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Freek T. Bakker Nationaal Herbarium Nederland Wageningen University branch

DNA barcoding: the CBOL perspective. Freek T. Bakker Nationaal Herbarium Nederland Wageningen University branch http://www.barcoding.si.edu. DNA barcoding. “ Using molecular data as species diagnostics isn’t new, but global standardization and scale of implementation are”.

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Freek T. Bakker Nationaal Herbarium Nederland Wageningen University branch

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  1. DNA barcoding: the CBOL perspective Freek T. Bakker Nationaal Herbarium Nederland Wageningen University branch http://www.barcoding.si.edu

  2. DNA barcoding “Using molecular data as species diagnostics isn’t new, but global standardization and scale of implementation are”

  3. 1.7 × 106 described species 10 barcodes per species ~20× 106 barcodes of 650bp each 10 × 106 more eukaryote species to go ~100 × 106 more barcodes of 650bp each In total this would be ~65,000,000,000 bp This is twice the total amount of bp currently in GenBank! To be completed within the decade (Hajibabaei & al., 2005) How many DNA barcodes do we need, or, what’s ahead?

  4. CBOL Member Organisations (May 2006) • 100+ Member organizations, 40 countries • 30 Member organizations from 20 developing countries

  5. Coordination/Facilitation of Bottom-Up activities Be a catalyst for DNA barcode activities globally Respond to applied user communities Minimalisim (organizational) – build on existing activities rather than constructing new ones Standardization, cost-effectiveness of generating DNA barcodes Global participation CBOL’s underlying principles

  6. CBOL Structure Member Organizations Executive Committee Secretariat Office Working Groups Scientific Advisory Board

  7. Database: Designing/constructing the Barcode Section of GenBank DNA: Protocols for formalin-fixed and old museum specimens; advice to new labs, LIMS for dissemination Data Analysis: Beyond phenetic methods; population genetics perspective Plants: Identify gene region(s) for barcoding CBOL’s Working Groups

  8. Barcode Records in GenBank Specimen Metadata Voucher Specimen Species Name Geo referenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalog of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI NameBank Publication links - New species Barcode Sequence Trace files Other Databases Literature(link to content or citation) PhylogeneticPopulation GeneticsEcological

  9. Barcode Records in GenBank EMBL Barcode Section of GenBank DDBJ BoLD, University of Guelph database Barcoders and Barcoding Labs

  10. Global initiatives to create reference library Enable users to adopt barcode ID systems All-species barcode database will: Strengthen specimen/species data Improve collections, tissue/DNA resources Attract users to barcoding for specimen IDs Regional Working Groups Small Steering Committees CBOL’s campaigns

  11. First barcoding publications in 2002 Cold Spring Harbor planning workshops in 2003 Sloan Foundation grant, launch in May 2004 Secretariat opens at Smithsonian, September 2004 First international conference February 2005 GenBank’s BARCODE section end 2005 Molecular Ecology Notes DNA barcode section Sloan Foundation Grant renewal March 2006 CBOL Milestones

  12. Now, an international affiliation of: 100+ Members Org’s, 40 countries, 6 continents Natural history museums, biodiversity organizations Users: e.g., government agencies Private sector biotech companies, database providers CBOL Milestones

  13. Four Working Groups FishBOL and All Birds Initiatives International Network for Barcoding Invasive and Pest Species (INBIPS) Created Steering Committees for: Tephritid fruit flies (agricultural pests) Mosquitoes (disease vectors) African bushmeat (endangered vertebrates) Current and Planned Projects

  14. Engaging collections, researchers and users Expand membership to 200 organizations Double participation in developing countries Four regional meetings in 2006 to expand awareness, assess needs, start networks in: Southern and eastern Africa South America Southern Asia Working with BioNET, development agencies Second International Barcode Conference, Southeast Asia, February 2007 CBOL 2008

  15. Poor representation of systematics infrastructure in Africa

  16. South Africa and Kenya involved from beginning of CBOL in May 2004 Southern African regional workshop April 2006 Eastern and Western regional workshops under discussion African involvement in global campaigns (e.g., birds, fish, mosquitos, fruit flies) Outreach to Africa

  17. Raise awareness Explore potential applications in the region Assess greatest needs and opportunities in the region (for instance, curation collections) Identify highest priorities, construct national and regional action plans Start intra-regional networks and intercontinental partnerships Goals of Regional Meetings

  18. In-country training Research training fellowships Infrastructure improvement: Lab equipment acquisition Collections Information technology Other forms of capacity-building identified during regional meetings Possible Follow-On Activities

  19. Users Bold/Genbank Taxon name Sequencing facility Collection Extraction facility Taxonomist Voucher

  20. Users Bold/Genbank Taxon name Sequencing facility Collection Extraction facility Taxonomist Voucher

  21. Bold/Genbank Collection Collection Taxon names Sequencingfacilities Collection Extraction facilities Identified vouchers = Taxonomist Taxonomist Taxonomist List of names Networks Model 1: by taxa

  22. National networks Canada: Canadian species France: Insects (Fulguromorpha, etc) France (+ Europe): EU pest insect species International networks ABBI FishBoL www.fishbol.org Mosquitoes Tephritidae Lepidoptera Networks Model 1: by taxa

  23. Bold/Genbank Collection Genoscope Taxon name MNHN Extraction facility Unidentifiedvouchers ‘morphospecies’ Identified voucher Research projects Panglao, Santo Researchproject BOA Networks Model 2: by location or ecosystem

  24. National networks model 2 = starting from field collections France: BOA, Marine tropical W Pacific taxa e.g. www.panglao-hotspot.org International networks model 2 Coral Reefs / CoML CoML = Census of Marine Life based both in ecosystems (Coral Reefs) and taxa (FishBoL) www.corocean.org Networks Model 2: by location or ecosystem

  25. Bold/Genebank Taxon name Institution Sequencing facility Institutions Institutions Institutions Collection Institutions Extraction facility Taxonomist Voucher Networks Model 3: by institution What is the role of institutions regarding DNA barcoding? • Maintaining infrastructure and human resources

  26. Institution Institutions Institutions Bold/Genebank Institutions Institutions Taxon name Sequencing facility Collection Extraction facility Taxonomist Voucher Networks Model 3: by institution What is the role of networks of institutions regarding multiform DNA barcoding networks? • Maintaining information flow and traceability of data EDIT = EU level CBoL = global

  27. European Distributed Institute of Taxonomy EU « Network of Excellence » = not specifically adressing Barcoding, but aiming at integration of research at institutions level 27 major taxonomic institutions working at Integration of policies Integration of research projects: making common tools (cybertaxonomy on the web) Integration of training + capacity building Integration of infrastructures Barcoding = ECBoL Networks Model 3: EDIT

  28. National: NL-TAF (The Netherlands): Fungi: CBS Plants: Nationaal Herbarium Animals: Naturalis, Univ. of Amsterdam Zoology, Wageningen Univ. Nematology clade and region-based approaches DNA bank International: EDIT www.mnhn.fr/edit CBoL www.barcoding.si.edu Networks Model 3: by institution

  29. Thank you for your attention!

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