Overview of Consortium for the Barcode of Life (CBOL)

1. Overview of Consortium for the Barcode of Life (CBOL) David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu;http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938

2. Species Identification Matters • Endangered/protected species • Agricultural pests/beneficial species • Invasive species • Disease vectors/pathogens • Hazards (e.g., bird strikes on airplanes) • Environmental quality indicators • Unsustainable harvesting • Fidelity of cell lines/culture collections

3. Global Taxonomy Initiative • Established by Convention on Biological Diversity in 2002 (COP6) • Purpose is to remove or reduce the ”taxonomic impediment”

4. The taxonomic impediment • Knowledge gaps in our taxonomic system • Shortage of trained taxonomists and curators • Impact of these deficiencies on our ability to conserve, use and share the benefits of biological diversity

5. Operational objectives of GTI • Assess taxonomic needs and capacities • Build and maintain human resources, systems and infrastructure • Facilitate improved and effective infrastructure for access to taxonomic information • Include taxonomic objectives in CBD work programmes and cross-cutting issues

6. What is an effective infrastructure for taxonomy? • Taxonomists • Training • Access to information • Literature • Primary data • Research tools • Bandwidth • Other computing resources • Links to other biological web-based resources (e-biology/e-biodiversity)

7. Infrastructure of Taxonomy:Fragmented, Disconnected • Collections and databases of specimens • Seedbanks, culture/cell line collections • Compilations of taxonomic names • Floristic and faunistic surveys/inventories • Monographs, Taxonomic revisions • Data repositories (characters, gene sequences, images, trees) • The (undigitized) Taxonomic Literature

8. What do we mean by primary biodiversity data? • Label data on ~ 1.5 - 3.0 billion specimens in natural history collections, herbaria, botanical gardens, etc. • Associated notes, recordings, publications, etc. • Observational data (e.g. bird banding data) • These data have been amassed over ~ 300 years; most not digital • Big legacy data problem

9. Biodiversity Informatics:Fragmented, Unconnected

10. Growth of Biodiversity Databases Museum databases of associated data Authority files of taxonomic names

16. Databases of Species Distributions Museum databases of associated data Databases of species occurrences and distribution Authority files of taxonomic names

18. DNA Barcodes:A Key Variable for Biodiversity Informatics Museum databases of associated data Databases of species occurrences and distribution (OBIS) Authority files of taxonomic names

19. Some existing e-biodiversity resources • DNA sequence databases (GenBank et al.) (www.ncbi.nlm.nih.gov/Genbank) • Protein Data Bank (www.rcsb.org/pdb) • BOLD (www.barcodinglife.org) • Catalogue of Life (spice.sp2000.org) • Zoological Record (http://scientific.thomson.com/products/zr) • GBIF (www.gbif.net) • Cyber Infrastructure for Phylogenetic Research (CIPRES) (www.phylo.org) • Long-Term Ecological Research (LTER) Network (www.lternet.edu)

20. Emerging e-biodiversity resources • European Distributed Institute for Taxonomy (EDIT) • Biodiversity Heritage Library: Digitizing Taxonomic Literature (www.bhl.si.edu) • Encyclopedia of Life: Web pages for every species

21. Uses of DNA Barcodes Research tool for improving species-level taxonomy: • Associating all life history stages, genders • Testing species boundaries, finding new variants Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Environmental indicators, protected species • Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: • Undescribed and cryptic species

22. Uses of DNA Barcodes Research tool for improving species-level taxonomy: • Associating all life history stages, genders • Testing species boundaries, finding new variants Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Environmental indicators, protected species • Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: • Undescribed and cryptic species

23. Uses of DNA Barcodes Research tool for improving species-level taxonomy: • Associating all life history stages, genders • Testing species boundaries, finding new variants Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Environmental indicators, protected species • Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: • Undescribed and cryptic species

24. Using a Million Barcodes A critical mass of standardized data for: • Biogeographic patterns, habitat dynamics • Phylogeography • Niche modelling • Ecological relationships • Dynamics of molecular evolution • Complementing Tree of Life • Long-term biodiversity monitoring • Understanding and preserving biodiversity

25. Consortium for the Barcode of Life: Major Points • Mission: Promoting DNA barcoding as a global standard for species identification • History of development • Recent origin, rapid growth • Mode of operation as an international initiative • Compromise between bottom-up, democratic (slow) and top-down, centrally-managed (nimble) organization • Distributed activity that seeks global participation • Minimal bureaucracy, highly user-driven • Focused on projects with near- and mid-term results

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

27. CBOL Member Organizations: 2007 • 150+ Member organizations, 45 countries • 30+ Member organizations from 20+ developing countries

28. Consortium for the Barcode of Life (CBOL) • 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 • Now an international affiliation of: • Natural history museums, biodiversity organizations • Users: e.g., government agencies • Private sector biotech companies, database providers

29. CBOL-Initiated Projects • Fish Barcode of Life (FISH-BOL) • 30,000 marine/freshwater species by 2010 • All Birds Barcoding Initiative (ABBI) • 10,000 species by 2010 • Tephritid fruit flies • 2,000 pest/beneficial species and relatives by 2008 • Mosquitoes • 3,300 species by 2008 • African scale insects, lake fish, stem-borers

30. Logistical Issues • The Organization: By taxonomy? Geography? Application? • The Taxonomic Framework: Consensus list of species • The Sampling Strategy • The Supply Chain • The Data: Assembling and comparing data • The Funding • The Resulting Publications

31. Projects initiated by others • Marine zooplankton (CMarZ): Marine habitat, multiple taxa • All-Leps: Multiple regions/habitats, single taxon • BioCode, Moorea: Single location, multiple habitats, multiple taxa

32. Major Challenges • Lack of funding to acquire, identify, curate specimens • Assembling, managing, editing, QA for BARCODE-compliant data are labor-intensive • Technical problems with data transfer to BOLD, barcoding workbench at Guelph • GenBank’s BarSTool is new • Aversion to sharing data pre-publication

33. Support from CBOL • ABBI, FISH-BOL, TBI, MBI get $50K per year • Internships for data management • Travel/consulting by taxonomists for specimen identification • Assistance in proposal writing • Interactions with Working Groups • “Leading Lab” initiative to improve lab and data management protocols

34. CBOL’s Working Groups • Database: Data standards and interoperability • DNA: Lab protocols • Data Analysis: New analytical methods; population genetics perspective • Plants: Identify gene region(s) for barcoding

35. Taipei Barcode Conference • Second International Barcode Conference • Academia Sinica, week of 17 September • Regional Barcode Meeting for South/East Asia • CBOL Working Groups • FISH-BOL/Marine Fisheries workshop • Short course on lab and data protocols