Welcome to the FishPopTrace e-Newsletter

Message from the Coordinator

The December issue of the FishPopTrace e-newsletter brings a further year of Consortium activity to a close. In advance of highlighting various recent and forthcoming events, it seems fitting to reflect on some significant milestones within the FishPopTrace project during 2009.

The Consortium enjoyed two opportunities during 2009 for full project meetings: the first was in Funchal, Madeira during February, and the second in Palma, Mallorca during September. Both events provided a valuable opportunity to review the progress and priorities, as well as developing and extending our links to organisations with an interest in traceability and conservation of fish resources. For example, at the Funchal workshop, we were fortunate to include representatives from the FAO, Det Norske Veritas (DNV), and the PEW Foundation. In addition, we had the pleasure of meeting the FishPopTrace Scientific Officer Dr Stamatis Varsamos, at the Palma meeting. As will be evident from previous and current FishpopTrace e-news, the Consortium has engaged effectively since its inception in various external endeavours.

On the scientific front, major progress has been made in the generation of our single nucleotide polymorphism (SNP) database for all target species. The current status is that genotyping of cod, hake and herring is underway, and due to be completed during December, and the full screening of sole SNPs is expected to take place early in the New Year. In addition to the various scientific challenges associated with generating new and informative molecular markers, numerous other requirements were addressed successfully during the year, including the need to tender our SNP genotyping to an appropriate sub-contractor, GenProbe. While SNPs form a major component of the framework for traceability studies and mapping of population structure in FishPopTrace, information from otolith microchemistry and shape analysis represent integral components of our outputs. Advances in the forensic validation of otolith data is well advanced, and we have also achieved an efficient complementarity between target otolith and SNP datasets. Work on the development of gene expression proteomics, fatty acid analysis and the use of a novel platform for assaying SNPs is underway, and initial data from the three novel tools provide encouraging signatures for fish traceability.

As you will see from the current issue, there have been various meetings in which FishPopTrace partners have participated. As well as training opportunities, such as engagement in the Ecological Genomics workshop in the University of Bologna, activities have included contributions to the Informal Workshop on the Use of Forensic Technologies in Fisheries Monitoring, Control and Surveillance (MCS) organised by the FAO in Rome, and a workshop on DNA barcoding, including a presentation of FishPopTrace fisheries genetics, in Malaysia. Jann Martinsohn chaired the Informal Workshop in Rome, and Einar Nielsen, Rob Ogden and Gary Carvalho were invitees to the meeting. The FAO initiative represents a global attempt to promote the use of available forensic techniques especially by developing countries, as a core component of MCS in tackling Illegal, Unregulated and Unreported Fishing (IUU). Discussions focused on the most appropriate techniques and approaches to develop traceability tools, as well as considerable discussion on the requirement for stringent forensic validation. A full report will be provided in due course. Such activities not only underlie the global importance of the context of FishPopTrace and associated activities, but also the role that partners are playing internationally. Such engagement necessarily focuses aspects of our own work on key priorities, including the need for effective technology transfer to end–users.

Plans for Workshop 4 are now well under way, and will take place from 22nd – 24th April 2010, at the coordinating Institute, Bangor University, UK. A key focus for the workshop will be discussion of the SNP data and integration with outputs from the otoliths. A Partner Workshop has also been organised to discuss the analysis and status of SNP data in advance of the workshop to be hosted by Partner 2, DTU-AQUA, between 23rd – 25th February 2010. The workshop will provide an opportunity to identify patterns from the emerging dataset as well as priorities for analysis in advance of Workshop 4.

Although we are yet to receive formal feedback of our first Periodic Report, it is almost time to start planning our Second Report. We aim to ensure a full draft is available in advance of Workshop 4 so that the finally edited version is ready for submission by 1st May 2010. There will be changes to the procedures for acquiring information from project partners and work package leaders, in an attempt to achieve greater harmony and standardisation in format, as well as ease of collation.

Having almost completed the second major phase of FishPopTrace which has focussed on the characterisation and validation of primary and novel tools, we are well placed for our third and key phase: the analysis of the large and integrated SNP and otolith datasets. In the meantime, thanks to all Consortium members for their continued commitment and generous contributions to the project, and especially the level of cooperation and collective support throughout. Greetings for a Happy Christmas: we are looking forward to continuing our partnership in what I am sure will be an enjoyable and productive New Year.

Gary Carvalho g.r.carvalho@bangor.ac.uk


1. Project update

1.1: Leuven WP3/5

The list of SNps to be genotyped has been sent to Illumina for the manufacture of the chips for all 4 species. The DNA samples have been sent to GenProbe for three of the species (Cod, Herring and Hake) and results are expected before Christmas

The DNA samples for sole are on their way to GenProbe three of the species and results are expected mid January.

Most otoliths have been sent to Audrey and will be processed this winter.


1.2: Bremen WP7

Dr. Kristina Kappel produced and tested the first padlock-based SNP-array using 5 artificial DNA targets. The results are straightaway positive and encouraging.


1.3: UiB WP5

Audrey Geffen visited Filipe Volckaert, Gregory Maes, and Els Cuveliers at their laboratory in September to finish revision on one of Els’ manuscripts and discuss FPT progress.

Marco Stagioni from the University of Bologna, Fano Marine Biological Laboratory visited Bergen for 10 days in November to learn about otolith preparation and to help with processing samples for the otolith morphometrics measurements (OTOMP). The first part of the OTOMP validation exercise was also completed during this visit.



The preparation and sending of hake DNA for SNP genotyping has been accomplished on schedule.

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2. Personnel News

2.1: Departures from FishPopTrace


Dr. Marc Kochzius left University of Bremen as his employment contract ended but he has kept a guest status at Prof. Blohm’s research group.


After the retirement of Prof. Blohm in March 2009 an extension of his contract with the University of Bremen until February 2011 has been agreed.


2.2: New additions to FishPopTrace


Eveline Diopere, a new PhD student started in October 2009, to work on FishPopTrace. She will be responsible for the mining and screening of functional genetic variation in sole in time and space. She will also perform the inheritance and validation study in an aquaculture panel.


Jeroen Van Houdt left the museum of Tervuren to take a post-doc position at the Genomics Core Facility in Leuven (Medical department). As such, he will stay involved in genomics projects of our lab and participate in further data-analysis /publication of the raw 454-sequencing data



2.3: UiB

After many delays and false starts, we have moved into the new Biology buildings at “Marineholmen” (watch the youtube promo! – they forgot the rain! http://www.youtube.com/user/Marineholmen). The move was a bit stressful for Mei-Yu and Audrey, packing and unpacking our lab twice since August. However, we were happy to pack and move one final time into our new lab on November 30th.


Packing the temporary lab for the 2nd time


Up and running in our new lab


 But not completely organized yet!


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3. Reports on meetings and conferences

3.1: FishPopTrace establishes contact to the European Parliament Committee of Fisheries (PECH) –14/10/09


The Joint Research Centre (P8) was delighted to welcome Isabella Lövin, a member of the European Parliament and Committee of Fisheries (PECH) to its premises. Isabella Lövin is a renowned Swedish journalist on environmental issues. In 2007 she published “Tyst hav" ("Silent Seas"), a book on Swedish and European overfishing which has had an overwhelming success in Sweden, and led to a vehement public debate on this topic. Her book has won 14 awards, amongst which "The Great Journalism Prize", "The Environmental journalist of the year", "The Golden Spade Prize of Investigative Journalism", "The Consumers Unions Award", "Journalist Prize of  the Organisation for the Protection of Animals", and most recently "The 2009 Baltic  Sea Foundation prize". It is currently translated into English.

Isabella Lövin is member of the Swedish Green Party, and since the 2009 election has been a member of the European Parliament (MEP).

During her one day visit, Ms. Lövin gave a presentation on “The Impact of Overfishing in the Baltic Sea”, a highly informative and interesting account of the disastrous effects of lacklustre fisheries management in the Baltic Sea. During her presentation Ms. Lövin focussed on Baltic cod, but also spoke about the devastating collapse of the cod stocks off the east coast of Newfoundland and the troubled European eel stocks. She furthermore stressed the global dimension of overfishing, pointing out the massive over-exploitation along the West-African coastline. Her extremely well attended talk was followed by a vivid discussion with the audience, covering a wide range of topics such as eel fisheries management, alternative management schemes, aquaculture, illegal fishing activities, and nutritional aspects.

Subsequently Ms. Lövin visited the Maritime Affairs Unit to discuss activities related to fisheries management and regulations. In this context FishPopTrace was introduced by a presentation, along with a general overview on applications based on forensic genetics and chemistry for fisheries management, control and enforcement. It is envisioned to build a contact between the FishPopTrace consortium and PECH, and Ms. Lövin kindly agreed to be our point of liaison.

Jann Martinsohn


3.2: 5th International Forum on Illegal, Unreported and Unregulated (IUU) Fishing 15/10/2009

Gary Carvalho attended the fifth in the series of international forums on IUU fishing was held at Chatham House, London on 15th-16th October 2009. Many topics were covered including the new EU regulation on IUU fishing, the economic implications of IUU fishing, addressing IUU fishing in Africa and the Asia-Pacific region, controlling and monitoring IUU fishing, and fisheries governance. At the beginning of the Conference, the film ‘The End of The Line’ was screened, hosted by Chatham House and the World Wildlife Foundation. The author of the associated book, Charles Clover, attended the occasion, and provided an opportunity for a Forum discussion on the status of over fishing and global fish stocks. Gary was able to provide background to the FishPopTrace project during discussions as well as establishing additional international links with fisheries bodies and various research organizations.


More details of the meeting are now available here including copies of all the presentations.


3.3: Three Fish Pop Tracers attend a ConGen course in Ecological genomics, 20-24th October.



During October the European ConGen consortium sponsored a course in state of the art methods in the upcoming field of “ecological genomics”. The course was organized by the University of Bologna and took place in a charming castle on the top of a hill in the small village of Bertinoro. One after the other, various experts shared and passed on their knowledge and experience within their respective fields (incl. SNP genotyping, gene expression, next generation sequencing and many other exciting topics). Gathered from all over the world some 30 young and promising post docs and Ph.D students soaked up all the impressions. Minds were reloaded with motivation and inspiration for future work and endeavours. Among the young and promising scientists in spe were three Fish Pop Tracers personified by Alessia Cariani (UNIBO), Sarah Helyar (MEFGL) and Morten Limborg (DTU Aqua). During the course each participant were humbly allocated a slot of three minutes to present their own research. However, the three Fish Pop Tracers were not late to grasp the chance of merging their slots and give a joint nine minute presentation of the Fish Pop Trace project (incl. handing out flyersJ). Our project invoked a lot of interest and impressed many leading characters within the field. The course also allowed us to meet up with other interesting scientists and get a feel for their respective projects (including a guy involved with the cod genome project).

At the end of the week and after some cloudy days the weather cleared up and revealed a clear and astonishing view from the top of the hill which was very symptomatic for the feeling we all had when saying the usual “good byes” and “see you later’s”. In the end we went home with renewed energy and a strong feeling that we’re part of a truly revolutionizing project within the field of applied genomics in non model organisms.

Morten Limborg


The computer labs: appropriately housed in the dungeons!


3.4: DNA Barcoding Workshop: Centre of Marine and Coastal Studies (CEMACS), 9th – 12th November 2009.


Martin Taylor and Gary Carvalho organized a DNA barcoding workshop at CEMACS, Malaysia, with a focus on the application of barcoding technologies to fish biology and fisheries management. A key application of the barcoding pipeline was it’s use in traceability in fisheries forensics, and there was also the opportunity to present aspects of the FishPopTrace project to workshop participants, as well as seminars in the Fisheries Research Institute, Department of Fisheries, Malaysia, the University of Malaya in Kuala Lumpur and the Centre of Research for Computational Science and Informatics in Biology, based at the University of Malaya and the Malaysian Fisheries Department in Penang. The format of the workshop included seminars and hands-on experience of the BOLD database, which also forms a component of the FishPopTrace traceability framework. In addition to the workshop and various meetings, there was the opportunity for Martin and Gary to collect samples of marine fish from Malaysian waters in connection with a Bangor-based PhD student.


Gary on field work in Malaysia!


3.5: Informal Workshop on the Use of Forensic Technologies in Fisheries Monitoring, Control and Surveillance: FAO, Rome, 8th – 11th December 2009.

A meeting was held at the FAO to discuss the use of forensic approaches in the context of MCS and IUU fishing. An invitation was received from Michelle Kuruc, who attended the FPT Madeira workshop, for four members of FishPopTrace to participate: Jann Martinsohn (subsequently elected as Chair of the workshop), Rob Ogden, (who delivered an introductory lecture on forensic technology in monitoring, control and surveillance), Einar Nielsen and Gary Carvalho, as participants. The aim of the workshop was to identify the most appropriate traceability tools for use within a forensic framework, and to generate a set of recommendations for taking the approach forward within a global context. The workshop included broad representation from a variety of nations and backgrounds, including forensic biologists, fisheries compliance officers, Directorates for fish inspection quality control, and various research organizations and Universities with experience in the development and application of advanced tools, as well as their implementation to fisheries. The workshop provided a key opportunity for profiling the objectives and progress of FishPopTrace, which was deemed a significant international effort in the quest to tackle IUU and promote consumer protection.                                                                                                                         Back to the top...

4. Plans for next Workshop

Plans are progressing well for the next FishPopTrace workshop  which as you are all aware is being held  at

the Environment Centre Wales (ECW), School of Biological Sciences in Bangor University from 20th - 22nd April 2010. We will be sending out further details of the accommodation and the booking procedure in the New Year. We are looking forward to welcoming  the consortium to Bangor and would be grateful if you could begin to consider the options available for travel  as soon as possible. Once you have booked flights, if you could complete the travel template sent out with the email, it would help us to begin to organise transfers.

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5. Funding Opportunities

5.1: Marine Genomics 2

KULeuven is involved in the preparation of a FP7-Conserted Action (MG4U), aiming at the valorisation to the industry of Marine Genomics data and results (Marine Genomics 2). Although limited in funding, this will enable the continuation of a broad marine genomics network and the preparation for larger scale projects in the marine genomics science (implementation of forensic tools, further functional/environmental genomics initiatives). Although the core group is limited, the involvement of all partners interested in Marine Genomics will be solicited as users group (for courses, etc).

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6. Relevant future meetings

6.1: SNP Workshop III: SNP discovery and applications in non-model organisms.

Seattle, Washington, USA, March 22-24, 2010

The International Program for study of Salmon Ecological Genetics at the University of Washington, School of Aquatic and Fishery Science, is planning a two and one-half day SNP Workshop III in Seattle, Washington, USA, March 22-24, 2010.  Both oral and poster presentations will be considered, and a subset invited for peer review and potential publication in a Special Issue of Molecular Ecology Resources to appear in early 2011.


6.2: Climate Change Effects on Fish and Fisheries: Forecasting impacts, assessing ecosystem responses, and evaluating management strategies Sendai, Japan, April 26 – 29, 2010

Audrey Geffen submitted the abstract: “High latitude climate variability and its implications for fish resources as revealed by fossil otoliths of cod (Gadus morhua)” which uses otolith characteristics (shape, growth record, composition) to analyse the cod populations fished by medieval communities in northern Norway


6.3: Australian Society for Fish Biology 2010 Annual Conference

Melbourne Museum Carlton Gardens, Melbourne, Australia 12-14 July 2010

Covers areas as wide as fish biodiversity, biogeography, phylogeography, community ecology, population biology, ecology, conservation, sustainability and resource management.


6.4: The FSBI Annual Conference

Queen's University, Belfast, UK 26-30 July 2010

The meeting will examine the influence of climate change on fish at different levels of biological organisation. Sessions will be organised to examine the role of climate change on the biology of fish at the genetic, cellular, individual, population, community and ecosystem levels. This will be a meeting where a wide variety of fish biologists (e.g. ecologists, fisheries biologists, physiologists and geneticists) can meet to present and discuss the issues of climate change effects on fish so as to develop a synthesis across scales and levels of biological organisation.

***Abstract deadline extended to 15th January 2010***

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7. Consortium Publications (as a result of FishPopTrace activity):

7.1: Juvenile sole otoliths Els Cuveliers paper on a first assessment of microchemistry as a tool to discriminate sole nurseries was accepted in MEPS: Cuveliers, E.L., Geffen, A.J, Guelinckx, J., Raeymaekers, J,  Skadal, J., Volckaert, F.A.M and Maes. G.E. Microchemical variation in juvenile sole (Solea solea) otoliths as a powerful tool for studying connectivity in the North Sea.  MEPS Accepted

7.2: VLIZ 2009

Eveline Diopere presented a poster partly on the FishPopTrace aims in sole at the national “10 year VLIZ” meeting, Ostend, Belgium. VLIZ is Flanders Marine Institute, coordinating/archiving marine projects and their data.

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8. Other useful Related Publications

8.1: Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

Looks at variation in 98 gene-associated SNPs for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution.

Einar E Nielsen, Jakob Hemmer-Hansen, Nina A Poulsen, Volker Loeschcke, Thomas Moen, Torild Johansen, Christian Mittelholzer, Geir-Lasse Taranger, Rob Ogden and Gary R Carvalho. BMC Evolutionary Biology

8.2: A Validated Methodology for Genetic Identification of Tuna Species (Genus Thunnus)

Tuna species of the genus Thunnus, such as the bluefin tunas, are some of the most important and yet most endangered trade fish in the world. Identification of these species in traded forms, however, may be difficult depending on the presentation of the products, which may hamper conservation efforts on trade control. In this paper, we validated a genetic methodology that can fully distinguish between the eight Thunnus species from any kind of processed tissue.

Viñas, Jordi., and Tudela, Sergi. PLoS One

8.3: Taxonomic confusion and market mislabelling of threatened skates: important consequences for their conservation status


The common skate is not at all common: this large marine fish has 'critically endangered' status. That it turns out to be not one species, but two, is a sharp reminder that good taxonomy must underpin conservation

Iglésias, S.P.  Lucile Toulhoat, Daniel Y. Sellos (online early) Aquatic Conservation: Marine and Freshwater Ecosystems

The paper was also reviewed in Nature: Biodiversity: Skates on thin ice. Nicholas K. Dulvy & John D. Reynolds Nature 462, 417 (26 November 2009)



8.4: Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: A largely untapped resource for applied conservation and evolution.

 Waples, R. S., and C. Do. Evolutionary Applications (published Online Early 26 November 2009).


8.5: Actinopterygians from the North-eastern Atlantic and the Mediterranean

Pdf version of a book project based on diversity, identification and classification of fishes (Actinopterygians) from the North-eastern Atlantic, the Mediterranean and adjacent areas. This new version includes 200 species belonging to 95 families.

8.6: Chondrichthyans from the North-eastern Atlantic and the Mediterranean


The third Pdf version of a book project based on diversity, identification and classification of sharks, rays & chimaeras (Chondrichthyans) from the North-eastern Atlantic, the Mediterranean and adjacent areas. This new version includes 84 species belonging to 23 families.


8.7: The DEFRA yearbooks


These 2 books (one for environment and one covering fisheries) highlight a range of marine biodiversity, environment and fisheries projects to illustrate the range of research Defra funded from April 2008 to March 2009.



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9. EU Developments on Traceability Related Issues 

9.1: The Commission’s guidance handbook for combating IUU fishing regulation

The European Commission has also recently published the implementing rules and guidance handbook for combating IUU fishing regulation.


For further information see the Commission's website: http://ec.europa.eu/fisheries/cfp/external_relations/illegal_fishing_en.htm


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10. Other EU Developments


10.1: The Commission’s proposal for Total Allowable Catches for 2010

The European Commission is proposing new levels of total allowable catch (TAC) and fishing effort for fish stocks available to Community fishing vessels mainly in the Atlantic and the North Sea. This proposal is based on scientific advice about the quantities of fish that can be caught sustainably. The Commission has also discussed working methods with Member States and the fishing sectors, and as a result of their advice has in many cases limited reductions to no more than 15% since last year.

For further information see the Commission's website: http://ec.europa.eu/fisheries/press_corner/press_releases/2009/com09_54_en.htm


10.2: Cod quotas

The European Commission is calling for cuts of up to 25 per cent in the amount of cod fishers can catch in 2010. Officials warned that the fish is nearing extinction in some major European fishing zones. “We are not that far away from a situation of complete collapse.”



10.3: Norway- Scotland talks collapse

European Union (EU) and Norwegian fishing fleets have been booted out of each other's waters, which they normally share, after talks on quotas collapsed.


10.4 Spain pursues greater hake TAC

The Spanish Government will solicit a 7 per cent increase (as opposed to the 10 per cent decrease advised) in hake captures in Northern waters during the meeting of the European Union (EU) Council of Fisheries Ministers, where 2010 fishing quotas will be negotiated as of next Monday.

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11. Other

11.1: Copenhagen SummitA couple of links to the marine aspects:http://copenhagendiagnosis.org/ http://www.guardian.co.uk/environment/2009/dec/10/ocean-acidification-epoca


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