Overview of DNA Barcoding and the Barcode of Life Initiative

1. Overview of DNA Barcoding and the Barcode of Life Initiative Scott E. Miller, Chair, CBOL Executive Committee National Museum of Natural History Smithsonian Institution MillerS@si.edu; http://www.barcoding.si.edu

2. Poor representation of systematics infrastructure in Africa

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

4. Outreach to Africa • South Africa and Kenya involved from beginning of CBOL in May 2004 • Southern African regional workshop now • Eastern and Western regional workshops under discussion • African involvement in global campaigns (e.g., birds, fish, mosquitos, fruit flies)

5. 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.”

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

7. D-Loop Small ribosomal RNA Large ribosomal RNA Cyt b ND1 ND6 COI COI ND5 L-strand ND2 H-strand ND4 COI ND4L COII ND3 ATPase subunit 8 COIII ATPase subunit 6 The Mitochondrial Genome

8. Uses of DNA Barcodes Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Environmental indicators, protected species Research tool for assigning specimens to known species, including: • Life history stages, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: • Undescribed and cryptic species

9. 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

10. Uses of DNA Barcodes Research tool for assigning specimens to known species, including: • Life history stages, damaged specimens, gut contents, droppings

11. Uses of DNA Barcodes Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Environmental indicators, protected species Research tool for assigning specimens to known species, including: • Life history stages, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: • Undescribed and cryptic species 23% marine species in Pearl Harbor are alien or cryptogenic

12. What DNA Barcoding is NOT • Barcoding is not DNA taxonomy; no single gene (or character) is adequate • Barcoding is not Tree of Life; barcode clusters are not phylogenetic trees • 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 • NEVERTHELESS, Barcoding is helping to create a 21st century research environment for taxonomy

13. Wider Impacts of Barcoding: 2008 • Catalyzing interoperability of databases • Barcode data standards link sequences, specimens, species names and publications • Renewing the mission of museums • DNA recovery from formalin-fixed specimens • Promoting the growth of DNA banks • Expanding analytical toolbox for taxonomy • Improving the information infrastructure • Digital library initiative in taxonomy

14. Digitizing Taxonomic Literature • CBOL’s catalytic efforts: • Library-Laboratory meeting in London on electronic access to taxonomic literature • Led to formation of Biodiversity Heritage Library initiative • Proactive steps with PubMed to add taxonomic journals to online abstracts • Aggressive negotiation with publishers of barcoding papers

15. The Vision: Enabling research, product development, and dissemination Ideally, all data should be accessible: • From any location • In formats appropriate to users • With a single query for each data type • Using simple links • Interoperable across data sets … digitally

16. Species web pages

17. Collaborating with International Initiatives • Global Biodiversity Information Facility (GBIF) • Global Taxonomy Initiative (GTI) of Convention on Biological Diversity • BioNet International • Projects such as SABONET • Digital library • Genbank/EMBL/DDBJ • Leveraging “north” and “south” funding?

18. Planned Outreach • Regional meetings in: • Cape Town, South Africa, 7-8 April 2006, SANBI • Brazil, 2nd quarter 2006 • Southern Asia, mid-2007 • Nairobi, Kenya, October 2006 • Second International Barcode Conference • Southeast Asia, February 2007 • Support from CBOL, host governments and international development agencies