Data Analysis Working Group, DIMACS, 26 Sept 2005 DNA Barcoding and the Consortium for the Barcode of Life David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution 202/ ; fax 202/

Data Analysis Working Group, DIMACS, 26 Sept 2005 Species Identification Matters Endangered/protected species Agricultural pests Invasive species Disease vectors/pathogens Hazards (e.g., bird strikes on airplanes) Environmental quality indicators Unsustainable harvesting Fidelity of cell lines/culture collections

Data Analysis Working Group, DIMACS, 26 Sept 2005 Specimens Characters Distributions of Character Variation Taxonomic Decision- Making Socioeconomic Decisions Specimens Concerns/ Regulations The Practice of Taxonomy Taxonomists The Uses of Taxonomy

Data Analysis Working Group, DIMACS, 26 Sept 2005 The Problem… Taxonomists are a limited resource Taxonomic infrastructure is not widely available Taxonomic decisions are difficult for non- specialists Therefore, the practice of taxonomy does not scale up to meet the needs of society (or ecology, ecosystem studies, etc.)

Data Analysis Working Group, DIMACS, 26 Sept 2005 A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species

Data Analysis Working Group, DIMACS, 26 Sept 2005 Uses of DNA Barcodes “Triage” tool for flagging potential new species: Undescribed and cryptic species Research tool for assigning specimens to known species, including: Life history stages, damaged specimens, gut contents, droppings Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Protected species, CITES listed, trade-sensitive

Data Analysis Working Group, DIMACS, 26 Sept 2005 The Mitochondrial Genome Cyt b D-Loop ND5 H-strand ND4 ND4L ND3 CO III CO I L-strand ND6 CO I ND2 ND1 CO II Small ribosomal RNA Large ribosomal RNA ATPase subunit 8 ATPase subunit 6

Data Analysis Working Group, DIMACS, 26 Sept 2005 How much information is there in a DNA Barcode? Human genome: –Contains 3 billion base-pairs –Identified by 648 bp COI barcode sequence –Content-to-label ratio: 5 X 10 6 Oxford English Dictionary, 2 nd Ed.,1989: –20 volumes, 21,730 pages, 500,000 entries, 59 million words, 350 million print characters –Identified by 10-character ISBN –Content-to-label ratio: 4 X 10 7

Data Analysis Working Group, DIMACS, 26 Sept 2005 Current Norm: High throughput ABI 3100 capillary automated sequencer Large capacity PCR and sequencing reactions

Data Analysis Working Group, DIMACS, 26 Sept 2005 Future Norm? A taxonomic GPS Link to reference database Usable by non- specialists.

Data Analysis Working Group, DIMACS, 26 Sept 2005

Consortium for the Barcode of Life (CBOL) An international affiliation of: –80+ Members Org’s, 35+ countries, 6 continents –Natural history museums, biodiversity organizations –Users: e.g., government agencies –Private sector biotech companies, database providers 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

Data Analysis Working Group, DIMACS, 26 Sept 2005 CBOL Member Organizations (as of May 2005)

Data Analysis Working Group, DIMACS, 26 Sept 2005 CBOL’s Working Groups Database: Designing/constructing the Barcode Section of GenBank DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination Data Analysis: Beyond phenetic methods; population genetics perspective Plants: Identify gene region(s) for barcoding

Data Analysis Working Group, DIMACS, 26 Sept 2005 CBOL’s Goals Create a reference barcode database Identify high-priority taxa and societal needs Promote/facilitate barcoding projects and ‘CBOL campaigns’ Improve methods, address shared obstacles through WGs Populate database from collections More portability, less time/expense Improve taxonomic research environment

Data Analysis Working Group, DIMACS, 26 Sept 2005 Recent and Planned Activities Data standards, Barcode records in GenBank Launch of FishBOL, All Birds Initiatives International Network for Barcoding Invasive and Pest Species (INBIPS) APEC Workshop on Invasives, Beijing Mosquitoes and disease vectors Plans for CITES species, endangered Vertebrates, Bushmeat

Data Analysis Working Group, DIMACS, 26 Sept 2005 Barcode Sequence Voucher Specimen Species Name Specimen Metadata Literature (link to content or citation) Barcode Section of GenBank Indices - Catalog 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