Linking Linking Barcode Data to Barcode Data to

Multiple UsersMultiple UsersDavid E. Schindel, Executive SecretaryDavid E. Schindel, Executive SecretaryNational Museum of Natural HistoryNational Museum of Natural History

Smithsonian InstitutionSmithsonian Institution

SchindelD@si.eduSchindelD@si.edu;; http://www.barcoding.si.eduhttp://www.barcoding.si.edu202/633-0812; fax 202/633-2938202/633-0812; fax 202/633-2938

A DNA barcode is a A DNA barcode is a short gene sequence short gene sequence

taken from taken from standardized portions standardized portions

of the genome,of the genome, used to identify used to identify

speciesspecies

The Mitochondrial Genome

Cyt bCyt b

D-Loop

ND5

H-strand

ND4

ND4LND3

COIII

COICOIL-strand

ND6

COI

ND2

ND1

COII

Small ribosomal RNA

Large ribosomal RNA

ATPase subunit 8

ATPase subunit 6

The Barcode Assembly LineFreshly collected

specimens

Frozen tissue

Young museum specimens

BOLD

GenBank

BARCODE Records

Users with unidentified specimens

Taxonomic Identifications and BARCODE Data

Standards

• Promote barcoding as a global standard

• Build participation

• Working Groups

• BARCODE standard

• International Conferences

• Increase production of public BARCODE records

Projects, Networks, Organizations

Uses of DNA BarcodesUses of DNA BarcodesResearch tool for species-level taxonomy, ecology:Research tool for species-level taxonomy, ecology: 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

““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species Taxonomic groups with few morphological Taxonomic groups with few morphological

featuresfeatures

New Sources of New Sources of Taxonomic/Ecological DataTaxonomic/Ecological Data

Immature stages, damaged specimensImmature stages, damaged specimens Trophic webs from gut contentsTrophic webs from gut contents Fecal droppingsFecal droppings Non-invasive sampling (catch/release, Non-invasive sampling (catch/release,

shed feathers, moults, fin clips)shed feathers, moults, fin clips) Rapid ecological sampling and Rapid ecological sampling and

ecosystem assessmentecosystem assessment Ecogenomic mixturesEcogenomic mixtures

Uses of DNA BarcodesUses of DNA BarcodesResearch tool for species-level taxonomy, ecology:Research tool for species-level taxonomy, ecology: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variants Testing 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

““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species Taxonomic groups with few morphological Taxonomic groups with few morphological

featuresfeatures

Uses of DNA BarcodesUses of DNA BarcodesResearch tool for species-level taxonomy, ecology:Research tool for species-level taxonomy, ecology: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variants Testing 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

““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species Taxonomic groups with few morphological Taxonomic groups with few morphological

featuresfeatures

Species sampled

Specimens per species

Total # specimens sequenced

# gene regions

Total sequence length per

species

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

Eco-genomics

105-106 (?)NA - no vouchers

NA - no vouchers

? NA

What DNA Barcoding is What DNA Barcoding is NOTNOT

Barcoding is not DNA taxonomy;Barcoding is not DNA taxonomy; no no single gene (or character) is adequatesingle gene (or character) is adequate

Barcoding is not Tree of Life;Barcoding is not Tree of Life; barcode barcode clusters are not phylogenetic treesclusters are not phylogenetic trees

Barcoding is not just COI;Barcoding is not just COI; standardizing on one region has benefits standardizing on one region has benefits and limitsand limits

Molecules in taxonomy is not new;Molecules in taxonomy is not new; but but large-scale and standardization large-scale and standardization are neware new

What DNA Barcoding is What DNA Barcoding is NOTNOT

Barcoding is not DNA taxonomy;Barcoding is not DNA taxonomy; no no single gene (or character) is adequatesingle gene (or character) is adequate

Barcoding is not Tree of Life;Barcoding is not Tree of Life; barcode barcode clusters are not phylogenetic treesclusters are not phylogenetic trees

Barcoding is not just COI;Barcoding is not just COI; standardizing on one region has benefits standardizing on one region has benefits and limitsand limits

Molecules in taxonomy is not new;Molecules in taxonomy is not new; but but large-scale and standardization large-scale and standardization are neware new

CBOL’s HistoryCBOL’s History Sloan Foundation support for two Banbury Sloan Foundation support for two Banbury

planning workshops in 2003planning workshops in 2003 Sloan 2-year inaugural CBOL grant, May 2004Sloan 2-year inaugural CBOL grant, May 2004 Secretariat opens at Smithsonian, September Secretariat opens at Smithsonian, September

20042004 International conference London, February International conference London, February

20052005 $1.55 million 2-year renewal in April 2006$1.55 million 2-year renewal in April 2006 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 Private sector biotech companies, database

providersproviders

CBOL Member Organizations: 2007

• 160+ Member organizations, 50 countries

• 54 Member organizations from 23 developing countries

CBOL’s Mission:CBOL’s Mission:Promoting DNA BarcodingPromoting DNA Barcoding

as a Global Standard as a Global Standard1.1. Developing/raising community standardsDeveloping/raising community standards2.2. Barcode projects to populate databaseBarcode projects to populate database3.3. Global participation and coordinationGlobal participation and coordination4.4. Acceptance by taxonomic communityAcceptance by taxonomic community5.5. Adoption by regulatory agenciesAdoption by regulatory agencies6.6. Excitement in other fields of science Excitement in other fields of science 7.7. Product development by private Product development by private

companiescompanies

Barcode Sequence

Voucher Specimen

Species Name

Specimen Metadata

Literature(link to content or

citation)

BARCODE Records in INSDC

Indices - Catalogue of Life - GBIF/ECAT

Nomenclators - Zoo Record - IPNI - NameBank

Publication links - New species

GeoreferenceHabitat

Character setsImages

BehaviorOther genes

Trace filesOther

DatabasesPhylogenetic

Pop’n GeneticsEcological

Primers

Databases - Provisional sp.

CBOL’s Mission:CBOL’s Mission:Promoting DNA BarcodingPromoting DNA Barcoding

as a Global Standard as a Global Standard1.1. Developing/raising community standardsDeveloping/raising community standards2.2. Barcode projects to populate databaseBarcode projects to populate database3.3. Global participation and coordinationGlobal participation and coordination4.4. Acceptance by taxonomic communityAcceptance by taxonomic community5.5. Adoption by regulatory agenciesAdoption by regulatory agencies6.6. Excitement in other fields of scienceExcitement in other fields of science7.7. Product development by private Product development by private

companiescompanies

CBOL-Initiated ProjectsCBOL-Initiated Projects Tephritid fruit flies (USDA)Tephritid fruit flies (USDA)

2,000 pest/beneficial species and relatives by 2,000 pest/beneficial species and relatives by 20082008

Mosquitoes 3,300 species by 2008Mosquitoes 3,300 species by 2008 Fish Barcode of Life, FISH-BOLFish Barcode of Life, FISH-BOL

30,000 marine/freshwater species by 201030,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (aviation All Birds Barcoding Initiative (aviation

agencies)agencies) 10,000 species by 201010,000 species by 2010

Water quality assessment (USEPA)Water quality assessment (USEPA) Scale insects, commercial fish, hardwoodScale insects, commercial fish, hardwood

CBOL’s Mission:CBOL’s Mission:Promoting DNA BarcodingPromoting DNA Barcoding

as a Global Standard as a Global Standard1.1. Developing/raising community standardsDeveloping/raising community standards2.2. Barcode projects to populate databaseBarcode projects to populate database3.3. Global participation and coordinationGlobal participation and coordination4.4. Acceptance by taxonomic communityAcceptance by taxonomic community5.5. Adoption by regulatory agenciesAdoption by regulatory agencies6.6. Excitement in other fields of scienceExcitement in other fields of science7.7. Product development by private Product development by private

companiescompanies

Geographic Outreach Geographic Outreach ActivitiesActivities

Regional meetings in:Regional meetings in: Cape Town, South Africa, 7-8 April 2006, Cape Town, South Africa, 7-8 April 2006,

SANBISANBI Nairobi, Kenya, 18-19 October 2006 Nairobi, Kenya, 18-19 October 2006 Brazil, February 2007Brazil, February 2007 Taiwan, September 2007Taiwan, September 2007

Assess technical/scientific capacityAssess technical/scientific capacity Identify high-priority barcoding projectsIdentify high-priority barcoding projects Initiate regional networks, partnershipsInitiate regional networks, partnerships Partnership with BioNET-INTERNATIONALPartnership with BioNET-INTERNATIONAL

Leading Lab NetworkLeading Lab NetworkTaipei Short Course, September Taipei Short Course, September

20072007

BioCode

STRI SI-LAB

CCDB

BOLD GenBank

New CBOL Activities, New CBOL Activities, 2008-20092008-2009

Leading Lab NetworkLeading Lab Network ““Phase 2” support for regional networksPhase 2” support for regional networks Offer to promote Fungal Barcoding InitiativeOffer to promote Fungal Barcoding Initiative Outreach to west/central Africa, India, ChinaOutreach to west/central Africa, India, China More direct communication with Member More direct communication with Member

OrganizationsOrganizations Promote acceptance by CBD, developing Promote acceptance by CBD, developing

countriescountries Expand partnerships with GBIF, Encyclopedia Expand partnerships with GBIF, Encyclopedia

of Life, Census of Marine Life, Catalog of Lifeof Life, Census of Marine Life, Catalog of Life

CBOL’s Mission:CBOL’s Mission:Promoting DNA BarcodingPromoting DNA Barcoding

as a Global Standard as a Global Standard1.1. Developing/raising community standardsDeveloping/raising community standards2.2. Barcode projects to populate databaseBarcode projects to populate database3.3. Global participation and coordinationGlobal participation and coordination4.4. Acceptance by taxonomic communityAcceptance by taxonomic community5.5. Adoption by regulatory agenciesAdoption by regulatory agencies6.6. Excitement in other fields of science Excitement in other fields of science 7.7. Product development by private Product development by private

companiescompanies

Adoption by RegulatorsAdoption by Regulators US Federal Aviation Administration – All BirdsUS Federal Aviation Administration – All Birds US Environmental Protection AgencyUS Environmental Protection Agency

$250K pilot test, water quality bioassessment$250K pilot test, water quality bioassessment US Food and Drug Administration US Food and Drug Administration

Reference barcodes for commercial fishReference barcodes for commercial fish FISH-BOL and fish regulatory agenciesFISH-BOL and fish regulatory agencies

CBOL workshop in Taipei, September 2007CBOL workshop in Taipei, September 2007 FAO International Plant Protection CommissionFAO International Plant Protection Commission

Proposal for Diagnostic Protocols for fruit flies Proposal for Diagnostic Protocols for fruit flies CITES, National Agencies, Conservation NGOsCITES, National Agencies, Conservation NGOs

International Steering Committee, identifying pilot International Steering Committee, identifying pilot projectsprojects

CBOL’s Mission:CBOL’s Mission:Promoting DNA BarcodingPromoting DNA Barcoding

as a Global Standard as a Global Standard1.1. Developing/raising community standardsDeveloping/raising community standards2.2. Barcode projects to populate databaseBarcode projects to populate database3.3. Global participation and coordinationGlobal participation and coordination4.4. Acceptance by taxonomic communityAcceptance by taxonomic community5.5. Adoption by regulatory agenciesAdoption by regulatory agencies6.6. Excitement in other fields of science Excitement in other fields of science 7.7. Product development by private Product development by private

companiescompanies

Intellectual Outreach Intellectual Outreach ActivitiesActivities

BOLI/Assembling the Tree of Life meetingBOLI/Assembling the Tree of Life meeting Building operational collaborationsBuilding operational collaborations Seeking database interoperabilitySeeking database interoperability Identifying research opportunitiesIdentifying research opportunities

EMBO Workshop on Molecular EMBO Workshop on Molecular Biodiversity and DNA BarcodesBiodiversity and DNA Barcodes Behavior of molecular markers across taxaBehavior of molecular markers across taxa

Banbury 3 workshop on molecular Banbury 3 workshop on molecular evolutionevolution Barcode data in research on speciation, Barcode data in research on speciation,

phylogeography, DNA dynamicsphylogeography, DNA dynamics