barcode conference

8/3/2019 Barcode Conference

1/23

Workshop

Identifying & Protecting European

Biodiversity using DNA Barcoding

EuroBioForum, Strasbourg, France

19 September 2008

Joining forces for barcoding in Europe


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Workshop Agenda | EuroBioForum 19 September 2008

Welcome and Opening

Pedro Crous

Director CBS Fungal Biodiversity Centre, the Netherlands

Tour de Table

Introduction and expression of interest in this initiative

iBOL, the international Barcode of Life Project

Paul Hebert

Director Biodiversity Institute of Ontario, University of Guelph, Canada

Canadian Centre for DNA Barcoding

Setting up and Managing an International Initiative

Christian Burks

President & CEO Ontario Genome Institute, Canada

CETAF, EDIT and the French National Barcoding Campaign

Simon Tillier

EDIT/CBOL/Musum national dHistoire naturelle. Paris, France

The ECBOL proposal

Pedro Crous

Why ECBOL?

Short introduction to the business plan: what, who, how, when

Alignment of activities

What is the optimal structure for implementation?

Conclusions


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Workshop Participants

Arnedo Miquel Universitat de Barcelona Spain

Bakker Freek Wageningen University/Nationaal Herbarium Nederland Netherlands

Burks Christian Ontario Genomics Institute Canada

Bussmann Vincent PROTEUS France

Buys Charles Netherlands Organisation for Scientific Research NWO Netherlands

Byrne Pamela Department of Agriculture, Fisheries & Food Ireland

Costa Filipe Minho University Portugal

Crous Pedro CBS Fungal Biodiversity Center Netherlands

Dijkhof Jan NWO- The Netherlands Netherlands

D'Onghia Anna Maria CIHEAM/Medirranean Agronomic Institute of Bari Italy

Gashi Berat Center For Academic Development and Medical Research France

Guissart Franois Belgian Federal Science Policy Belgium

Hbert Paul University of Guelph Canada

Ihle Sonja DFG Germany

Jaillon Olivier Genoscope - CEA France

Kallio Arja European Science Foundation France

Kriegsman Leo Marcel Naturalis Netherlands

Kruess Andreas Federal Agency for Nature Conservation Germany

Lahtinen Hannele Academy of Finland FinlandLane Richard Natural History Museum United Kingdom

Lucas Candida Molecular and Environmental Research Centre (CBMA) Portugal

Marks John European Science Foundation France

Mourad Daniel Ministry of Education, Culture and Science Netherlands

Nagy Zoltan Tamas Royal Belgian Institute of Natural Sciences Belgium

Nandi Owi Ivar Phytax Ltd. Switzerland

Natzer Eva Bavarian State Ministry of Sciences, Research and the Art Germany

Rasplus Jean-Yves Institut National de la Recherche Agronomique France

Razumas Valdemaras Institute of Biochemistry Lithuania

Remacle Jacques European Commission Belgium

Resende Catarina FCT Portugal

Rieke Volker Federal Ministry for Education and Research Germany

Slot Marjanne Spects Special Projects Netherlands

Smolders Hans Ministry of Agriculture, Nature and Foodquality Netherlands

Sundstrm Michael Novo Nordisk Foundation Center for Protein Research Denmark

Tillier Simon EDIT France

Vomero Vincenzo Musei Scientifici di Roma (Museo di Zoologia) Italy

Vuorio Eero Ilkka University of Turku Finland

Wnning Tschol Ingrid Robert Bosch Stiftung GmbH Germany


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September 2008

Identifying & Protecting European Biodiversity using

DNA Barcodes

The total number of species estimated to exist on earth varies from 3M to 50M or

more. Over the past 250 years, more than 1.6M has been described. There is growing

awareness that human activities are causing large-scale habitat fragmentation and

hence extinction at an ever higher rate. The call to protect our planets biodiversity is

widespread and gets stronger every day. But how can we protect our biodiversity ifwe dont know what we are protecting or worse, what we are destroying?

What is the barcode of life?

The task of species recognition has become

more complex; classic taxonomic methods are

no longer sufficient to recognise all cryptic

species, so more advanced methods are

needed. Since 2003, the technique of DNA

barcoding (species identification based on

short DNA sequences) has drawn

considerable attention from the international

scientific community, government agencies,

and the public. Large-scale investigations

have demonstrated its effectiveness in a wide

variety of applications.

DNA barcoding is no longer simply an

academic exercise. The complexities in

gaining species identifications have

immediate serious economic, societal and

environmental implications. Customs officers,

public health officials, ecologists, resource

managers and many others desire an

unequivocal answer to the question of what

species an organism belongs to. The answer

is often critical to health and prosperity of

society. Applications could be in forensics,

conservation, or ecosystem monitoring, by for

instance:

protecting endangered species

identifying invasive organisms

sustaining natural resources

controlling agricultural pests

stopping disease vectors

monitoring environmental quality

ECBOL joining forces for barcoding

in Europe

Europe has been in the front l ine of the

evolution of DNA barcoding; the first

international scientific conference was held in

London in 2005. European taxonomists and

bioinformatics specialists have formedthemselves into young, effective networks that

gather, identify and curate specimens and

analyse barcoding results and make them

available in state of the art repositories. By

adding high-capacity research infrastructures,

these networks will be able to function at an

unprecedented level.

To join these forces in Europe and thus form

an active participating partner in the

International Barcode of Life Initiative (iBOL),

the European Distributed Institute of

Taxonomy (EDIT) has initiated ECBOL(European Consortium for the Barcode of

Life), a large-infrastructure proposal to

calibrate Europes biodiversity using DNA

barcodes.

Within ECBOL a network of leading labs for

DNA barcoding will be set up across Europe.

Furthermore, a centralised bioinformatics hub

is planned to make information, present in

national databases, available through a

single, integrated interface.

European Consortium For The Barcode Of Life


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September 2008

Collaboration is needed with private

companies to develop point-of-contact

barcode analysis and massive barcode

screens. Estimations show that existing

European collections already approach the

number of one billion specimens. The

resulting sequence and barcode reference

library will enable a highly effective, globally

accessible identification system for those

species that are encountered by humanity.

Aside from the library the infrastructure will

have to be developed that is needed for

application to real world problems such as

forensics, conservation and ecosystem

monitoring.

Creating a barcode reference library will, next

to an efficient identification system for

organisms, lead to the discovery of many new

species. It will cause the identification process

to become more precise and automated. The

vast amount of DNA barcoding data will be an

important impetus for the understanding of

mechanisms of evolution as studied in the

field of evolutionary biology.

Applications taking advantages of DNA

barcodes will be developed in dialogue with

the stakeholders; taxonomists will engage

with users (government agencies for public

health, agriculture, environment and species

protection) to design and implement

large-scale barcoding projects.

Since 2004 the Consortium for the Barcode of

Life (CBOL) has played a critical role in

bringing together 150 biodiversity

organisations from more than 45 countries all

over the world with an interest in barcoding.

The rapid growth of this consortium shows

that DNA barcoding has become a leading

standard in the identification of species;

barcode records have already been gathered

for 350,000 specimens representing more

than 35,000 species.

The members of ECBOL will offer training

courses in barcoding-related taxonomic

subjects leading to an integrated European

training programme. In parallel, public

education will increase awareness of the vital

contribution that DNA barcoding can make to

improve the quality of life.

The ultimate goal of barcoding is to assemble

the sequence library and the technology

necessary to identify organisms rapidly and

inexpensively.

Membership of ECBOL

Natural history museums

Zoological and botanical gardens and

herbaria together with university

departments

Private biotech companies

Policy-directed bodies (such as

biodiversity organisations and

governmental and intergovernmental

organisations)

ECBOL consortium chair

Pedro Crous

CBS Fungal Biodiversity Centre

Prof. dr. Pedro W. Crous, director

Uppsalalaan 8, 3584 CT Utrecht

The Netherlands

W www.ecbol.org

E [email protected]

T +31 (30)2122643

European Consortium For The Barcode Of Life


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| Business Plan

|Business Plan |Identifying and Protecting European

Biodiversity using DNA Barcodes

September 2008

European Consortium for the Barcode Of LifeEuropean Consortium for the Barcode Of Life


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CONTENTS

Overview .........3

1. Background on Biodiversity ....4

2. Background on DNA Barcoding.....................................................4

3. Background on Practical Applicability of DNA Barcoding...5

3.1 Protecting Endangered Species..............................5

3.2 Invasive Organisms.................................................5

3.3 Sustaining Natural Resources.................................5

3.4 Controlling Agricultural Pests..6

3.5 Stopping Disease Vectors...6

3.6 Monitoring Environmental Quality.....................................6

4. Research Plans.......................6

5. Education, Outreach and Impact...........................8

6. Scientific Impact.9

6.1 DNA Barcodes and Species Diversity...9

6.2 DNA Barcodes and Genomics..10

7. Financing10

8. The ECBOL consortium and the Network of European Leading Laboratories

NELL..11

8.1 Structure...11

8.2 Governance ....11

9. Linkages...13

9.1 EDIT (European Distributed Institute of Taxonomy).13

9.2 CETAF.13

9.3 LifeWatch13

9.4 CBOL / iBOL...14

9.5 Synthesys II FP7 (infrastructure grant)...14

10. ECBOL Policy Commitments.....15

10.1 Data Repositories and Release..15

10.2 Taxonomic Assignments.....15

10.3 Audit Trail...15

10.4 DNA Extracts.15

10.5 Convention on Biological Diversity..15

Summary .15


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Overview

Calibrating Europes Biodiversity using DNA Barcodes (ECBOL) is a large-infrastructure proposal driven

by a European consortium of biodiversity and taxonomy researchers (ECBOL consortium), which is an

initiative of the European Distributed Institute of Taxonomy (EDIT).The ECBOL consortium envisages a

network of leading labs for DNA barcoding across Europe (NELL). These high-throughput labs will

barcode specimens from existing European natural history collections and specimens acquired by

ATBIs (All Taxa Biodiversity Inventories) or from targeted taxonomic sampling. A centralised

bioinformatics hub is planned to make information present in national databases (i.e. collection

databases, taxonomic resources, sequence repositories) available through a single, integrated interface.

Applications taking advantages of DNA barcodes will be developed in dialogue with stakeholder needs

and with CBOLs (Consortium for the Barcode of Life) working groups. ECBOL also aims to represent

the European central node of the international Barcode of Life (iBOL) initiative, which aspires to barcode

5M specimens representing 500k species within 5 years.


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1 Background on Biodiversity

When Linnaeus published his Systema Naturae in 1758, it initiated the scientific registration of

species diversity on earth. He provided names for slightly more than 5000 species using a binomial

system (e.g. Homo sapiens) that has become the standard. Aside from names, he provided brief

morphological descriptions to aid others in recognising these species. More than 1.6M species have

been described over the past 250 years, and the total number of species estimated to exist varies

from 3M to 50M or more. However, the task of species recognition has become more complex.

This has been caused partly by the fact that not enough new professional taxonomists are being

trained, and by integrating new kinds of evidence for species limits, for instance DNA sequence

divergence. It is expected that an overwhelming amount of eukaryotic species still awaits

description. Among these are many species that are unidentifiable by classic taxonomic methods or

because of being unculturable or invisible to the naked eye.

There is growing awareness that human activities are causing large-scale habitat fragmentation and

hence extinction at an ever higher rate. The call for intensified efforts to document and protect

Earths biodiversity was a key policy declaration in the 1992 Convention on Biological Diversity.

Some of these areas have already been addressed by other pan-European efforts like EDIT

(unifying taxonomy) and LifeWatch. Calibrating Europes Biodiversity using DNA Barcodes

(ECBOL) will be complementary to these initiatives, and will be in fact the European contribution to

the global iBOL project. It will cut the costs by up-scaling and centralising the production of

reference data, while at the same time providing a basis for molecular-based biodiversity monitoring

in areas relevant for conservation.

2 Background on DNA Barcoding

Since its first appearance in 2003, DNA barcoding has drawn considerable attention from the

international scientific community, government agencies, and the public. Although it generated

some controversy in the first years, DNA barcoding has gained increasing scientific momentum as

large-scale investigations have demonstrated its effectiveness in a wide variety of taxa.

The substantial funding commitments and the rapid growth in the Barcode of Life Initiative (BOLI),

supported and expedited by the Consortium for the Barcode of Life (CBOL, 150 member

organizations in 45 countries) indicate that DNA barcoding has moved from concept to a global

programme. Reflecting this deployment of resources and personnel, barcode records have already

been gathered for 350,000 specimens representing more than 35,000 species.

Europe was in the vanguard of the evolution of DNA barcoding, the first international scientific

conference on barcoding was held in Europe (London) in 2005. Furthermore, we have the raw

material, the expertise, and the expert workforce needed to contribute in a major way to the

barcode initiative as well as to the use of barcode data. In contrast to the worlds other main DNA

barcode centres, in the US and Canada, Europe presently still lacks the capital investment to

support DNA barcoding on an industrial scale.


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3 Background on Practical Applicability of DNA Barcoding

DNA barcoding is not just an academic exercise. The complexities in gaining species identifications

have immediate serious economic, societal and environmental implications. Customs officers,

public health officials, ecologists, resource managers and many others desire an unequivocal

answer to the question what species an organism belongs to. The answer is often critical to the

health and prosperity of society.

The ECBOL proposal aims firstly at providing the infrastructure for enabling European biodiversity

collections to conduct DNA barcoding on an industrial scale. Secondly it will also build a DNA library

that can be used as a tool in various focused subjects, a few of which are outlined below.

3.1 Protecting Endangered Species

Trade in endangered species is illegal. This has been ratified by all EU-countries signing CITES

(Convention on International Trade in Endangered Species of Wild Fauna and Flora). Yet customs

officials at points of entry are faced daily with the challenge to identifying illegal imports of wildlife

and products thereof. Bushmeat, for example, is both sold locally and exported as processed but

raw meat or as dried and smoked meat making it difficult to make reliable species identification

using morphology. DNA barcode data set the stage to an improved control of illegal international

trade.

3.2 Invasive Organisms

Invasive species, brought into Europe via trade or changing climatic conditions present a threat to

agriculture, watercourses, human health and indigenous biodiversity. Unfortunately they rarely

present themselves in a form or life stage that can be easily identified (e.g. larval stages in ship

ballast water). Rapid and accurate identification through interception mechanisms or regular

environmental monitoring is crucial in monitoring their spread a service that barcoding with its

global perspective and universal technology can provide.

3.3 Sustaining Natural Resources

Human population growth continues to put pressure on natural resources. Barcoding can improve

monitoring of organismal population size and growth. It also enables resource managers and

government regulators to monitor how much of each species is being used because processed

products such as fish filets and lumber can be identified using barcode data. Data on population

growth and use form the basis of improved policies for sustainable harvesting.


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3.4 Controlling Agricultural Pests

Agricultural pests endanger the livelihood of farmers world-wide, influencing the sustainability of

cultures, the success of agricultural companies, and friendly trade relations among nations.

Decisions involving agricultural pests start with the fundamental question: What species is it?

Without a reliable identification, effective counter-measures cannot be taken in the field,

and governments cannot establish well-informed trade agreements and restrictions.

3.5 Stopping Disease Vectors

As global trade and travel increase, public health officials face the growing challenge of identifying

alien diseases and their vectors. Potentially all incoming shipments, returning travellers or

migrating plants or animals can carry or be a vector of infectious diseases, like dengue fever,

western Nile virus or bird flu. Once a disease has been introduced into a country, containment and

eradication are huge and expensive challenges. DNA barcoding will become an invaluable

resource for monitoring and preventing the spread of disease-bearing organisms in local

populations. In addition, more accurate identification can minimise the use of for example

insecticides by eradication programmes.

3.6 Monitoring Environmental Quality

Bio assessment is an accepted system for monitoring the health of natural environments such as

streams, rivers, and wetlands. Biological samples are collected, the plant and animal species are

identified, and the number of individuals per species is counted, from which an index of

environmental health is calculated. Specimens in the samples have been identified using

morphology-based identification keys, but frequently only a small fraction of the species can be

identified this way. Most of the specimens in the samples are juveniles or have been damaged andcan only be assigned to a genus or family. The US Environmental Protection Agency is conducting

a two-year test of DNA barcoding as part of its Advanced Monitoring Initiative to test the accuracy

and cost-effectiveness of barcoding. Likewise barcoding also promises to be an incredibly valuable

tool to monitor the changing biodiversity in Europe.

4 Research Plans

In the short history of barcode analysis the initial barriers have largely been overcome.

Scientific counterarguments have been refuted, costs have been reduced and its applicability has

been shown in various geographic settings in almost all taxonomic groups and in several practical

applications. It has also become apparent, however, that DNA barcoding can only become a

success if handled on an industrial scale.


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European taxonomists and bioinformatics specialists have formed themselves into young but

effective networks that gather, identify and curate specimens and analyse barcoding results and

make them available in state of the art repositories. By adding high-capacity research

infrastructures, these networks will be able to function at an unprecedented level. For the first time,

taxonomists will be able to engage with users (e.g., government agencies for public health,

agriculture, environment and species protection) to design and implement large-scale barcoding

projects that can be completed in a reasonably short time. Also collaboration is needed with private

companies to develop point-of-contact barcode analysis and massive barcode screens.

This massive up-scaling represents a paradigm shift for biodiversity science which has, until now,

been largely advanced through lone investigators or small collaborations.

Estimations of CETAF (Consortium of European Taxonomic Facilities) show that existing

European collections already approach the number of one billion specimens. The resulting

sequence and barcode reference library will enable a highly effective, globally accessible

identification system for those eukaryote species that are encountered by humanity. Aside fromthis library the infrastructure will have to be developed that is needed for application to real world

problems, such as forensics, conservation, and ecosystem monitoring. The strategy for doing so is:

Convene a high-level Barcoding Council from EDIT (www.e-taxonomy.eu) and CETAF

(www.cetaf.org), as well as applied organisations in government departments that routinely

use DNA barcoding technology

Convene a Users Council with representatives of different sectors (agriculture,

environment, health, etc.) divided into interest-based sub councils

Create a network of European barcoding laboratories equipped with high-throughput

robotics for DNA extraction and sequencing, and a well-trained technical staff. These

facilities will handle DNA extraction, sequencing, archiving and databasing on an industrial

scale, as is the case with the Biodiversity Institute of Ontario in Guelph, Canada

Establish a permanent infrastructure for DNA biobanking which will provide Europe and

the global scientific community with access to DNA extracts, archived specimens and

databases

Create companion bioinformatics nodes at the barcoding laboratories

Design five-year barcoding initiatives within each subcouncil, drawing on existing

collections in museums and herbaria supplemented by new collections

Conduct coordinated, systematic surveys of biological monitoring sites in critical

ecosystems throughout Europe. These sentinel sites will be part of a monitoring system

for studying the long-term impact of global climate change and other human-induced

impacts on the environment

Build on the networks of databases, experts and research projects already underway,

e.g. LifeWatch, with support of national research councils and the European Commission

to create a seamless data-sharing environment that connects the new barcode factory

with users such as border inspectors, public health officials, agriculture specialists and the

general public


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5 Education, Outreach and Impact

Despite the availability of a well developed taxonomic infrastructure, European taxonomic

research, including in its collection management aspects, increasingly relies on an aging

taxonomic community, with permanent staff often over 50 years old and with a significant input by

retired researchers and skilled amateurs who frequently have to self-fund their research. Efforts to

find enthusiastic young people with an interest in becoming qualified taxonomists are thwarted by

insufficient training opportunities and a lack of long-term professional prospects. It is therefore

important to start arousing interest at an early age. ECBOL will investigate the possibility to interest

schools for and let schools participate in its research programs, for instance in collecting samples

for barcoding.

Following the initiative started within EDIT, the members of ECBOL will offer training courses in

barcoding-related taxonomic subjects leading to an integrated European training programme.

In parallel, public education will increase the awareness of the vital contribution that DNA

barcoding can make to taxonomy and thus to biodiversity and ecosystem research.

Consistent lobbying will contribute to maintain the interest of the various decision-makers and

funding agencies.

It is important that the impact of DNA barcoding on biodiversity, health and economy is made

public. ECBOL will actively encourage the barcoding community to publish its results not only in

scientific literature, but also in periodicals aimed at the general public. Especially the institutions

directed at the general public have an excellent opportunity to raise public awareness by

organizing temporal exhibitions or extending permanent exhibitions with themes explaining the

impact of DNA barcoding on society. Also a possible cooperation with ALTER-Net (a network of

European biodiversity scientists with public awareness as one of the topics) will be investigated.

Furthermore the societal impact of DNA barcoding will be investigated in one of the work

packages.


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6 Scientific Impact

Creating a barcode reference library will, next to an efficient identification system for organisms,

lead to the discovery of many new species. It will cause the identification process to become both

more precise and automated. This automation will truly revolutionise our understanding of

biodiversity especially when it can be developed into portable systems to be used in the field.

Many specimens of rare or even extinct species have been stored in museum collections for

decades, some even for centuries. Researchers are faced with the challenge to develop novel

solutions for recovering DNA sequence information from degraded DNA. Other solutions will be

found for retrieving DNA from single cells and environmental mixtures. The vast amount of DNA

barcoding data will be an important impetus for the understanding of mechanisms of evolution as

studied in the field of evolutionary biology.

Finally the setting up of a network of DNA-banks will create an invaluable resource for future

genomic studies. It allows the rapid mobilisation of investigations involving issues ranging from

single genes to whole genomes. The research that lies ahead will lead to a whole new field of study,

namely Environmental Genomics. Academic institutions will set up courses in the fields related to

this research topic and private companies will develop dedicated applications. These

developments will prove the impact of DNA barcoding on medicine, agriculture and education.

6.1 DNA Barcodes and Species Diversity

Since Linnaeus started describing species, the toolset of taxonomy has hardly changed.

Species are recognised by morphological characteristics, aided by microscopy, but the

fundamental building blocks intrinsically defining a species have not been identified until molecular

taxonomy and finally DNA barcoding entered the arena. This identification procedure allows

anyone who can operate the necessary equipment to pinpoint any (described) form of life.

Also DNA barcoding promises industrial scale throughput of the taxa awaiting description.

These two developments will lead to two remarkable new breakthroughs in biodiversity science.

Firstly the question as to how many species exist on our planet will receive an answer that is far

more accurate then any answer to date. The best studied groups will see their species counts

increased by a mere 5-10 percent, but other groups may stunningly increase their numbers many

times. This was shown already in an investigation into Costa Rican tachinid flies, where the once

determined 16 species proved to be actually 74 once barcoded. These results will also give rise to

investigations into hitherto unaddressed problems such as why some parasitoids attack many

different species, while others confine themselves to one single host.

Secondly many biological research initiatives are hampered by the inability to identify large

numbers of species at one given time or place. DNA barcoding will give us insight into long

standing questions of food-web ecology, ecosystem integrity and resilience to expected climate

change.


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6.2 DNA Barcodes and Genomics

The ECBOL research will capture several billions of base pairs of sequence information.

The impact of this information on genomics will be considerable. Instead of presenting all the

information of all genes of one taxon, DNA barcoding presents a cross section of the genes of a

series of taxa. This presentation will give a completely new point of view for studies into the

genomic variation between species. Apart from this the availability of DNA in a European DNA

banks network will be of great interest to genome investigators. Importantly, an alternative point of

entry into conventional genomics resources such as this will provide explicit logical connections

between taxon-based and genomics data; while both of these domains already offer a wealth of

information, each is separated from the other through lack of any consistent means of connection.

7 Financing

A major cost is the initial setup of the DNA barcode reference library. Subsequent routine

identification costs that generate DNA barcodes from unknown samples can either be borne by

local labs, or charged for (like routine sequencing) by either private or public sector labs.

An estimation of the costs of the aforementioned plans is given below:

Description Costs

Network of European Leading Laboratories for DNA extraction and biobanking 62 M

ATB projects (All Taxon Barcoding) in various European National Heritage sites

(in coordination with existing All Taxon Biodiversity Projects) 10 M

Ancient DNA lab (specializing in developing techniques and extracting DNA from

the valuable type collections housed in various European collections) (In

coordination with the research activities of Synthesys II in FP7) 5 M

Administration, management, coordination, public relations and outreach 5 M

Training and education 3 M

Running costs for laboratories in each work package 25 M

Costs for specimen supply and data management 15 M

Total 125 M


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In the future ECBOL will continue its activities. The financing of the Network of Leading

Laboratories after the first phase of the consortium will come from funds needed to perform core

activities, such as regional (national) European and other international barcoding projects and also

from external revenues. Envisaged are industrial support linked to the products generated from the

barcodes generated in phase one, and selling of barcoding products to industry, conservation

agencies, agriculture, health organizations, etc. As a result of the outreach of ECBOL, structural

government funds should become available to maintain the daily operation of the barcoding

laboratories and the activities resulting thereof.

8 ECBOL and the Network of European Leading Laboratories (NELL)

8.1 Structure

ECBOL aims at having member organisations (contractors) from as many as possible European

countries. Member organisations are typically natural history museums, zoological and botanical

gardens and herbaria together with university departments, private biotech companies and other

policy-directed bodies such as biodiversity organisations and governmental and intergovernmental

organisations. The member organisations can be involved in research networks, such as NELL.

8.2 Governance

ECBOL is financed by European available funds. These funds will be used for the activities

assigned to the different Work Packages. The separate institutions are represented in the Board of

Directors, an advisory body. Each institution is represented in the Steering Committee and will

have voting rights equalling the amount of funding received by that institution. Voting rights for

institutions that have received common funding will be shared equally by these institutions.

The institutions participate in NELL by signing the consortium agreement and binding themselves

to the Joint Program of Activities (JPA). The JPA is subdivided in Work Packages (WP) that is

executed by one or more contracting members and is approved by the Board of Funding Partners.

The Board of Funding Partners will convene at regular intervals to monitor compliance with project

objectives and ensure good governance.

The ECBOL consortium advises institutions of a specific country to form national networks.

A national network can apply for and use country specific funds. Funds available for a specific

country or institution will not give voting rights in the Steering Committee of NELL unless the

activities and facilities financed by these funds can be made available to all national networks.


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The NELL Office, with the Project Leader as director, is responsible for the daily affairs of NELL.

The Project Leader answers to the Steering Committee.

NELL has three advisory bodies, CETAF, the Board of Directors and the Scientific Advisory

Council.

Funding Partners

Stakeholders

ScientificAdvisory Council

Network of European

Laboratories (NELL)Office Project Leader

Steering Committee(NELL)

WP1 European Type Collection

WP6 Biodiv. & Natural Products

WP7 Environmental Monitoring

WP8 Indoor Air & Food

WP9 Valorisation of Knowledge

WP10 Data Management (EMBL)

CETAF

Board of Directors(NELL)+ CETAF (chair)

BOLI

ECBOL

ManagementStructure

WP2 Nature Conservation

WP3 Plant Health & Quarantine

WP4 Forensics

WP5 Human HealthContractors

(Members ofNELL)


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9 Linkages

9.1 EDIT (European Distributed Institute of Taxonomy)

In 2006 a Network of Excellence was started under the EU 6th framework called EDIT, European

Distributed Institute of Taxonomy. The participants in EDIT belong to the leading taxonomic

facilities in Europe. EDITs goal is to reduce the fragmentation in European taxonomic research

and expertise and to coordinate the European contribution to the global taxonomic effort aimed at

improving societys capacity for biodiversity conservation. The EDIT proposal prominently included

a mandate for Organisation of the European contribution to the international DNA barcoding

efforts.

It should be noted that funding available for EDIT is principally for coordination and not for the

barcode infrastructure itself. ECBOL is a logical follow-up and extension of EDIT. The funding for

EDIT is granted for a period of five years and thus ends in 2011, but is very likely to continue after.

9.2 CETAF

CETAF is a networked consortium of scientific institutions in Europe formed to promote training,

research and understanding of systematic biology and palaeobiology. Together, CETAF institutions

hold very substantial biological (zoological and botanical), palaeobiological, and geological

collections and provide the resource for the work of thousands of researchers in a variety of

scientific disciplines. CETAF, having its very own expertise, is an advisory body to ECBOL.

9.3 LifeWatch

LifeWatch is a European plan to link ecological monitoring data collected from marine and

terrestrial environments with the vast amount of data in physical collections. The new infrastructure

will open up new areas of research and new services by providing access to the large data sets

from different (genetic, population, species and ecosystem) levels of biodiversity together with

analytical and modelling tools. LifeWatch plans to construct and bring into operation the facilities,

hardware and software as well as governance structures to create a biodiversity research

infrastructure with virtual laboratories with analytical and modelling tools, a service centre for users

and to promote research opportunities.


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9.4 CBOL / iBOL

Since 2004 the Consortium for the Barcoding Of Life (CBOL) has played a critical role in bringing

together 150 biodiversity organisations from all over the world with an interest in DNA barcoding.

Within CBOL working groups are active with drafting norms, assembling protocols, networking,

raising awareness, capacity building and lowering the barriers to barcode assembly. CBOL

however does not do the actual job of barcoding.

The ECBOL consortium fully supports and participates in the International Barcode of Life (iBOL)

initiative (www.dnabarcoding.org). The iBOL project has the goal of assembling the sequence

library and the technology necessary to identify organisms rapidly and inexpensively. iBOL will

construct the richly parameterised barcode library needed as the foundation for a DNA-based

identification system, which will include all barcode data generated in ECBOL; iBOL aims to

barcode 5M specimens representing 500k species within 5 years. iBOL will also delivertechnologies enabling both massive biodiversity screens and point-of-contact identifications.

Its work will be advanced through links to supporting initiatives such as ECBOL.

ECBOL will work closely together with iBOL in achieving common goals, including the organisation

of conferences and workshops and the establishment of new research collaborations.

9.5 Synthesys II FP7 (infrastructure grant)

Synthesys 2 has now been approved in principle, and presently is being negotiating with the

Commission. The grant includes a Joint Research Activity focusing on DNA extraction from stored

material, which will complement the goals of ECBOL.


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10 ECBOL Policy Commitments

10.1 Data Repositories and Release

All specimen and sequence data gathered by research(ers) under the NELL contract will be madepublicly available in public repositories such as European Nucleotide Archive at EMBL-EBI, BOLD,

GenBank, DDBJ and a to be developed ECBOL repository within 12 months following data

acquisition. The underlying trace files will be released to the European Nucleotide Archive or the

NCBI Trace Archive within three months of their acquisition.

10.2 Taxonomic Assignments

The ECBOL consortium gives high priority to the early release of sequence and specimen

information and to its coupling to a taxonomic designator. Because the taxonomic expertise to

assign barcoded specimens to a Linnaean binomial is sometimes hard to get, ECBOL will bind

itself to the iBOL registration system for barcode clusters. Barcode records will be assigned a

Barcode Identification Number (BIN) by the system.

10.3 Audit Trail

Critical evaluation of barcode records is only possible when specimens used for barcode analysis

are retained as vouchers and when they gain labels indicating that they were the source of the

tissue that produced a particular barcode sequence. As a consequence, members of the ECBOL

consortium will deposit specimens used for barcode analysis in curated collection facilities and

attach labels signalling their status as barcode vouchers.

10.4 DNA Extracts

The DNA extracts gathered by NELL will represent a valuable legacy for other research initiatives.

They may often comprise the only available DNA sample for a species. Because of this fact,

ECBOL participants will preserve all DNA extracts. Decisions in relation to access and use of such

extracts will be solely determined by national and institutional policies.

10.5 Convention on Biological Diversity

Members of NELL are committed to the regulatory framework established under the Convention on

Biological Diversity. Transactions between ECBOL members will respect all restrictions in relation

to biomaterials transfer.

Summary

ECBOL aims to establish a Network of European Leading Laboratories (NELL) among the major

biodiversity resource centres of Europe. This network will have an automated, high throughput

capacity to generate DNA barcodes of species at an industrial scale, to help identify life on earth.

Once established, the network has a goal to initially barcode 1M specimens, representing 100k

species within 5 years. Further initiatives will be launched to expand the barcode database in an

attempt to represent all known (and as yet unknown) life on Earth.


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European Consortium for the Barcode Of Life

ECBOL, 2008

ECBOL consortium chair | Professor Pedro Crous

CBS Fungal Biodiversity Centre

Professor P.W. Crous

Uppsalalaan 8 |3584 CT Utrecht | The Netherlands

W www.ecbol.org

E [email protected]

T +31 (30)2122643

Concept |ECBOL consortium

European Consortium for the Barcode Of Life


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Notes


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Notes

barcode conference

Documents