Freek T. Bakker Nationaal Herbarium Nederland Wageningen University branch DNA barcoding: the CBOL perspective

CoML meeting Amsterdam – 15 May ‘06 DNA barcoding “ Using molecular data as species diagnostics isn’t new, but global standardization and scale of implementation are”

CoML meeting Amsterdam – 15 May ‘ × 10 6 described species 10 barcodes per species ~20 × 10 6 barcodes of 650bp each 10 × 10 6 more eukaryote species to go ~100 × 10 6 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?

CoML meeting Amsterdam – 15 May ‘06

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

CoML meeting Amsterdam – 15 May ‘06 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

CoML meeting Amsterdam – 15 May ‘06 CBOL Structure Member Organizations Executive Committee Working Groups Scientific Advisory Board Secretariat Office

CoML meeting Amsterdam – 15 May ‘06 CBOL’s Working Groups 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

CoML meeting Amsterdam – 15 May ‘06 Barcode Sequence Voucher Specimen Species Name Specimen Metadata Literature (link to content or citation) Indices - Catalog of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI NameBank Publication links - New species Geo reference Habitat Character sets Images Behavior Other genes Trace files Other Databases Phylogenetic Population Genetics Ecological Barcode Records in GenBank

CoML meeting Amsterdam – 15 May ‘06 Barcode Section of GenBank EMBLDDBJ Barcoders and Barcoding Labs BoLD, University of Guelph database Barcode Records in GenBank

CoML meeting Amsterdam – 15 May ‘06 CBOL’s campaigns 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

CoML meeting Amsterdam – 15 May ‘06 CBOL Milestones 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

CoML meeting Amsterdam – 15 May ‘06 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

CoML meeting Amsterdam – 15 May ‘06 Current and Planned Projects 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)

CoML meeting Amsterdam – 15 May ‘06 CBOL 2008 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

CoML meeting Amsterdam – 15 May ‘06 Poor representation of systematics infrastructure in Africa

CoML meeting Amsterdam – 15 May ‘06 Outreach to Africa 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)

CoML meeting Amsterdam – 15 May ‘06 Goals of Regional Meetings 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

CoML meeting Amsterdam – 15 May ‘06 Possible Follow-On Activities In-country training Research training fellowships Infrastructure improvement: –Lab equipment acquisition –Collections –Information technology Other forms of capacity-building identified during regional meetings

CoML meeting Amsterdam – 15 May ‘06 Taxonomist Taxon name Voucher Extraction facility Sequencing facility Collection Bold/Genbank Users

CoML meeting Amsterdam – 15 May ‘06 Taxonomist Taxon name Voucher Extraction facility Sequencing facility Collection Bold/Genbank Users

CoML meeting Amsterdam – 15 May ‘06 Networks Model 1: by taxa Sequencing facilities = Taxon names Identified vouchers Extraction facilities Collection Bold/Genbank Taxonomist List of names Collection Taxonomist

CoML meeting Amsterdam – 15 May ‘06 National networks –Canada: Canadian species –France: Insects (Fulguromorpha, etc) –France (+ Europe): EU pest insect species International networks –ABBI –FishBoL –Mosquitoes –Tephritidae –Lepidoptera Networks Model 1: by taxa

CoML meeting Amsterdam – 15 May ‘06 Taxon name Identified voucher MNHN Extraction facility Genoscope Collection Bold/Genbank Research projects Panglao, Santo Research project BOA Unidentified vouchers ‘morphospecies’ Networks Model 2: by location or ecosystem

CoML meeting Amsterdam – 15 May ‘06 National networks model 2 = starting from field collections –France: BOA, Marine tropical W Pacific taxa e.g. International networks model 2 –Coral Reefs / CoML –CoML = Census of Marine Life based both in ecosystems (Coral Reefs) and taxa (FishBoL) Networks Model 2: by location or ecosystem

CoML meeting Amsterdam – 15 May ‘06 Taxonomist Taxon name Voucher Extraction facility Sequencing facility Collection Bold/Genebank Institution Institutions What is the role of institutions regarding DNA barcoding? Maintaining infrastructure and human resources Networks Model 3: by institution

CoML meeting Amsterdam – 15 May ‘06 Taxonomist Taxon name Voucher Extraction facility Sequencing facility Collection Bold/Genebank Institution Institutions EDIT = EU level CBoL = global 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

CoML meeting Amsterdam – 15 May ‘06 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 Networks Model 3: EDIT Barcoding = ECBoL

CoML meeting Amsterdam – 15 May ‘06 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 –CBoL Networks Model 3: by institution

CoML meeting Amsterdam – 15 May ‘06 Thank you for your attention!