Transcript Document
Potencials of DNA Barcoding in South America Robert Hanner, PhD Database Working Group Chair, CBOL Global Campaign Coordinator, FISH-BOL Associate Director, Canadian Barcode of Life Network Biodiversity Institute of Ontario, University of Guelph, Canada 19-20 March 2007 Biological specimens come in many forms Identifiable adults Juvenile stages Processed products Barcoding works on all forms First publication on fish barcoding: Rationale for FISH-BOL Fish comprise nearly half of all vertebrates, yet with ~30,000 described species they are still a manageable group for demonstrating the utility of barcoding. As the dominant source of protein in the human diet and with an estimated $200 billion USD annual value of fisheries worldwide, fishes are of major socio-economic importance. With ~300,000 names recorded for fishes world wide, harmonization of names across collections is needed. Challenge: establish an organizational infrastructure with clear sampling and analytical protocols. FISH-BOL Inaugural Fish Barcode of Life Workshop, 5-8 June 2005 FISH-BOL takes shape… Goal: • Coordinate the assembly of a reference sequence library for all fish species. Existing collections and anticipated sampling effort: About 33 million fish specimens reside in museum collections; their barcode analysis will ultimately aid both the resolution of cases of synonymy and help define species concepts. The fixation of these specimens in formalin has led to DNA damage that makes sequencing difficult. Serious effort needs to be directed to the collection of fresh specimens to ensure rapid progress. Plans call for the initial analysis of 5 specimens of each species from each major biogeographic region. Barcode Acquisition It will be necessary to analyze some 0.5M fishes to assemble a barcode library that provides adequate geographic coverage for the estimated 30,000 species of fishes. Analytical protocols are in place and costs are currently about $5 per specimen. Because of the volume of samples and expense of capillary sequencers, it is expected that much of the DNA sequencing will be done in large-scale facilities. Barcode Repository and Analysis The FISH-BOL initiative is assembling specimen records that encompass both a DNA barcode sequence and the provenance data associated with the specimen examined. The Barcode of Life Data (BOLD) System (www.barcodinglife.org) provides a web-based platform used for the assembly and analysis of these records. All of the sequence records and elements of the specimen data will subsequently migrate to GenBank and the other major genomics repositories upon publication of results. Organizational Structure The FISH-BOL campaign consists of individual projects coordinated by regional working groups that target FAO areas. There 10 of these regional groups, each is working to assemble and analyze fish samples from its region. Scientific interest will derive from comparisons that span continents and oceans, collaborations that will be fostered by the campaign. NATURE VOL 417, 2 MAY 2002 “Is it time for taxonomy to break with tradition and unify on the Internet?” Methods Digital Characterization: e-Vouchers Enhance access to collections Reduce wear on specimens Document identity when no morphological voucher exists Detailed View E-vouchers: Macrouridae rattails, grenadiers Coryphaenoides: 12 species of grenadier in the New Zealand EEZ Coryphaenoides subserrulatus Four rayed grenadier Coryphaenoides striaturus Striate grenadier Imaging Fishes $200 Flatbed Scanner 30 Images per Hour Voucher Specimen Labeling is Critical Specimen labels • ‘DNA barcode’ labels needed on vouchers (genetic epitypes). important for bidirectional linkage between barcode records & museum collections. Campaign Data – From BOLD to FISH-BOL Distributed Information Aggregation FISH-BOL Website CCDB Barcoding Node BOLD Smithsonian Barcoding Node BOLNET Website All-Birds Website Individualized Data Feeds for Campaign Management FISH-BOL Campaign web site: www.fishbol.org FISH-BOL Species Lists Global and Regional Lists FISH-BOL Progress FISH-BOL Progress FISH-BOL Progress FISH-BOL Regional Chairs Meeting, May 2006 Amsterdam Priority taxa (goals) Source of specimens Identification and curation of vouchers Sample preparation and sequencing Timetable Support Regional Working Groups FAO Area critical to tracking regional progress Central America (Areas 02, 31, 77) South America (Areas 03, 41, 87) New Collaborators Protocol Available Regional Progress: Region # Species # Barcoded Progress Africa Australia C. America Europe India N. America NE Asia Oceania* S. America SE Asia 8720 7953 7383 1929 10181 7805 9483 5411 8353 11034 635 1105 552 312 866 860 283 619 403 863 7% 14% 7% 16% 9% 11% 3% 11% 5% 8% Expected Benefits: Standardize the application of names. Facilitate species identification for all users, particularly in cases where traditional methods are not applicable. Highlight specimens that represent a range expansion of known species. Flag unrecognized or cryptic diversity. Demonstrate the value of collections and taxonomists contributing to the campaign. Summary As a tool for taxonomists, DNA barcoding and FISH-BOL are pivotal for dealing with both synonymy and species discovery. The resulting registry of sequence accessions will unite a diverse assemblage of specimens, collections and species information. It will also enable the rapid identification of larval, fragmentary or otherwise ambiguous samples for regulatory and other purposes.