Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
From DNA Barcoding to the Encyclopedia of Life: Initiatives in Biodiversity Informatics David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution [email protected]; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938 Species Identification Matters Environmental quality indicators Managing for sustainable harvesting Consumer protection, ensuring food quality Endangered/protected species Invasive species (e.g., in ballast water) Basic research on evolution, ecology Agricultural pests/beneficial species Disease vectors/pathogens Fidelity of cell lines/culture collections EPA/RTP – 8 April 08 Encyclopedia of Life Taxonomic revisions, biotic surveys Published species descriptions Public database records Description/revision not yet published Data not yet released Not yet described Not yet in specimen catalog Not yet examined Not yet curated Not yet collected EPA/RTP – 8 April 08 Infrastructure of Taxonomy Collections and databases of specimens Seedbanks, culture/cell line collections Compilations of taxonomic names Floristic and faunistic surveys/inventories Monographs, Taxonomic revisions Data repositories (gene sequences, characters, images, trees) The (undigitized) Taxonomic Literature EPA/RTP – 8 April 08 Biodiversity Informatics: Fragmented, Unconnected Specimens Journal Publications Species Names EPA/RTP – 8 April 08 Data providers: DNA data: Barcoding Specimens: Specify, KE-EMu, ARCTOS Publications: Biodiversity Heritage Library Tools and Value-adders: Improving georeference data: BioGeomancer Collecting, preparing data: EDIT ScratchPads Building consensus taxonomies: CATE Aggregators Reviewed lists of taxonomic names: ITIS, Species2000 Assembling occurrence reports: OBIS One-stop access to distributed data: GBIF EOL – Knowledge space EPA/RTP – 8 April 08 Biodiversity Heritage Library www.biodiversitylibrary.org Scanning and OCR converting the out-ofcopyright taxonomic literature Now Online: 7,660 volumes; 2,942,044 pages American Museum of Natural History (New York) Field Museum (Chicago) Natural History Museum (London) Smithsonian Institution (Washington) Missouri Botanical Garden (St. Louis) New York Botanical Garden (New York) Royal Botanic Garden, Kew Botany Libraries, Harvard University Ernst Mayr Library of the Museum of Comparative Zoology, Harvard University Marine Biological Laboratory / Woods Hole Oceanographic Institution James Dwight Dana Zoophytes. Atlas, 1849 EPA/RTP – 8 April 08 Growth of Biodiversity Databases Voucher Specimen Biodiversity Heritage Library Journal Publication Museum databases of associated data Species Name Authority files of taxonomic names EPA/RTP – 8 April 08 What? Where? When? Distributed Database serving data through nodes and partners Census of Marine Life (CoML) and the Ocean Biogeographic Information System (OBIS) Voucher Specimen Museum databases of associated data Databases of species occurrences and distribution Journal Publication Species Name Authority files of taxonomic names EPA/RTP – 8 April 08 EPA/RTP – 8 April 08 Global Biodiversity Information Facility (GBIF) Voucher Specimen Museum databases of associated data Databases of species occurrences and distribution Journal Publication Species Name Authority files of taxonomic names EPA/RTP – 8 April 08 www.eol.org On-line resource—plants, animals, microorganisms Web pages for all 1.8 million known species Plus millions more yet to be described Common format Customizable by user Freely available Accessible from a common portal Never completed EPA/RTP – 8 April 08 Components of the Encyclopedia of Life (EOL) Each site consists of several components – Species page for the general public Draft pages assembled via mashup technology Drafts authenticated by experts (“curators”) using controlled wikis Information submitted by public – Anyone can comment on the information and or suggest things to add – Curators will examine these suggestions and may move some of the information to the protected part EPA/RTP – 8 April 08 EPA/RTP – 8 April 08 DNA Barcodes: A Key Variable for Biodiversity Informatics Voucher Specimen Museum databases of associated data Databases of species occurrences and distribution (OBIS) Barcode Sequence Journal Publication Species Name Authority files of taxonomic names EPA/RTP – 8 April 08 A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species Reactions to Barcoding: 2004 From ecologists and other users: “This is what we need! How soon can we get started?” From traditional taxonomists: “Species should be based on lots of characters, not just barcodes” From forward-looking taxonomists: “Using molecular data as species diagnostics isn’t new, but standardization and broad implementation are great!” From barcoding practitioners: “I had my doubts at the beginning, but it really works as a tool for identification (96% accurate in a recent mollusc paper) and it is at least as good as traditional approaches to discovering new species.” EPA/RTP – 8 April 08 The Mitochondrial Genome D-Loop Small ribosomal RNA Large ribosomal RNA Cyt b ND1 ND6 ND5 L-strand COI COI ND2 H-strand ND4 COI ND4L ND3 COIII COII ATPase subunit 8 ATPase subunit 6 EPA/RTP – 8 April 08 Projects, Networks, Organizations • Promote barcoding as a global standard • Build participation • Working Groups • BARCODE standard • International Conferences • Increase production of public BARCODE records Uses of DNA Barcodes Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings Research tool for improving species-level taxonomy: Associating all life history stages, genders Testing species boundaries, finding new variants “Triage” tool for flagging potential new species: Undescribed and cryptic species EPA/RTP – 8 April 08 Associating Life Stages, Processed Parts, Dimorphic Genders The Barcoding Pipeline Building the reference library: – Well-identified specimen – Tissue subsample – DNA extraction, PCR amplification – DNA sequencing – Data submission to GenBank Using the reference library: – Unidentified specimen – Tissue, DNA, sequencing – Comparison with reference sequences EPA/RTP – 8 April 08 Producing Barcode Data: 2008 Faster, more portable: Hundreds of samples per hour Integrated DNA microchips Table-top microfluidic systems EPA/RTP – 8 April 08 Producing Barcode Data: 2010? Barcode data anywhere, instantly Data in seconds to minutes Pennies per sample Link to reference database A taxonomic GPS Usable by nonspecialists EPA/RTP – 8 April 08 Consortium for the Barcode of Life (CBOL) First barcoding publications in 2002 Cold Spring Harbor planning workshops in 2003 Sloan Foundation 2-year grant for $800K May 2004 Secretariat opens at Smithsonian, September 2004 First international conference February 2005 $1.55 million 2-year renewal in April 2006 Now an international affiliation of: – Natural history museums, biodiversity organizations – Users: e.g., government agencies – Private sector biotech companies, database providers EPA/RTP – 8 April 08 CBOL Member Organizations: 2007 • 150+ Member organizations, 45 countries • 30+ Member organizations from 20+ developing countries EPA/RTP – 8 April 08 CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. 2. 3. 4. 5. 6. 7. Developing/raising community standards Barcode projects to populate database Global participation and coordination Adoption by regulatory agencies Acceptance by taxonomic community Excitement in other fields of science Product development by private companies EPA/RTP – 8 April 08 BARCODE Records in INSDC Specimen Metadata Georeference Habitat Character sets Images Behavior Other genes Other Databases Phylogenetic Pop’n Genetics Ecological Voucher Specimen Barcode Sequence Trace files Primers Literature (link to content or citation) Species Name Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Databases - Provisional sp. EPA/RTP – 8 April 08 Structured Link to Vouchers Institutional Acronym : Collection Code : Catalog ID EPA/RTP – 8 April 08 Link from GenBank to Museums EPA/RTP – 8 April 08 CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. 2. 3. 4. 5. 6. 7. Developing/raising community standards Barcode projects to populate database Global participation and coordination Adoption by regulatory agencies Acceptance by taxonomic community Excitement in other fields of science Product development by private companies EPA/RTP – 8 April 08 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 EPA/RTP – 8 April 08 CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. 2. 3. 4. 5. 6. 7. Developing/raising community standards Barcode projects to populate database Global participation and coordination Adoption by regulatory agencies Acceptance by taxonomic community Excitement in other fields of science Product development by private companies EPA/RTP – 8 April 08 Outreach Activities Regional meetings in: – Cape Town, South Africa, 7-8 April 2006, SANBI – Nairobi, Kenya, 18-19 October 2006 – Brazil, February 2007 – Taiwan, September 2007 Second International Barcode Conference – Taiwan, September 2007 Support from CBOL, host governments and international development agencies EPA/RTP – 8 April 08 CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. 2. 3. 4. 5. 6. 7. Developing/raising community standards Barcode projects to populate database Global participation and coordination Adoption by regulatory agencies Acceptance by taxonomic community Excitement in other fields of science Product development by private companies EPA/RTP – 8 April 08 Adoption by Regulators Environmental Protection Agency – $250K pilot test, water quality bioassessment Food and Drug Administration – Reference barcodes for commercial fish NOAA/NMFS – $100K for Gulf of Maine pilot project – FISH-BOL workshop with agencies, Taipei, Sept 2007 Federal Aviation Administration – $500K for birds FAO International Plant Protection Commission – Proposal for Diagnostic Protocols for fruit flies CITES, National Agencies, Conservation NGOs – International Steering Committee, identifying pilot projects EPA/RTP – 8 April 08 US Wadeable Streams Assessment • National assessment of the condition of wadeable streams • 10 different taxonomic ID laboratories • 749 stream macroinvertebrate samples (sites) • All organisms identified to genus only • 10% random re-identification by independent taxonomist • Data quality objective – 85% repeatability Credible environmental decision-making depends on objectivity and repeatability of taxonomic results EPA/RTP – 8 April 08 EPA Advanced Monitoring Initiative Mark Bagley, USEPA/ORD, Cincinnati Project Goals • • • Develop a DNA barcode library for important aquatic indicator species (EPT) Ephemeroptera (Mayflies) Plecoptera (Stoneflies) Trichoptera (Caddisflies) Compare DNA barcodes to traditional bioassessments for EPT taxa from Maryland stream survey Cost, Speed, Objectivity, Accuracy, Precision How important is increased taxonomic precision? Determine how to efficiently incorporate DNA barcodes into a state bioassessment program