Robert Hanner, PhD

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Potencials of DNA Barcoding in South America
19-20 March 2007
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
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Biological specimens come in many forms
Identifiable adults
Juvenile stages
Processed products
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Barcoding works on all forms
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First publication on fish barcoding
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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.

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FISH-BOL
Inaugural Fish Barcode of Life Workshop, 5-8
June 2005
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FISH-BOL takes shape

• Goal
• Coordinate the assembly of a reference sequence
  library for all fish species.

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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.

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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.

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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.

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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.

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NATURE VOL 417, 2 MAY 2002
Is it time for taxonomy to break with tradition
and unify on the Internet?
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Methods
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Digital Characterization

• e-Vouchers
• Enhance access to collections
• Reduce wear on specimens
• Document identity when no morphological voucher
  exists

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Detailed View
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E-vouchers

Macrouridae rattails, grenadiers
Coryphaenoides 12 species of grenadier in the New Zealand EEZ

Coryphaenoides subserrulatus Four rayed grenadier
Coryphaenoides striaturus Striate grenadier
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Imaging Fishes
200 Flatbed Scanner
30 Images per Hour
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Voucher Specimen Labeling is Critical

• Specimen labels
• DNA barcode labels needed on vouchers (genetic
  epitypes).
• important for bidirectional linkage between
  barcode records museum collections.

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Campaign Data From BOLD to FISH-BOL
Distributed Information Aggregation
FISH-BOL Website
CCDB
Barcoding Node
BOLNET Website
BOLD
Smithsonian
All-Birds Website
Barcoding Node
Individualized Data Feeds for Campaign Management
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FISH-BOL Campaign web site www.fishbol.org
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FISH-BOL Species Lists
Global and Regional Lists
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FISH-BOL Progress
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FISH-BOL Progress
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FISH-BOL Progress
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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

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Regional Working Groups
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FAO Area critical to tracking regional progress

• Central America (Areas 02, 31, 77)
• South America (Areas 03, 41, 87)

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New Collaborators Protocol Available
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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
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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.

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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.