DNA Barcoding and the Consortium for the Barcode of Life Scott Miller Smithsonian Institution

Why systematics and taxonomy? Basic tool for describing and explaining biological diversity Historical framework for biocontrol, biogeography, ecology, evolution, etc. -predictive value of phylogeny- Communication of knowledge

Species Identification Matters Basic research on evolution, ecology Agricultural pests/beneficial species Invasive species Environmental quality indicators Managing for sustainable harvesting Endangered/protected species Disease vectors/pathogens Hazards (e.g., bird strikes on airplanes) Fidelity of cell lines/culture collections

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

Barcoding for Animals - COI 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

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

Associating Life Stages, Processed Parts, Dimorphic Genders

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

CBOL Member Organizations: Member organizations, 45 countries 30+ Member organizations from 20+ developing countries

CBOL’s Strategy Collaborate with existing biodiversity initiatives Work to connect existing systems with new data standards; avoid “reinventing the wheel” Rely on GenBank, EMBL and DDBJ as archival data repositories BOLD as LIMS and barcode database/analysis Global participation Engage taxonomists and applied user communities Set tangible, realistic goals, near-term results

Linking to International Initiatives through CBOL Global Biodiversity Information Facility (GBIF) ISIS/ZIMS (zoos) Taxonomic databases (Species 2000, ITIS) Voucher specimen databases (EMu) Biodiversity Heritage Library Genbank/EMBL/DDBJ partnership Encyclopedia of Life (new –

CBOL Taxon Focused 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

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

Driving Cultural Change Integrating databases: –Sequences, vouchers, species names Accelerating taxonomic outputs –Digital libraries, Encyclopedia of Life –Species registration, ZooBank Promoting open access to data –The barcode “data commons” –Creating a reward system for data publication –PLoS One “data release” papers –Community feedback for data curation

CBOL Formalin Workshop May 8-9, 2006 workshop in Washington, U.S. National Research Council Chemists, biochemists, biophysicists, biomedical researchers Literature survey of DNA recovery protocols from formalin-fixed specimens Create a new research agenda Follow-on with SPNHC as major partner

CBOL Outreach Activities Regional meetings in: –Cape Town, South Africa, 7-8 April 2006, SANBI –Nairobi, Kenya, October 2006 –Brazil, February 2007 –Taiwan, September 2007 Second International Barcode Conference –Taiwan, September 2007 Support from CBOL, host governments and international development agencies

Goals of Regional Meetings Raise awareness Explore potential applications in the region Assess greatest needs and opportunities in the region Identify highest priorities, construct national and regional action plans Start intra-regional networks and intercontinental partnerships

Taipei Barcode Conference Second International Barcode Conference Academia Sinica, week of 17 September Regional Barcode Meeting for South/SE Asia CBOL Working Groups FISH-BOL/Marine Fisheries workshop Short course on biodiversity informatics

Methods

Producing Barcode Data: 2006 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 Pennies per sample Link to reference database A taxonomic GPS Usable by non- specialists

What DNA Barcoding is NOT Barcoding is not DNA taxonomy; no single gene (or character) is adequate Barcoding is not “Tree of Life”; we focus on species diagnosis not phylogeny Barcoding is not just COI; standardizing on one region has benefits and limits Molecules in taxonomy is not new; but large-scale and standardization are new Barcoding can help to create a 21 st century research environment for taxonomy

For additional information, see More CBOL members welcome!