ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Overview of DNA Barcoding David E. Schindel, Executive Secretary Consortium for the Barcode of Life National

ABBI/FISH-BOL meeting, Buenos Aires, March 2007

Overview of DNA Barcoding

David E. Schindel, Executive SecretaryDavid E. Schindel, Executive SecretaryConsortium for the Barcode of LifeConsortium for the Barcode of Life

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


DNA Barcodes:A Key Variable for Biodiversity

Informatics

Journal Publication

Species Name

Voucher Specimen

Barcode Sequence

Authority files of taxonomic

names

Museum databases of

associated dataDatabases of species

occurrences and distribution (OBIS)


• Background onBackground on• DNA BarcodingDNA Barcoding• The DNA Barcode InitiativeThe DNA Barcode Initiative• Consortium for the Barcode of Life Consortium for the Barcode of Life

(CBOL)(CBOL)• Current and planned activitiesCurrent and planned activities• Data standards for barcode dataData standards for barcode data• Challenges to CBOL projectsChallenges to CBOL projects• Support from CBOLSupport from CBOL


A DNA barcode is a short gene sequence

taken from standardized portions

of the genome, used to identify

species


Reactions to Barcoding: 2004• From ecologists and other users:From ecologists and other users:

“This is what we need! How soon can we get started?”“This is what we need! How soon can we get started?”• From traditional taxonomists:From traditional taxonomists:

“Species should be based on lots of characters, “Species should be based on lots of characters, not just barcodes” not just barcodes”

• From forward-looking taxonomists:From forward-looking taxonomists:“Using molecular data as species diagnostics isn’t “Using molecular data as species diagnostics isn’t

new, but standardization and broad implementation are new, but standardization and broad implementation are great!”great!”

• From barcoding practitioners:From barcoding practitioners:“I had my doubts at the beginning, but it really works “I had my doubts at the beginning, but it really works

as a tool for identification (96% accurate in a recent mollusc as a tool for identification (96% accurate in a recent mollusc paper) and it is at least as good as traditional approaches to paper) and it is at least as good as traditional approaches to discovering new species.”discovering new species.”


Uses of DNA BarcodesResearch tool for improving species-level taxonomy:Research tool for improving species-level 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, gut Using minimal samples, damaged specimens, gut

contents, droppingscontents, droppings

““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species:• Undescribed and cryptic speciesUndescribed and cryptic species


Associating Life Stages, Processed Parts, Dimorphic Genders



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, gut Using minimal samples, damaged specimens, gut





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, gut Using minimal samples, damaged specimens, gut




Using 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 biodiversityUnderstanding and preserving biodiversity


What DNA Barcoding is NOT

• Barcoding is not DNA taxonomy;Barcoding is not DNA taxonomy; no single no single gene (or character) is adequategene (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 standardizing on one region has benefits and limitsone region has benefits and 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 NOT

• Barcoding is not DNA taxonomy;Barcoding is not DNA taxonomy; no single no single gene (or character) is adequategene (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 standardizing on one region has benefits and limitsone region has benefits and 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


Consortium for the 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 2004Secretariat opens at Smithsonian, September 2004• First international conference February 2005First international conference February 2005• Now an international affiliation of:Now an international affiliation of:

• 150 Members Org’s, 45 countries, 6 continents150 Members Org’s, 45 countries, 6 continents• 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


Consortium for the Barcode of Life (CBOL)Smithsonian Institution/Sloan Foundation150 Member Organizations, 45 Countries as of March 07


Outreach Activities• Regional meetings in:Regional meetings in:

- Cape Town, South Africa, 7-8 April 2006, SANBICape Town, South Africa, 7-8 April 2006, SANBI- Nairobi, Kenya, 18-19 October 2006 Nairobi, Kenya, 18-19 October 2006 - Brazil, March 2007Brazil, March 2007- Taiwan, September 2007Taiwan, September 2007

• Support from CBOL, host governments and Support from CBOL, host governments and international development agenciesinternational development agencies

• Second International Barcode ConferenceSecond International Barcode Conference- Taiwan, September 2007Taiwan, September 2007


Goals of Regional Meetings

• Raise awareness Raise awareness • Explore potential applications in the regionExplore potential applications in the region• Assess greatest needs and opportunities Assess greatest needs and opportunities

in the regionin the region• Identify highest priorities, construct Identify highest priorities, construct

national and regional action plans national and regional action plans • Start intra-regional networks and Start intra-regional networks and

intercontinental partnershipsintercontinental partnerships


CBOL-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 20082,000 pest/beneficial species and relatives by 2008• MosquitoesMosquitoes

• 3,300 species by 20083,300 species by 2008• African Scale InsectsAfrican Scale Insects• Endangered vertebrates (bushmeat) Endangered vertebrates (bushmeat)


Projects initiated by others

• CMarZ: Marine habitat, multiple taxaCMarZ: Marine habitat, multiple taxa• All-Leps: Multiple regions/habitats, single All-Leps: Multiple regions/habitats, single

taxontaxon• BioCode, Moorea: Single location, BioCode, Moorea: Single location,

multiple habitats, multiple taxamultiple habitats, multiple taxa


CBOL’s Working Groups

• Database:Database: Designing/constructing the Designing/constructing the Barcode Section of GenBankBarcode Section of GenBank

• DNA:DNA: Protocols for formalin-fixed and old Protocols for formalin-fixed and old museum specimens; Producing LIMS for museum specimens; Producing LIMS for disseminationdissemination

• Data Analysis:Data Analysis: Beyond phenetic Beyond phenetic methods; population genetics perspectivemethods; population genetics perspective

• Plants: Plants: Identify gene region(s) for Identify gene region(s) for barcodingbarcoding


Barcode Data Standards• Consensus results of Front Royal meetingConsensus results of Front Royal meeting

• GBIFGBIF ITIS ITIS GRIN GRIN• NBIINBII Species2000 Species2000 IPNI IPNI• ICZNICZN ZooRecord ZooRecord OBIS OBIS

• Structured link to voucher specimenStructured link to voucher specimen• Species name selected from authoritySpecies name selected from authority• Online access to metadataOnline access to metadata• Trace files and quality scoresTrace files and quality scores• Minimum sequence lengthMinimum sequence length


Barcode Sequence

Voucher Specimen

Species Name

Specimen Metadata

Literature(link to content or

citation)

BARCODE Records in INSDC

Indices - Catalog of Life - GBIF/ECAT

Nomenclators - Zoo Record - IPNI - NameBank

Publication links - New species

Databases - Provisional sp.

GeoreferenceHabitat

Character setsImages

BehaviorOther genes

Trace filesOther

DatabasesPhylogenetic

Pop’n GeneticsEcological

Primers


Digitizing Taxonomic Literature• CBOL’s catalytic efforts:CBOL’s catalytic efforts:

• Library-Laboratory meeting in London, 2005, Library-Laboratory meeting in London, 2005, on electronic access to taxonomic literatureon electronic access to taxonomic literature

• Led to formation of Biodiversity Heritage Led to formation of Biodiversity Heritage Library initiativeLibrary initiative

• Proactive steps with PubMed to add Proactive steps with PubMed to add taxonomic journals to online abstractstaxonomic journals to online abstracts

• Aggressive negotiation with publishers of Aggressive negotiation with publishers of barcoding papersbarcoding papers

• Involvement in Encyclopedia of LifeInvolvement in Encyclopedia of Life








CBOL Formalin Workshop• May 8-9, 2006 workshop in Washington, May 8-9, 2006 workshop in Washington,

National Research CouncilNational Research Council• Chemists, biochemists, biophysicists, Chemists, biochemists, biophysicists,

biomedical researchersbiomedical researchers• Literature survey of DNA recovery Literature survey of DNA recovery

protocols from formalin-fixed specimensprotocols from formalin-fixed specimens• Create a new research agendaCreate a new research agenda• Follow-on with SPNHC as major partnerFollow-on with SPNHC as major partner


CBOL’s Working Groups• Database:Database: Designing/constructing the Designing/constructing the

Barcode Section of GenBankBarcode Section of GenBank• DNA:DNA: Protocols for formalin-fixed and old Protocols for formalin-fixed and old

museum specimens; Producing LIMS for museum specimens; Producing LIMS for disseminationdissemination








• Plants: Plants: Identify gene region(s) for Identify gene region(s) for barcoding by December 2006barcoding by December 2006


Progress toward Plant Barcode

• Kress 2005 proposal for ITS and trnh-psbAKress 2005 proposal for ITS and trnh-psbA• Kew Garden receives Sloan/Moore Kew Garden receives Sloan/Moore

Foundation support, early 2005Foundation support, early 2005• Phase 1 screens 100 genes across 50 Phase 1 screens 100 genes across 50

sibling species pairssibling species pairs• Phase 2 tests of matK, rpcoC1, rpoB, ndhJ, Phase 2 tests of matK, rpcoC1, rpoB, ndhJ,

and accDand accD• Canadian proposal for rbcLCanadian proposal for rbcL• CBOL protocols for approving barcode CBOL protocols for approving barcode

regionsregions


Wider Impacts of Barcoding• Catalyzing interoperability of databasesCatalyzing interoperability of databases

• Barcode data standards link sequences, Barcode data standards link sequences, specimens, species names and publicationsspecimens, species names and publications

• Improving the information infrastructureImproving the information infrastructure• Digital library initiative in taxonomyDigital library initiative in taxonomy

• Expanding analytical toolbox for taxonomy Expanding analytical toolbox for taxonomy • Renewing the mission of museumsRenewing the mission of museums

• DNA recovery from formalin-fixed specimensDNA recovery from formalin-fixed specimens• Promoting the growth of DNA banksPromoting the growth of DNA banks


Major 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-intensiveBARCODE-compliant data are labor-intensive• Technical problems with data transfer to Technical problems with data transfer to

BOLDBOLD• GenBank’s BarSTool is newGenBank’s BarSTool is new• Aversion to sharing data pre-publicationAversion to sharing data pre-publication


Support from CBOL• ABBI and FISH-BOL get $50K per yearABBI and FISH-BOL 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• Formalin projectFormalin project• ““Leading Lab” initiative to improve lab and Leading Lab” initiative to improve lab and

data management protocolsdata management protocols


Taipei Barcode Conference

• Second International Barcode Conference Second International Barcode Conference • Academia Sinica, week of 17 SeptemberAcademia Sinica, week of 17 September• Regional Barcode Meeting for South/SE Regional Barcode Meeting for South/SE

AsiaAsia• CBOL Working GroupsCBOL Working Groups• FISH-BOL/Marine Fisheries workshopFISH-BOL/Marine Fisheries workshop• Short course on biodiversity informaticsShort course on biodiversity informatics

Documents

ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Overview of DNA Barcoding David E. Schindel, Executive Secretary Consortium for the Barcode of Life National