Robert Hanner, PhD Database Working Group Chair, CBOL Global Campaign Coordinator, FISH-BOL...
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Transcript of Robert Hanner, PhD Database Working Group Chair, CBOL Global Campaign Coordinator, FISH-BOL...
Robert Hanner, PhDDatabase Working Group Chair, CBOLGlobal Campaign Coordinator, FISH-BOLAssociate Director, Canadian Barcode of Life NetworkBiodiversity Institute of Ontario, University of Guelph, Canada
The Fish Barcode of Life InitiativeThe Fish Barcode of Life Initiative
ABBI/FISH-BOL Neotropical Working Group Meeting 14 March 2007
NATURE VOL 417, 2 MAY 2002
“Is it time for taxonomy to break with tradition and unify on the Internet?”
Fish
Barcoding
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 that will be 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.
Methods
www.Barcodinglife.org
FISH-BOL to create a valuable public resource
Electronic database:
• DNA barcodes
• Specimen images
• Collection locality information
• Linkage to voucher specimens
• Valid taxonomic names
• Other collateral information such as FAO area, collector, identifier, donor, etc.
www.Barcodinglife.org
Project Summary Page
Detailed View
Process Record
Trace File Browser
Nearest Neighbor Summary
Neighbor Joining Dendrogram
Detailed View
Detailed View
Digital Characterization:
e-Vouchers• Enhance access to
collections• Reduce wear on
specimens• Document identity
when no morphological voucher exists
E-vouchers:
Coryphaenoides: 12 species of grenadier in the New Zealand EEZ
Coryphaenoides striaturus Striate grenadier
Coryphaenoides subserrulatus Four rayed grenadier
Macrouridae rattails, grenadiers
Imaging Fishes
$200 Flatbed Scanner
30 Images per Hour
Specimen labels• ‘DNA barcode’ labels needed on vouchers (genetic epitypes).
important for bidirectional linkage between barcode records & museum collections.
Voucher Specimen Labeling is Critical
Campaign Data – From BOLD to FISH-BOL
BOLD
CCDBBarcoding Node
SmithsonianBarcoding Node
FISH-BOLWebsite
All-BirdsWebsite
BOLNETWebsite
Distributed Information Aggregation
Individualized Data Feeds for Campaign Management
FISH-BOL Campaign web site: www.fishbol.org
FISH-BOL Species Lists
Global and RegionalLists
Campaign Coordination and Community Consensus
First Case of Simultaneous Treatment by First Case of Simultaneous Treatment by
CoF/FishBase/ITISCoF/FishBase/ITIS
Acipenser multiscutatus
- not recognized by expert (V. Birstein)
- no types available
- unidentifiable name
Treated as nomen dubium, moved into synonymy table in ITIS and purged from all three checklists!
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
Model of Collaboration
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 8720 635 7%
Australia 7953 1105 14%
C. America 7383 552 7%
Europe 1929 312 16%
India 10181 866 9%
N. America 7805 860 11%
NE Asia 9483 283 3%
Oceania* 5411 619 11%
S. America 8353 403 5%
SE Asia 11034 863 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.
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.
Summary