThe Funding7.7. The Resulting PublicationsThe Resulting Publications
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Projects initiated by othersProjects initiated by others
Marine zooplankton (CMarZ): Marine zooplankton (CMarZ): Marine habitat, multiple taxaMarine habitat, multiple taxa
All-Leps: Multiple regions/habitats, All-Leps: Multiple regions/habitats, single taxonsingle taxon
BioCode, Moorea: Single location, BioCode, Moorea: Single location, multiple habitats, multiple taxamultiple habitats, multiple taxa
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Major ChallengesMajor Challenges Lack of funding to acquire, identify, curate Lack of funding to acquire, identify, curate
specimensspecimens Assembling, managing, editing, QA for Assembling, managing, editing, QA for
BARCODE-compliant data are labor-BARCODE-compliant data are labor-intensiveintensive
Technical problems with data transfer to Technical problems with data transfer to BOLD, barcoding workbench at GuelphBOLD, barcoding workbench at Guelph
GenBank’s BarSTool is newGenBank’s BarSTool is new Aversion to sharing data pre-publicationAversion to sharing data pre-publication
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Support from CBOLSupport from CBOL ABBI, FISH-BOL, TBI, MBI get $50K per yearABBI, FISH-BOL, TBI, MBI get $50K per year Internships for data managementInternships for data management Travel/consulting by taxonomists for Travel/consulting by taxonomists for
specimen identificationspecimen identification Assistance in proposal writingAssistance in proposal writing Interactions with Working GroupsInteractions with Working Groups ““Leading Lab” initiative to improve lab and Leading Lab” initiative to improve lab and
data management protocolsdata management protocols
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
CBOL’s Working GroupsCBOL’s Working Groups Database:Database: Data standards and Data standards and
interoperabilityinteroperability
DNA:DNA: Lab protocols Lab protocols
Data Analysis:Data Analysis: New analytical New analytical methods; population genetics methods; population genetics perspectiveperspective
Plants: Plants: Identify gene region(s) for Identify gene region(s) for barcodingbarcoding
South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
Taipei Barcode ConferenceTaipei Barcode Conference
Second International Barcode Second International Barcode Conference Conference
Academia Sinica, week of 17 SeptemberAcademia Sinica, week of 17 September Regional Barcode Meeting for Regional Barcode Meeting for
South/East AsiaSouth/East Asia CBOL Working GroupsCBOL Working Groups FISH-BOL/Marine Fisheries workshopFISH-BOL/Marine Fisheries workshop Short course on lab and data protocols Short course on lab and data protocols