census of marine life, amsterdam – 16 may 2006 the protocol chain for dna barcoding projects

Census of Marine Life, Amsterdam – 16 May 2006

The Protocol Chain for DNA Barcoding Projects


CBOL’s Underlying Principles

• Respond to taxonomists, other disciplines, Respond to taxonomists, other disciplines, applied user communitiesapplied user communities

• Coordination/Facilitation of Bottom-Up activitiesCoordination/Facilitation of Bottom-Up activities• Minimalism (organizational) – build on existing Minimalism (organizational) – build on existing

activities rather than constructing new onesactivities rather than constructing new ones• Standardization, cost-effectivenessStandardization, cost-effectiveness• Minimalism (scientific) – fewest possible regionsMinimalism (scientific) – fewest possible regions• Tangible, realistic goals, near-term resultsTangible, realistic goals, near-term results• Global participationGlobal participation


Different Projects, Different Goals

• Libraries of DNA barcodes allow us to:Libraries of DNA barcodes allow us to:• Compare unknown specimens to Compare unknown specimens to allall barcoded barcoded

species species • Assignment to a known speciesAssignment to a known species• Suggest affinity to species cluster, higher taxonSuggest affinity to species cluster, higher taxon

• Test the presence/absence of Test the presence/absence of particular particular species in an unknown or mix of unknownsspecies in an unknown or mix of unknowns

• Uncover Uncover newnew clusters, potential new species clusters, potential new species• Protocols will vary according to goals, state Protocols will vary according to goals, state

of taxonomy, completeness of the libraryof taxonomy, completeness of the library


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

• Endangered vertebrates (bushmeat) Endangered vertebrates (bushmeat) • Successive phases of African mammalsSuccessive phases of African mammals


Projects initiated by others

• CMarZ: CMarZ: Marine habitat, multiple taxaMarine habitat, multiple taxa

• All-Leps: All-Leps: • 2 families, multiple regions2 families, multiple regions• 4 4 regions/habitats, multiple taxaregions/habitats, multiple taxa

• BioCode, Moorea: BioCode, Moorea: Single location, multiple habitats, Single location, multiple habitats, multiple taxamultiple taxa


Launching CBOL Projects

Assembling Steering CommitteeAssembling Steering Committee• UsersUsers• Taxonomists, collection curatorsTaxonomists, collection curators• Service providers (BOLD, analytical labs)Service providers (BOLD, analytical labs)

• Plan for scope, timetable, logisticsPlan for scope, timetable, logistics• Pilot tests of primers, PCR amplificationPilot tests of primers, PCR amplification• Assemble pipeline of specimens to labAssemble pipeline of specimens to lab• Address other logistical issuesAddress other logistical issues


Logistical Issues1.1. The OrganizationThe Organization

2.2. The Taxonomic Framework: Consensus list of The Taxonomic Framework: Consensus list of species species

3.3. The Sampling StrategyThe Sampling Strategy

4.4. The Supply ChainThe Supply Chain

5.5. The Data: Assembling and comparing dataThe Data: Assembling and comparing data

6.6. The FundingThe Funding

7.7. The Resulting PublicationsThe Resulting Publications


The OrganizationBy taxonomy? Geography? Institution?By taxonomy? Geography? Institution?FISH-BOL and ABBI: FISH-BOL and ABBI: • Regional Working GroupsRegional Working Groups• Steering CommitteeSteering Committee• Campaign coordinatorCampaign coordinatorMosquitoes and Tephritids:Mosquitoes and Tephritids:• Highly centralized committee/coordinatorHighly centralized committee/coordinatorBushmeat:Bushmeat:• Mix of users, diverse taxonomistsMix of users, diverse taxonomists


Networks Model 2: by location or ecosystem

Taxon name

Identifiedvoucher

MNHNExtraction facility

GenoscopeCollection

Bold/GenBank

Research projectsPanglao, Santo

Research projectBOA

Unidentified vouchers ‘morphospecies’


The Taxonomic Framework

FISH-BOL catalyzed consensus list of:FISH-BOL catalyzed consensus list of:• FishBaseFishBase• Catalog of FishesCatalog of Fishes• Integrated Taxonomic Information SystemIntegrated Taxonomic Information System

ABBI uses a published species checklistABBI uses a published species checklist• Cross-check with Species2000, ITISCross-check with Species2000, ITIS

Mosquitoes and Tephritids:Mosquitoes and Tephritids:• Checklists developed by usersChecklists developed by users


The Sampling StrategyHow many specimens per species per area?How many specimens per species per area?• Under study by Data Analysis WGUnder study by Data Analysis WG• FISH-BOL, ABBI: FISH-BOL, ABBI:

• 5 per species from across geographic range5 per species from across geographic range• Minimum one whole voucher per speciesMinimum one whole voucher per species• Intensive sampling for some speciesIntensive sampling for some species

What qualifies as a voucher? Varies widely:What qualifies as a voucher? Varies widely:• Gold standard museum study specimensGold standard museum study specimens• Invasive non-destructive extraction samplingInvasive non-destructive extraction sampling• Totally destructive sampling with e-VoucherTotally destructive sampling with e-Voucher


The Supply Chain• Sources of specimens:Sources of specimens:

– Museum collections ($)Museum collections ($)– Piggyback on existing field programs ($$)Piggyback on existing field programs ($$)– Dedicated new collecting efforts ($$$$$)Dedicated new collecting efforts ($$$$$)

• Permits for collecting/international transferPermits for collecting/international transfer• Expert identificationExpert identification• Data capture, digital imaging, tissue samplingData capture, digital imaging, tissue sampling• Curation of voucher specimens, tissue samples, DNA Curation of voucher specimens, tissue samples, DNA

extractsextracts• Moving samples (or extracts or PCR products) to Moving samples (or extracts or PCR products) to

sequencerssequencers


The Data (1)

• Assembling and comparing dataAssembling and comparing data• CBOL recommends BOLD with subsequent CBOL recommends BOLD with subsequent

upload to INSDCupload to INSDC

• Curation and quality controlCuration and quality control• CBOL/INSDC have established standards, CBOL/INSDC have established standards,

capability to maintain data accuracycapability to maintain data accuracy• Long-term responsibility of barcoding Long-term responsibility of barcoding

communitycommunity


The Data (2)

• Ownership, pre-release accessOwnership, pre-release access• Project-specific policiesProject-specific policies• Attitudes range from very open to more Attitudes range from very open to more

protectiveprotective

• Timing of data releaseTiming of data release• Controlled by owner of dataControlled by owner of data• CBOL urges early release, except for tight CBOL urges early release, except for tight

connections to hypothesis-driven publicationsconnections to hypothesis-driven publications


The Funding

Engage the potential users from the start:Engage the potential users from the start:• On the Steering Committee, setting prioritiesOn the Steering Committee, setting priorities• Give repeated presentations to expanding Give repeated presentations to expanding

audiences; work toward top policy-makersaudiences; work toward top policy-makers• Keep them informed of progressKeep them informed of progress

Some foundations will take risks, act as catalystsSome foundations will take risks, act as catalysts

Other foundations will like low-risk projects of Other foundations will like low-risk projects of which they can take ownershipwhich they can take ownership


The Resulting Publications

• Pilot studies demonstrating effectiveness of Pilot studies demonstrating effectiveness of barcode region in a new taxonbarcode region in a new taxon

• Regional barcode surveys of a taxon, noting Regional barcode surveys of a taxon, noting trends toward lumping or splittingtrends toward lumping or splitting

• Use of barcodes in ecological, evolutionary Use of barcodes in ecological, evolutionary studies, applied projectsstudies, applied projects

• Progress reports from barcoding campaignsProgress reports from barcoding campaigns• Synthetic studies of regions, habitats, taxaSynthetic studies of regions, habitats, taxa• Formal taxonomic revisionsFormal taxonomic revisions


Call for ParticipationData Analysis Challenges Arising from

the DNA Barcode Initiative

National Museum of Natural History Paris, 6-8 July 2006

census of marine life, amsterdam – 16 may 2006 the protocol chain for dna barcoding projects

Documents

species cluster

pestbeneficial species

marinefreshwater species

consensus list of species

barcoded species assignment

unknown specimens

multiple habitats

multiple taxa biocode