South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Overview of Consortium for the Barcode of Life (CBOL) David E. Schindel, Executive

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


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


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”


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


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


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)


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


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


Biodiversity Informatics:Biodiversity Informatics:Fragmented, UnconnectedFragmented, Unconnected

Journal Publication

Species Name

Voucher Specimen


Growth of Biodiversity DatabasesGrowth of Biodiversity Databases

Journal Publication

Species Name

Voucher Specimen

Authority files of taxonomic

names

Museum databases of

associated data







Databases of Species Databases of Species DistributionsDistributions

Journal Publication

Species Name

Voucher Specimen


names

Museum databases of

associated dataDatabases of species

occurrences and distribution



DNA Barcodes:DNA Barcodes:A Key Variable for Biodiversity A Key Variable for Biodiversity

InformaticsInformatics

Journal Publication

Species Name

Voucher Specimen

Barcode Sequence


names

Museum databases of

associated dataDatabases of species

occurrences and distribution (OBIS)


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) )


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


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



taxonomy:taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variantsTesting species boundaries, finding new variants






taxonomy:taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variantsTesting species boundaries, finding new variants





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


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


CBOL StructureCBOL Structure

Member Organizations

Executive Committee

Working Groups

Scientific Advisory Board

Secretariat Office


CBOL Member Organizations: 2007

• 150+ Member organizations, 45 countries

• 30+ Member organizations from 20+ developing countries


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


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


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


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


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


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


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


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

Documents

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Overview of Consortium for the Barcode of Life (CBOL) David E. Schindel, Executive