Upload
akshaypaatra
View
234
Download
0
Embed Size (px)
Citation preview
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
8/3/2019 Barcode Conference
2/23
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
8/3/2019 Barcode Conference
3/23
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
8/3/2019 Barcode Conference
4/23
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
8/3/2019 Barcode Conference
5/23
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
T +31 (30)2122643
European Consortium For The Barcode Of Life
8/3/2019 Barcode Conference
6/23
1 |
| 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
8/3/2019 Barcode Conference
7/23
2 |
| Business Plan
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
8/3/2019 Barcode Conference
8/23
3 |
| Business Plan
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.
8/3/2019 Barcode Conference
9/23
4 |
| Business Plan
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.
8/3/2019 Barcode Conference
10/23
5 |
| Business Plan
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.
8/3/2019 Barcode Conference
11/23
6 |
| Business Plan
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.
8/3/2019 Barcode Conference
12/23
7 |
| Business Plan
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
8/3/2019 Barcode Conference
13/23
8 |
| Business Plan
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.
8/3/2019 Barcode Conference
14/23
9 |
| Business Plan
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.
8/3/2019 Barcode Conference
15/23
10 |
| Business Plan
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
8/3/2019 Barcode Conference
16/23
11 |
| Business Plan
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.
8/3/2019 Barcode Conference
17/23
12 |
| Business Plan
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)
8/3/2019 Barcode Conference
18/23
13 |
| Business Plan
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.
8/3/2019 Barcode Conference
19/23
14 |
| Business Plan
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.
8/3/2019 Barcode Conference
20/23
15 |
| Business Plan
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.
8/3/2019 Barcode Conference
21/23
16 |
| Business Plan
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
T +31 (30)2122643
Concept |ECBOL consortium
European Consortium for the Barcode Of Life
8/3/2019 Barcode Conference
22/23
Notes
8/3/2019 Barcode Conference
23/23
Notes