South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Overview of Consortium for the Barcode of Life (CBOL) David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution / ; fax 202/

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Species Identification Matters Endangered/protected species Endangered/protected species Agricultural pests/beneficial species Agricultural pests/beneficial species Invasive species Invasive species Disease vectors/pathogens Disease vectors/pathogens Hazards (e.g., bird strikes on airplanes) Hazards (e.g., bird strikes on airplanes) Environmental quality indicators Environmental quality indicators Unsustainable harvesting Unsustainable harvesting Fidelity of cell lines/culture collections Fidelity of cell lines/culture collections

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Global Taxonomy Initiative Established by Convention on Biological Diversity in 2002 (COP6) Established by Convention on Biological Diversity in 2002 (COP6) Purpose is to remove or reduce the ”taxonomic impediment” Purpose is to remove or reduce the ”taxonomic impediment”

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 The taxonomic impediment Knowledge gaps in our taxonomic system Knowledge gaps in our taxonomic system Shortage of trained taxonomists and curators Shortage of trained taxonomists and curators Impact of these deficiencies on our ability to conserve, use and share the benefits of biological diversity Impact of these deficiencies on our ability to conserve, use and share the benefits of biological diversity

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Operational objectives of GTI Assess taxonomic needs and capacities Assess taxonomic needs and capacities Build and maintain human resources, systems and infrastructure Build and maintain human resources, systems and infrastructure Facilitate improved and effective infrastructure for access to taxonomic information Facilitate improved and effective infrastructure for access to taxonomic information Include taxonomic objectives in CBD work programmes and cross-cutting issues Include taxonomic objectives in CBD work programmes and cross-cutting issues

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 What is an effective infrastructure for taxonomy? Taxonomists Taxonomists Training Training Access to information Access to information –Literature –Primary data –Research tools –Bandwidth –Other computing resources –Links to other biological web-based resources (e-biology/e-biodiversity)

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Infrastructure of Taxonomy: Fragmented, Disconnected Collections and databases of specimens Collections and databases of specimens Seedbanks, culture/cell line collections Seedbanks, culture/cell line collections Compilations of taxonomic names Compilations of taxonomic names Floristic and faunistic surveys/inventories Floristic and faunistic surveys/inventories Monographs, Taxonomic revisions Monographs, Taxonomic revisions Data repositories (characters, gene sequences, images, trees) Data repositories (characters, gene sequences, images, trees) The (undigitized) Taxonomic Literature The (undigitized) Taxonomic Literature

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 What do we mean by primary biodiversity data? Associated notes, recordings, publications, etc. Associated notes, recordings, publications, etc. Observational data (e.g. bird banding data) Observational data (e.g. bird banding data) Label data on ~ billion specimens in natural history collections, herbaria, botanical gardens, etc. Label data on ~ billion specimens in natural history collections, herbaria, botanical gardens, etc. These data have been amassed over ~ 300 years; most not digital These data have been amassed over ~ 300 years; most not digital Big legacy data problem Big legacy data problem

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Biodiversity Informatics: Fragmented, Unconnected Voucher Specimen Species Name Journal Publication

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Growth of Biodiversity Databases Authority files of taxonomic names Museum databases of associated data

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007

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

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007

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

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Some existing e-biodiversity resources DNA sequence databases (GenBank et al.) ( DNA sequence databases (GenBank et al.) ( Protein Data Bank ( Protein Data Bank ( BOLD ( BOLD ( Catalogue of Life (spice.sp2000.org) Catalogue of Life (spice.sp2000.org) Zoological Record ( Zoological Record ( GBIF ( GBIF ( Cyber Infrastructure for Phylogenetic Research (CIPRES) ( Cyber Infrastructure for Phylogenetic Research (CIPRES) ( Long-Term Ecological Research (LTER) Network ( Long-Term Ecological Research (LTER) Network (

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Emerging e-biodiversity resources European Distributed Institute for Taxonomy (EDIT) European Distributed Institute for Taxonomy (EDIT) Biodiversity Heritage Library: Digitizing Taxonomic Literature ( Biodiversity Heritage Library: Digitizing Taxonomic Literature ( Encyclopedia of Life: Web pages for every species Encyclopedia of Life: Web pages for every species

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Associating all life history stages, genders Testing species boundaries, finding new variants Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Disease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Associating all life history stages, genders Testing species boundaries, finding new variants Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Disease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Associating all life history stages, genders Testing species boundaries, finding new variants Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Disease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Using a Million Barcodes A critical mass of standardized data for: Biogeographic patterns, habitat dynamics Biogeographic patterns, habitat dynamics Phylogeography Phylogeography Niche modelling Niche modelling Ecological relationships Ecological relationships Dynamics of molecular evolution Dynamics of molecular evolution Complementing Tree of Life Complementing Tree of Life Long-term biodiversity monitoring Long-term biodiversity monitoring Understanding and preserving biodiversity Understanding and preserving biodiversity

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Mission: Promoting DNA barcoding as a global standard for species identification Mission: Promoting DNA barcoding as a global standard for species identification History of development History of development –Recent origin, rapid growth Mode of operation as an international initiative 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 Consortium for the Barcode of Life: Major Points

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 CBOL Structure Member Organizations Executive Committee Working Groups Scientific Advisory Board Secretariat Office

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 CBOL Member Organizations: Member organizations, 45 countries 30+ Member organizations from 20+ developing countries

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Consortium for the Barcode of Life (CBOL) First barcoding publications in 2002 First barcoding publications in 2002 Cold Spring Harbor planning workshops in 2003 Cold Spring Harbor planning workshops in 2003 Sloan Foundation grant, launch in May 2004 Sloan Foundation grant, launch in May 2004 Secretariat opens at Smithsonian, September 2004 Secretariat opens at Smithsonian, September 2004 First international conference February 2005 First international conference February 2005 Now an international affiliation of: Now an international affiliation of: –Natural history museums, biodiversity organizations –Users: e.g., government agencies –Private sector biotech companies, database providers

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 CBOL-Initiated Projects Fish Barcode of Life (FISH-BOL) Fish Barcode of Life (FISH-BOL) –30,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI) All Birds Barcoding Initiative (ABBI) –10,000 species by 2010 Tephritid fruit flies Tephritid fruit flies –2,000 pest/beneficial species and relatives by 2008 Mosquitoes Mosquitoes –3,300 species by 2008 African scale insects, lake fish, stem-borers African scale insects, lake fish, stem-borers

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Logistical Issues 1. The Organization: By taxonomy? Geography? Application? 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

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Projects initiated by others Marine zooplankton (CMarZ): Marine habitat, multiple taxa Marine zooplankton (CMarZ): Marine habitat, multiple taxa All-Leps: Multiple regions/habitats, single taxon All-Leps: Multiple regions/habitats, single taxon BioCode, Moorea: Single location, multiple habitats, multiple taxa BioCode, Moorea: Single location, multiple habitats, multiple taxa

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Major Challenges Lack of funding to acquire, identify, curate specimens Lack of funding to acquire, identify, curate specimens Assembling, managing, editing, QA for BARCODE-compliant data are labor-intensive Assembling, managing, editing, QA for BARCODE-compliant data are labor-intensive Technical problems with data transfer to BOLD, barcoding workbench at Guelph Technical problems with data transfer to BOLD, barcoding workbench at Guelph GenBank’s BarSTool is new GenBank’s BarSTool is new Aversion to sharing data pre-publication Aversion to sharing data pre-publication

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Support from CBOL ABBI, FISH-BOL, TBI, MBI get $50K per year ABBI, FISH-BOL, TBI, MBI get $50K per year Internships for data management Internships for data management Travel/consulting by taxonomists for specimen identification Travel/consulting by taxonomists for specimen identification Assistance in proposal writing Assistance in proposal writing Interactions with Working Groups Interactions with Working Groups “Leading Lab” initiative to improve lab and data management protocols “Leading Lab” initiative to improve lab and data management protocols

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 CBOL’s Working Groups Database: Data standards and interoperability Database: Data standards and interoperability DNA: Lab protocols DNA: Lab protocols Data Analysis: New analytical methods; population genetics perspective Data Analysis: New analytical methods; population genetics perspective Plants: Identify gene region(s) for barcoding Plants: Identify gene region(s) for barcoding

South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007 Taipei Barcode Conference Second International Barcode Conference Second International Barcode Conference Academia Sinica, week of 17 September Academia Sinica, week of 17 September Regional Barcode Meeting for South/East Asia Regional Barcode Meeting for South/East Asia CBOL Working Groups CBOL Working Groups FISH-BOL/Marine Fisheries workshop FISH-BOL/Marine Fisheries workshop Short course on lab and data protocols Short course on lab and data protocols