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