Census of Marine Life, Amsterdam – 16 May 2006 The Protocol Chain for DNA Barcoding Projects

Census of Marine Life, Amsterdam – 16 May 2006 CBOL’s Underlying Principles Respond to taxonomists, other disciplines, applied user communities Respond to taxonomists, other disciplines, applied user communities Coordination/Facilitation of Bottom-Up activities Coordination/Facilitation of Bottom-Up activities Minimalism (organizational) – build on existing activities rather than constructing new ones Minimalism (organizational) – build on existing activities rather than constructing new ones Standardization, cost-effectiveness Standardization, cost-effectiveness Minimalism (scientific) – fewest possible regions Minimalism (scientific) – fewest possible regions Tangible, realistic goals, near-term results Tangible, realistic goals, near-term results Global participation Global participation

Census of Marine Life, Amsterdam – 16 May 2006 Different Projects, Different Goals Libraries of DNA barcodes allow us to: Libraries of DNA barcodes allow us to: Compare unknown specimens to all barcoded speciesCompare unknown specimens to all barcoded 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 particular species in an unknown or mix of unknownsTest the presence/absence of particular species in an unknown or mix of unknowns Uncover new clusters, potential new speciesUncover new clusters, potential new species Protocols will vary according to goals, state of taxonomy, completeness of the library Protocols will vary according to goals, state of taxonomy, completeness of the library

Census of Marine Life, Amsterdam – 16 May 2006 CBOL-Initiated Projects Fish Barcode of Life (FISH-BOL) Fish Barcode of Life (FISH-BOL) 30,000 marine/freshwater species by ,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI) All Birds Barcoding Initiative (ABBI) 10,000 species by ,000 species by 2010 Tephritid fruit flies Tephritid fruit flies 2,000 pest/beneficial species and relatives by 20082,000 pest/beneficial species and relatives by 2008 Mosquitoes Mosquitoes 3,300 species by 20083,300 species by 2008 Endangered vertebrates (bushmeat) Endangered vertebrates (bushmeat) Successive phases of African mammalsSuccessive phases of African mammals

Census of Marine Life, Amsterdam – 16 May 2006 Projects initiated by others CMarZ: Marine habitat, multiple taxa CMarZ: Marine habitat, multiple taxa All-Leps: All-Leps: 2 families, multiple regions2 families, multiple regions 4 regions/habitats, multiple taxa4 regions/habitats, multiple taxa BioCode, Moorea: Single location, multiple habitats, multiple taxa BioCode, Moorea: Single location, multiple habitats, multiple taxa

Census of Marine Life, Amsterdam – 16 May 2006 Launching CBOL Projects Assembling Steering Committee UsersUsers Taxonomists, collection curatorsTaxonomists, collection curators Service providers (BOLD, analytical labs)Service providers (BOLD, analytical labs) Plan for scope, timetable, logistics Plan for scope, timetable, logistics Pilot tests of primers, PCR amplification Pilot tests of primers, PCR amplification Assemble pipeline of specimens to lab Assemble pipeline of specimens to lab Address other logistical issues Address other logistical issues

Census of Marine Life, Amsterdam – 16 May 2006 Logistical Issues 1. The Organization 2. The Taxonomic Framework: Consensus list of species 3. The Sampling Strategy 4. The Supply Chain 5. The Data: Assembling and comparing data 6. The Funding 7. The Resulting Publications

Census of Marine Life, Amsterdam – 16 May 2006 The Organization By taxonomy? Geography? Institution? FISH-BOL and ABBI: Regional Working Groups Regional Working Groups Steering Committee Steering Committee Campaign coordinator Campaign coordinator Mosquitoes and Tephritids: Highly centralized committee/coordinator Highly centralized committee/coordinatorBushmeat: Mix of users, diverse taxonomists Mix of users, diverse taxonomists

Census of Marine Life, Amsterdam – 16 May 2006 Networks Model 2: by location or ecosystem Taxon name Identified voucher MNHN Extraction facility Genoscope Collection Bold/GenBank Research projects Panglao, Santo Research project BOA Unidentified vouchers ‘morphospecies’

Census of Marine Life, Amsterdam – 16 May 2006 The Taxonomic Framework FISH-BOL catalyzed consensus list of: FishBase FishBase Catalog of Fishes Catalog of Fishes Integrated Taxonomic Information System Integrated Taxonomic Information System ABBI uses a published species checklist Cross-check with Species2000, ITIS Cross-check with Species2000, ITIS Mosquitoes and Tephritids: Checklists developed by users Checklists developed by users

Census of Marine Life, Amsterdam – 16 May 2006 The Sampling Strategy 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: 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

Census of Marine Life, Amsterdam – 16 May 2006 The Supply Chain Sources of specimens: Sources of specimens: – Museum collections ($) – Piggyback on existing field programs ($$) – Dedicated new collecting efforts ($$$$$) Permits for collecting/international transfer Permits for collecting/international transfer Expert identification Expert identification Data capture, digital imaging, tissue sampling Data capture, digital imaging, tissue sampling Curation of voucher specimens, tissue samples, DNA extracts Curation of voucher specimens, tissue samples, DNA extracts Moving samples (or extracts or PCR products) to sequencers Moving samples (or extracts or PCR products) to sequencers

Census of Marine Life, Amsterdam – 16 May 2006 The Data (1) Assembling and comparing dataAssembling and comparing data CBOL recommends BOLD with subsequent upload to INSDCCBOL recommends BOLD with subsequent upload to INSDC Curation and quality controlCuration and quality control CBOL/INSDC have established standards, capability to maintain data accuracyCBOL/INSDC have established standards, capability to maintain data accuracy Long-term responsibility of barcoding communityLong-term responsibility of barcoding community

Census of Marine Life, Amsterdam – 16 May 2006 The Data (2) Ownership, pre-release accessOwnership, pre-release access Project-specific policiesProject-specific policies Attitudes range from very open to more protectiveAttitudes range from very open to more protective Timing of data releaseTiming of data release Controlled by owner of dataControlled by owner of data CBOL urges early release, except for tight connections to hypothesis-driven publicationsCBOL urges early release, except for tight connections to hypothesis-driven publications

Census of Marine Life, Amsterdam – 16 May 2006 The Funding Engage the potential users from the start: On the Steering Committee, setting priorities On the Steering Committee, setting priorities Give repeated presentations to expanding audiences; work toward top policy-makers Give repeated presentations to expanding audiences; work toward top policy-makers Keep them informed of progress Keep them informed of progress Some foundations will take risks, act as catalysts Other foundations will like low-risk projects of which they can take ownership

Census of Marine Life, Amsterdam – 16 May 2006 The Resulting Publications Pilot studies demonstrating effectiveness of barcode region in a new taxon Pilot studies demonstrating effectiveness of barcode region in a new taxon Regional barcode surveys of a taxon, noting trends toward lumping or splitting Regional barcode surveys of a taxon, noting trends toward lumping or splitting Use of barcodes in ecological, evolutionary studies, applied projects Use of barcodes in ecological, evolutionary studies, applied projects Progress reports from barcoding campaigns Progress reports from barcoding campaigns Synthetic studies of regions, habitats, taxa Synthetic studies of regions, habitats, taxa Formal taxonomic revisions Formal taxonomic revisions

Census of Marine Life, Amsterdam – 16 May 2006 Call for Participation Data Analysis Challenges Arising from the DNA Barcode Initiative National Museum of Natural History Paris, 6-8 July 2006