Introduction to the Consortium for the Barcode of Life (CBOL) Scott Miller Smithsonian Institution and Consortium for the Barcode of Life

Two views of genomics Vertical: Complete genomes, deep but narrow knowledge Vertical: Complete genomes, deep but narrow knowledge Few species and few individuals Few species and few individuals But evolving in humans, Drosophila, crops But evolving in humans, Drosophila, crops Horizontal: Short targeted sequences, shallow but broad knowledge Horizontal: Short targeted sequences, shallow but broad knowledge Many species and many individuals Many species and many individuals DNA barcoding as an example DNA barcoding as an example

Species Identification Matters Agricultural pests/beneficial species Agricultural pests/beneficial species Managing trade (e.g., IPPC) Managing trade (e.g., IPPC) Consumer protection, ensuring food quality Consumer protection, ensuring food quality Invasive species Invasive species Environmental quality indicators Environmental quality indicators Quality of cell lines/culture collections Quality of cell lines/culture collections Globilization increasing invasive species spread Globilization increasing invasive species spread Changes of host and range with climate change Changes of host and range with climate change

Species Identification Matters (2) 80% CGIAR impact in Africa ($17 billion) from 4 biocontrol programs 80% CGIAR impact in Africa ($17 billion) from 4 biocontrol programs Cassava mealybug, mango mealybug, water hyacinth, cassava green mite Cassava mealybug, mango mealybug, water hyacinth, cassava green mite All involved significant taxonomic challenges in pest and/or biocontrol agent All involved significant taxonomic challenges in pest and/or biocontrol agent Maredia & Raitzer 2006 Maredia & Raitzer 2006

Historic challenges Problems with species concepts and their application Problems with species concepts and their application Problems with species identifications Problems with species identifications Character systems – morphology, genetics, etc. Character systems – morphology, genetics, etc. Access to existing knowledge Access to existing knowledge Decline in expertise Decline in expertise Decline in service availablity Decline in service availablity Genomics and Internet offer new options Genomics and Internet offer new options

Poor representation of systematics infrastructure in Africa

Human resources also thinly distributed Stuckenberg (1964): most systematics done outside of Africa, but only 7% of world entomologists working on Africa Stuckenberg (1964): most systematics done outside of Africa, but only 7% of world entomologists working on Africa Gaston & May (1992): only 4% of ecologists and 7% of systematists in Africa Gaston & May (1992): only 4% of ecologists and 7% of systematists in Africa Surveys by CABI (1993), ICIPE (1996), and SAFRINET (1998) show same trends Surveys by CABI (1993), ICIPE (1996), and SAFRINET (1998) show same trends

Associating Life Stages, Processed Parts, and Dimorphic Genders

A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species

An Internal ID System for All Animals Typical Animal Cell Mitochondrion DNA mtDNA D-Loop ND5 H-strand ND4 ND4L ND3 CO III L-strand ND6 ND2 ND1 CO II Small ribosomal RNA ATPase subunit 8 ATPase subunit 6 Cytochrome b CO I The Mitochondrial Genome

How Barcoding Works Building the reference library: Building the reference library: Well-identified specimen (vouchers) Well-identified specimen (vouchers) Tissue subsample Tissue subsample DNA extraction, PCR amplification DNA extraction, PCR amplification DNA sequencing DNA sequencing Data submission to GenBank Data submission to GenBank Using the reference library: Using the reference library: Unidentified specimen Unidentified specimen Tissue, DNA, sequencing Tissue, DNA, sequencing Comparison with reference sequences Comparison with reference sequences

How Barcoding is Done From specimen to sequence to species Voucher Specimen DNA extractionCO1 geneDNA sequencing Trace file Database of Barcode Records Collecting ND3ND3 COIIICOIII ND2ND2 ND1ND1

Example: Moths in Africa Noctuid stem borers are species complexes Noctuid stem borers are species complexes ICIPE and IRD studies ICIPE and IRD studies Their tachinid parasites are also (Dittrich et al 2006) Their tachinid parasites are also (Dittrich et al 2006) Leguminivora ptychora on legumes is as species complex (Miller unpubl. from IITA samples) Leguminivora ptychora on legumes is as species complex (Miller unpubl. from IITA samples) But some pests are widespread, e.g., Spoladea recurvalis and Maruca vitrata But some pests are widespread, e.g., Spoladea recurvalis and Maruca vitrata

Quick and efficient Hawk moths (Sphingidae) sampled on IITA Ibadan campus (agroscape and forest) Hawk moths (Sphingidae) sampled on IITA Ibadan campus (agroscape and forest) 49 species in six months, almost all the local fauna 49 species in six months, almost all the local fauna DNA barcodes all well resolved in local context and almost well resolved in global context DNA barcodes all well resolved in local context and almost well resolved in global context Local sequence libraries can be assembled quickly and contribute to global library Local sequence libraries can be assembled quickly and contribute to global library

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Coordination with other fields of science 6. Adoption by regulatory agencies 7. Product development by private companies

2008: CBOL Member Organizations 170+ Member organizations, 50+ countries 54 Member organizations from 20+ developing countries

Growth of CBOL Activities Executive Committee from 4 continents Executive Committee from 4 continents Implementation Board of 19 Members Implementation Board of 19 Members  Working Groups  Campaigns  GenBank, BOLD  Related Initiatives Outreach meetings to Africa, South/Central America, Asia Outreach meetings to Africa, South/Central America, Asia Network of 15 “Leading Labs” in 9 countries Network of 15 “Leading Labs” in 9 countries Strong partnerships with GenBank/EMBL/DDBJ, GBIF, EOL Strong partnerships with GenBank/EMBL/DDBJ, GBIF, EOL

CBOL’s Global 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 ,000 pest/beneficial species and relatives by 2008 Mosquitoes Mosquitoes 3,300 species by ,300 species by 2008 Endangered species Endangered species Trees of the world Trees of the world

Preview of the Third International Barcode Conference (2009) 1 million barcode records from 100,000 species 1 million barcode records from 100,000 species Rapid progress on plant and fungal barcoding Rapid progress on plant and fungal barcoding Identifying unknowns in 30 minutes for less than US$1 Identifying unknowns in 30 minutes for less than US$1 Port inspectors starting to test unknowns with barcodes in several countries Port inspectors starting to test unknowns with barcodes in several countries Portable sequencing ? Portable sequencing ? Completion of the first local barcode biotic inventory Completion of the first local barcode biotic inventory

Overview of DNA barcoding and its relations to other biodiversity initiatives Scott Miller Smithsonian Institution and Consortium for the Barcode of Life

How Barcoding is Done From specimen to sequence to species Voucher Specimen DNA extractionCO1 geneDNA sequencing Trace file Database of Barcode Records Collecting ND3ND3 COIIICOIII ND2ND2 ND1ND1

Producing Barcode Data: 2007 ABI 3100 capillary automated sequencer Hundreds of samples per day Dimes to dollars per sample Polymerase Chain Reaction Amplification units

Producing Barcode Data: 2008 Faster, more portable: Hundreds of samples per hour Integrated DNA microchipsTable-top microfluidic systems

Producing Barcode Data: 2010? Barcode data anywhere, instantly Data in seconds to minutes Data in seconds to minutes Pennies per sample Pennies per sample Link to reference database Link to reference database A taxonomic GPS A taxonomic GPS Usable by non- specialists Usable by non- specialists

Barcode Sequence Voucher Specimen Species Name Specimen Metadata Literature (link to content or citation) BARCODE Records in GenBank Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Georeference Habitat Character sets Images Behavior Other genes Trace files Other Databases Phylogenetic Pop’n Genetics Ecological Primers Databases - Provisional sp.

GenBank, EMBL, and DDBJ Global, Open Access to Barcode Data

Linking GenBank to Vouchers

Specimen Webpage

Sequence Webpage

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Coordination with other fields of science 6. Adoption by regulatory agencies 7. Product development by private companies

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Coordination with other fields of science 6. Adoption by regulatory agencies 7. Product development by private companies

CBOL’s Global 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 ,000 pest/beneficial species and relatives by 2008 Mosquitoes Mosquitoes 3,300 species by ,300 species by 2008 Endangered species Endangered species Trees of the world Trees of the world

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Coordination with other fields of science 6. Adoption by regulatory agencies 7. Product development by private companies

Leading Labs Network BioCode STRISI-LAB CCDB BOLDGenBank

Linking to International Initiatives through the Consortium for the Barcode of Life (CBOL) Global Biodiversity Information Facility (GBIF) Global Biodiversity Information Facility (GBIF) Taxonomic databases (Species 2000, ITIS) Taxonomic databases (Species 2000, ITIS) Voucher specimen databases Voucher specimen databases BioNet International BioNet International CBD Global Taxonomy Initiative CBD Global Taxonomy Initiative Projects such as SABONET & BOZONET Projects such as SABONET & BOZONET Biodiversity Heritage Library/Encyclopedia of Life Biodiversity Heritage Library/Encyclopedia of Life Genbank/EMBL/DDBJ partnership Genbank/EMBL/DDBJ partnership

Access and Benefit Sharing November 2008 international workshop on non-commercial biodiversity research; workshop goals: Develop code of conduct for researchers Develop code of conduct for researchers Develop off-the-shelf options for: Develop off-the-shelf options for: Standard PICs, MATs, MTAs (Plant Treaty as model?) Standard PICs, MATs, MTAs (Plant Treaty as model?) Release of barcode and specimen data Release of barcode and specimen data Publication of results Publication of results Ownership and safeguarding of voucher specimens Ownership and safeguarding of voucher specimens Access to tissue for barcoding Access to tissue for barcoding Restrictions on subsequent use of DNA Restrictions on subsequent use of DNA

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Coordination with other fields of science 6. Adoption by regulatory agencies 7. Product development by private companies

Old and new techniques CBOL builds on existing taxonomic knowledge CBOL builds on existing taxonomic knowledge Sequence library built on vouchered specimens Sequence library built on vouchered specimens Voucher specimens make science testable and repeatable; vital to quality control Voucher specimens make science testable and repeatable; vital to quality control Voucher specimens link historic, current and future research Voucher specimens link historic, current and future research

Building Collaborations Beyond Taxonomy Workshops withWorkshops with  Assembling the Tree of Life projects  Population biologists (“Banbury 3”) EMBO Conference on Molecular BiodiversityEMBO Conference on Molecular Biodiversity Co-sponsor of e-Biosphere 09 Conference on Biodiversity Informatics, June 2009, LondonCo-sponsor of e-Biosphere 09 Conference on Biodiversity Informatics, June 2009, London

Links to Taxonomic Literature London meeting on electronic access to taxonomic literature, 2005 London meeting on electronic access to taxonomic literature, 2005 Catalyzed Biodiversity Heritage Library Catalyzed Biodiversity Heritage Librarywww.biodiversitylibrary.org Proactive steps with PubMed to add taxonomic journals to online abstracts Proactive steps with PubMed to add taxonomic journals to online abstracts Aggressive negotiation with publishers of barcoding papers Aggressive negotiation with publishers of barcoding papers Involvement in Encyclopedia of Life Involvement in Encyclopedia of Life

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Coordination with other fields of science 6. Adoption by regulatory agencies 7. Product development by private companies

Adoption by Regulators International: FISH-BOL and fish regulatory agencies FISH-BOL and fish regulatory agencies  CBOL workshop in Taipei, September 2007 FAO and International Plant Protection Convention FAO and International Plant Protection Convention  Proposal for Diagnostic Protocols for fruit flies CITES, National Agencies, Conservation NGOs CITES, National Agencies, Conservation NGOs  International Steering Committee, identifying pilot projects National examples from USA: Federal Aviation Administration – Birds Federal Aviation Administration – Birds Environmental Protection Agency – Aquatic insects Environmental Protection Agency – Aquatic insects Nat’l Oceanic and Atmospheric Administration - Fish Nat’l Oceanic and Atmospheric Administration - Fish Department of Agriculture – Fruit flies Department of Agriculture – Fruit flies

Promote barcoding as a global standard Build participation Working Groups BARCODE standard International Conferences Increase production of public BARCODE records Projects, Networks, Organizations BOLI versus CBOL versus iBOL??

BOLI, CBOL, iBOL and BOLD BOLI is the umbrella term BOLI is the umbrella term Includes projects, networks, organizations Includes projects, networks, organizations CBOL is a catalytic organization CBOL is a catalytic organization Launched in 2004 Launched in 2004 Now in its third grant period ( ) Now in its third grant period ( ) iBOL is a $25M Genome Canada proposal iBOL is a $25M Genome Canada proposal Part of $150M project plan, with a 3:1 match Part of $150M project plan, with a 3:1 match Proposal submitted September 2008 Proposal submitted September 2008 BOLD is a system of databases at Guelph BOLD is a system of databases at Guelph Open access workbench Open access workbench