Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection of samples from fisheries products for genetic analysis : final report.
Date: 2020-09-17
Institutions: Executive Agency for Small and Medium-sized Enterprises
Subjects: DNA, authorised catch, by-catch, fish, fishery product, fishery research, fishing controls, fishing fleet, genetics, report, research method, traceability, zoology

Study to produce an 
International Manual of 
Procedures (IMP) to be used 
in the NAFO Regulatory Area 
to guide the collection of 
samples from fisheries 
products for genetic analysis 

European Maritime and Fisheries Fund (EMFF) 

[Written  by  Narcisa  Maria  Bandarra  (IPMA),  Ricardo  Alpoim  (IPMA),  Carlos  Cardoso  (BioAtlantis, 
Ltd.), Fernando González-Costas (IEO), Alma Hernandez de Rojas (IEO), Naiara Rodríguez-Ezpeleta 
(AZTI), Haritz Arrizabalaga (AZTI) [September – 2020] 

 
 
 
 
 
 
 
 
 
 
 
 
 
This report should be cited as: 

Bandarra,  NM,  Alpoim  R,  Cardoso,  C.,  González-Costas  F.,  Rojas,  A.  H.,  Rodriguez-
Ezpeleta,  N.,  Arrizabalaga,  H.,  2020.  Study  to  produce  an  International  Manual  of 
Procedures  (IMP)  to  be  used  in  the  NAFO  Regulatory  Area  to  guide  the  collection  of 
samples  from  fisheries  products  for  genetic  analysis.  Final  Report.  European 
Commission.  Specific  Contract  No.  15  EASME/EMFF/2019/1.3.2.2  under  Framework 
Contract No. EASME/EMFF/2016/008. 77 pp. 

“The information and views set out in this study are those of the author(s) and 
do not necessarily reflect the official opinion of EASME or of the Commission. 
Neither  EASME,  nor  the  Commission  can  guarantee  the  accuracy  of  the  data 
included  in  this  study.  Neither  EASME,  nor  the  Commission,  or  any  person 
acting on their behalf may be held responsible for the use which may be made 
of the information contained therein.” 

EUROPEAN COMMISSION 

Executive Agency for Small and Medium-sized Enterprises (EASME) 

Unit Department A - COSME, H2020 SME and EMFF 

Unit A3 EMFF 

Contact: EASME EMFF A.3; Rocío Suárez Jiménez  

E-mail:  EASME-EMFF-CONTRACTS@ec.europa.eu; Rocío.Suárez-Jiménez@ec.europa.eu  

European Commission 
B-1049 Brussels 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection of 
samples from fisheries products for genetic analysis" 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Specific Contract No 15  

EASME/EMFF/2019/1.3.2.2  

FRAMEWORK CONTRACT 
EASME/EMFF/2016/008   

Provision of Scientific Advice for 
Fisheries Beyond EU Waters  

Study to produce an 
International Manual of 
Procedures (IMP) to be used 
in the NAFO Regulatory Area 
to guide the collection of 
samples from fisheries 
products for genetic analysis 

Final Report 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

 
 
  
  
 
 
 
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This document has been prepared for the European Commission however it reflects the views only of the 
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Luxembourg: Publications Office of the European Union, 2020 

PDF 

ISBN 978-92-9460-210-7  doi: 10.2826/018413 

EA-02-20-644-EN-N 

© European Union, 2020 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

4 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Contents 

EXECUTIVE SUMMARY ................................................................................................... 1 

RÉSUMÉ EXÉCUTIF ........................................................................................................ 1 

RESUMEN EJECUTIVO .................................................................................................... 2 

1. 

INTRODUCTION ..................................................................................................... 4 

1.1  GENERAL INTRODUCTION TO THE SPECIFIC CONTRACT ............................................ 4 

1.2  OBJECTIVE AND STRUCTURE OF THE FINAL REPORT ................................................. 6 

2.  OBJECTIVES, METHODS, PROGRESS AND MAIN RESULTS BY TASK .............................. 7 

2.1  TASK 1 – LITERATURE REVIEW ............................................................................... 7 

2.1.1.  OBJECTIVES ................................................................................................... 7 

2.1.2.  METHODOLOGY ............................................................................................... 7 

2.1.3. 

RESULTS ........................................................................................................ 8 

2.1.3.1. 

BACKGROUND ............................................................................................. 9 

2.1.3.2. 

ALTERNATIVE METHODOLOGIES FOR FISH PRODUCT AUTHENTICITY ................ 10 

2.1.3.3. 

DNA-BASED SPECIES ASSIGNMENT .............................................................. 18 

2.1.3.4. 

ONGOING STUDIES AND RESEARCH PROJECTS .............................................. 21 

2.1.3.5. 

EMERGING TECHNOLOGIES.......................................................................... 21 

2.1.3.6. 

CHALLENGES AND MITIGATION .................................................................... 22 

2.1.3.7. 

FUTURE PERSPECTIVES ............................................................................... 23 

2.2  TASK 2 – MANUAL OF PROCEDURES ....................................................................... 24 

2.2.1.  OBJECTIVES .................................................................................................. 24 

2.2.2.  METHODOLOGY .............................................................................................. 24 

2.2.3. 

RESULTS ....................................................................................................... 25 

2.2.3.1. 

SUB-TASK  2.1  -  ANALYSIS  OF  THE  PORTUGUESE  MANUAL  OF 

PROCEDURES ....................................................................................................... 25 

2.2.3.1.1.  TRANSLATED AND REVISED PORTUGUESE MANUAL OF PROCEDURES ............... 25 

2.2.3.1.2.  CRITICAL APPRAISAL OF THE PORTUGUESE MANUAL OF PROCEDURES ............. 26 

2.2.3.2. 

SUB-TASK  2.2  -  PREPARATION OF DESCRIPTIVE  ANALYSIS OF FISHING 

FLEETS ................................................................................................................ 27 

2.2.3.2.1.  STATUS OF THE SUB-TASK 2.2 ..................................................................... 27 

2.2.3.2.2.  INTRODUCTION TO NAFO ............................................................................ 28 

2.2.3.2.3.  NAFO CONSERVATION AND ENFORCEMENT MEASURES (NAFO, 2019A) ............. 31 

2.2.3.2.4.  NAFO FLEETS/FISHERIES ............................................................................. 38 

2.2.4. 

SUB-TASK 2.3 – ELABORATION OF MANUAL OF PROCEDURES ............................. 79 

3.  TIMETABLE FOR THE IMPLEMENTATION ................................................................... 85 

4.  LIST OF DELIVERABLES ......................................................................................... 87 

5.  LIST OF MEETINGS ................................................................................................ 88 

6.  LIST OF MILESTONES ............................................................................................ 89 

7.  REFERENCES ........................................................................................................ 90 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

5 

 
 
 
1.  EXECUTIVE SUMMARY 

Within 

the 

scope 

of 

the 

Specific 

Contract  No 

15 

EASME 

/EMFF/2019/1.3.2.2/02/15/SI2.807287 

FRAMEWORK 

CONTRACT 

EASME/EMFF/2016/008,  several  actions  were  undertaken  with  the  final  purpose  of 

generating  an  International  Manual  of  Procedures  (IMP)  on  “FISH  PRODUCTS 

SAMPLING  FOR  DNA  TESTING”.  This  involved  three  main  previous  steps: 

conduction  of  a  thorough  Literature  Review  on  the  state-of-the-art  of  the  analytical 

methodologies  and  related  sampling  issues;  translation  of  the  Portuguese  Manual  of 

Procedures (PMP) to English with the necessary adjustments to the EU wide reality and 

incorporating Portuguese Inspectors’ criticisms and experience in the application of the 

PMP;  and  preparation  of  a  Descriptive  Analysis  of  Fishing  Fleets  operating  in  NAFO 

RA. On the basis of these three components, the IMP was prepared. However, further 

component  incorporation,  refinement,  and  improvements  were  necessary,  namely, 

concerning  response  to  the  shortcomings  of  the  PMP  document  and  inspectors’ 

criticisms as well as detailing sample preparation and DNA analysis procedures for the 

production of a holistic and integrated IMP, which will be able to serve as an effective 

guide  to  all  professionals  involved  in  the  identification  of  fish  species  in  the  fishing 

fleets  operating  in  the  NAFO  Regulatory  Area.  Finally,  it  must  be  stressed  that  the 

generated IMP is open to additional changes as experience in the field is gathered and 

more information is collected. Hence, this IMP is above all other things a working tool 

for EU inspectors, analysts, other involved personnel, competent authorities, and other 

sector stakeholders. 

2.  RÉSUMÉ EXÉCUTIF 

Dans 

le 

cadre 

du 

Contrat 

Spécifique 

n° 

15 

EASME 

/EMFF/2019/1.3.2.2/02/15/SI2.807287  CONTRAT-CADRE  EASME/EMFF/2016/008, 

plusieurs actions ont été entreprises dans le but final de générer un Manuel International 

de  Procédures  (MIP)  sur  "L'échantillonnage  des  produits  de  la  pêche  pour  les  tests 

ADN".  Cela  a  impliqué  trois  étapes  préalables  :  la  réalisation  d'une  analyse 

documentaire  approfondie  sur  l'état  de  l'art  des  méthodes  d'analyse  et  les  questions 

d'échantillonnage connexes ; la traduction du Manuel de Procédures portugais (MPP) en 

anglais avec les ajustements nécessaires à la réalité de l'UE et l'intégration des critiques 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

1 

 
 
 
 
et de l'expérience des inspecteurs portugais dans l'application du MPP ; et la préparation 

d'une  analyse  descriptive  des  flottes  de  pêche  opérant  dans  la  Zone  de  Régulation 

OPANO.  C'est  sur  la  base  de  ces  trois  éléments  que  le  MIP  a  été  préparé.  Toutefois, 

d'autres éléments ont dû être incorporés, affinés et améliorés, en l’occurrence en ce qui 

concerne la réponse aux lacunes du document du MPP et aux critiques des inspecteurs, 

ainsi que le détail des procédures de préparation des échantillons et d'analyse de l'ADN 

pour la production d'un MIP holistique et intégré, qui pourra servir de guide efficace à 

tous les professionnels impliqués dans l'identification des espèces de poissons dans les 

flottes de pêche opérant dans la ZR OPANO. Enfin, il convient de souligner que le MIP 

généré est ouvert à des modifications supplémentaires à mesure que l'expérience sur le 

terrain  est  acquise  et  que  davantage  d'informations  sont  recueillies.  Par  conséquent, 

cette  MPI  est  avant  tout  un  outil  de  travail  pour  les  inspecteurs  UE,  les  analystes,  les 

autres personnels concernés, les autorités compétentes et les autres acteurs du secteur. 

3.  RESUMEN EJECUTIVO 

En 

el 

marco 

del 

Contrato 

Específico 

Nº 

15 

EASME 

/EMFF/2019/1.3.2.2/02/15/SI2.807287 

FRAMEWORK 

CONTRACT 

EASME/EMFF/2016/008,  se  emprendieron  varias  acciones  con  el  propósito  final  de 

generar  un  Manual  Internacional  de  Procedimientos  (MIP)  sobre  "MUESTREO  DE 

PRODUCTOS DE PESCADO PARA LA PRUEBA DE ADN". Ello supuso tres pasos 

previos  principales:  un  examen  exhaustivo  de  la  bibliografía  sobre  el  estado  de  las 

metodologías  analíticas  y  las  cuestiones  de  muestreo  relacionadas;  traducer  el  Manual 

de Procedimientos portugués (MPP) al inglés con los ajustes necesarios a la realidad de 

toda  la  UE  y  la  incorporación  de  las  críticas  y  la  experiencia  de  los  inspectores 

portugueses  en  la  aplicación  del  MPP;  y  preparar  un  análisis  descriptivo  de  las  flotas 

pesqueras  que  operan  en  el  Área  Regulatoria    NAFO.  Sobre  la  base  de  estos  tres 

componentes, se preparó el MIP. Sin embargo, fue necesario incorporar, perfeccionar y 

mejorar  ciertos  componentes,  sobre  todo  en  lo  que  respecta  a  la  respuesta  a  las 

deficiencias  del  documento  del  MPP  y  las  críticas  de  los  inspectores,  así  como  a  la 

preparación detallada de las muestras y los procedimientos de análisis del ADN para la 

elaboración de un MIP holístico e integrado, que pueda servir de guía eficaz a todos los 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

2 

 
 
 
 
 
profesionales  que  participan  en  la  identificación  de  las  especies  de  peces  en  las  flotas 

pesqueras que operan en la zona de regulación de la NAFO. Por último, cabe destacar 

que  el  MIP  generado  está  abierto  a  cambios  adicionales  a  medida  que  se  reúna  más 

experiencia  en  la  materia  y  más  información.  Por  lo  tanto,  este  MIP  es,  ante  todo,  un 

instrumento de trabajo para los inspectores de la Unión Europea, los analistas, otro tipo 

de personal implicado, las autoridades competentes y otros interesados del sector. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

3 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1.  INTRODUCTION 

1.1 GENERAL INTRODUCTION TO THE SPECIFIC CONTRACT 

EASME has commissioned the IPMA led consortium (IPMA, AZTI, and IEO) to fulfil 

the  request  under  the  Framework  Contract  EASME/EMFF/2016/008  on  "Scientific 

advice  for  fisheries  beyond  EU  waters".  The  present  draft  final  report  refers  to  the 

Specific  Contract  (SC)  Nº  15  within  this  framework,  aiming  at  the  production  of  an 

International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to 

guide the collection of samples from fisheries products for genetic analysis. 

Indeed,  the  Northwest  Atlantic  Fisheries  Organisation  (NAFO),  in  its  2019  edition  of 

the  Control  and  Enforcement  Measures  (CEM),  has  included  the  provisions  for  DNA 

analysis  in  an  effort  to  develop  a  solid  approach  to  fight  issues  related  with  species 

misidentification. NAFO has also emphasized the capacity of inspectors to take samples 

for  DNA  analysis  as  an  additional  tool  in  fighting  illegal,  unreported  and  unregulated 

fishing and fishing fraud by vessels operating in NAFO Regulatory Area (RA). Thus, a 

protocol  to  guide  the  collection  and  the  chain  of  custody  process  of  the  samples  to 

ensure  the  integrity  and  reliability  of  the  results  has  been  ensured  through  the 

preparation of the  International Manual of Procedures (IMP) “Fish Products Sampling 

for DNA Testing”. 

On  the  other  hand,  the  EU  experience  with  DNA  analysis  is  at  the  forefront  of  the 

experiences of other contracting parties. As such, as a NAFO contracting party, the EU 

wanted to build on previous experience and bring forth an international protocol for the 

collection  of  samples  for  DNA  analysis  in  the  NAFO  RA.  This  international  protocol 

will be presented for adoption during the 2019 NAFO Annual meeting, in its STATIC 

Committee. 

Precisely, the Specific Contract No. 15 has drawn on previous experience and expertise 

and put forward an IMP to guide in the collection of samples from fisheries products for 

genetic  analysis.  In  doing  this,  it  has  performed  a  literature  review  that  comprised 

already  established  methodologies  and  emergent  techniques,  representing  the  state-of-

the-art of the genomics. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

4 

 
 
 
 
 
 
 
The  final  report  is  a  key  piece  in  the  process  of  accomplishing  the  activities 

programmed for the Specific Contract No. 15, making a balance of what has been done 

and highlighting the challenges that were overcome in the preparation of the IMP. 

In order to fulfil the main purpose mentioned above, the following tasks were proposed 

and were developed: 

Task 1 - Literature review: 

Preparation of an updated review on molecular DNA-based analysis adequate to assign 

species to fish product and how these tools have been used worldwide to support fishing 

traceability  and  compliance.  This  review 

took 

into  account 

the  most  recent 

advancements,  including  the  identification  of  ongoing  studies  and  research  projects, 

taking  special  care  in  analysing  the  state-of-the-art  in  the  field.  This  enabled  the 

identification  of  the  strengths  and  weaknesses  of  these  techniques  and  emergent  ones 

that are relevant for consideration in future developments. Additionally, this document 

contained  a  section  dedicated  to  identify  the  practical  problems  that  are  faced  when 

implementing  the  procedures  and  identify  relevant  mitigation  measures  as  well  as 

measures to prevent possible future problems. 

Task 2 - Manual of procedures: 

Development of an International Manual of Procedures (IMP) to support the collection 

of  samples  from  fisheries  products  by  inspectors  during  their  operation  in  NAFO 

vessels. This manual of procedures is meant to be easily applied by inspectors from any 

NAFO Contracting Party in the context of their duties. 

The manual set scientifically grounded principles for the collection of samples on-board 

fishing vessels. The manual took into consideration the specificities of each fishing fleet 

operating  in  the  NAFO  RA  such  as  stowage  plans,  volumes  of  fishing  products  by 

species, type of processing presentation,  type of  fishing gear, and other characteristics 

deemed relevant. This was essential to ensure that the sampling protocol may be applied 

in  different  situations,  not  only  conforming  to  the  best  scientific  guidelines,  but  also 

producing the best results in practice. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

5 

 
 
 
 
 
 
 
This  IMP took  into account  the experience and current  practices of the EU MS in  the 

NAFO  RA  for  the  collection  of  samples  to  perform  DNA  analysis  and  on  possible 

extend build on the available experience. For such purpose, the Portuguese Manual of 

Procedures currently in place was reviewed. 

The  contractor  has  met  the  objectives  of  this  task  through  undertaking  the  following 

specific sub-tasks: 

Sub-task 2.1: 

Analysis  of  the  Portuguese  manual  of  procedures  to  identify  potential 

weaknesses to be addressed and the areas still requiring development and improvement 

in  order  to  produce  a  Manual  universally  applicable  to  any  fishing  activity  in  NAFO 

RA. 

Sub-task 2.2: 

Preparation of a descriptive analysis of the fishing fleets operating in the NAFO 

RA, their characteristics and the identification of relevant factors to take into account in 

each  of  those  for  the  designing  of  specific  sampling  schemas  and  other  specific 

necessary adaptations to each type of fleet. 

Sub-task 2.3: 

Production of the Manual of Procedures, taking into full consideration the results 

from the previous two sub-tasks, therefore expanding in the areas the current manual of 

procedures does not  deliver, and ensuring the implementation  of appropriate sampling 

techniques  (e.g.  collection  process,  setting  sample  dimensions)  for  each  type  activity 

performed in the NAFO RA. 

On the basis of these tasks it was possible to have a practical and reliable IMP for the 

NAFO RA. 

1.2 OBJECTIVE AND STRUCTURE OF THE FINAL REPORT 

The main goal of this Final Report is to provide an update on the progress made and the 

main results and outcomes achieved, specifying in detail the work undertaken under the 

specific Tasks 1 to 2, comprising all Sub-Tasks 2.1-2.3. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

6 

 
 
 
 
 
 
 
 
In this report we also inform about any problems that have occurred during the course 

of  the  SC15,  how  the  Consortium  addressed  them  and  the  final  objectives  were 

achieved. 

2.  OBJECTIVES, METHODS, PROGRESS AND MAIN RESULTS BY TASK 

2.1 TASK 1 – LITERATURE REVIEW 

2.1.1.  OBJECTIVES 

The  objective  of  this  Task  was  to  prepare  a  literature  review  comprising  available 

studies  and  methodologies  describing  the  relevance  of  molecular  analysis  to  reliably 

assign species names to fisheries products. This literature review provided examples of 

current application of these techniques in the world. The literature review comprised not 

only  the  genomic  techniques,  but  also  delved  into  the  possibilities  offered  by 

proteomics,  metabolomics,  and  lipidomics.  Ongoing  projects  in  this  scientific  area, 

practical applications, and case-studies were also included. 

2.1.2.  METHODOLOGY 

This  was basically  a desk-based Task  aiming at  finding, revising,  and organizing  new 

knowledge  available  and  data.  The  literature  review  was  performed  using  scientific 

peer-reviewed studies, book chapters, and other relevant documents, such as reports and 

documents  from  International  bodies,  including  Non-Governmental  Organizations 

(NGOs). These documents were attained through a thorough search of the World Wide 

Web using Google as search engine and, in particular, taking advantage of the Google 

Scholar.  Moreover,  specific  sources  of  scientific  publications  were  screened,  namely, 

ScienceDirect/Elsevier,  Springer  Verlag,  Wiley  Publishers,  Taylor  and  Francis 

Publishers,  the  Royal  Society  of  Chemistry,  and  OMICS  International.  Finally,  the 

reference  documents  that  were  used  to  perform  the  literature  review  concerning  the 

studies  using  molecular  analyses  to  reliably  assign  species  to  fisheries  products  were 

collected  from  bibliographic  databases  of 

indexed 

journals  such  as  PubMed 

(https://www.ncbi.nlm.nih.gov 

› 

pubmed) 

or 

Science 

Direct 

(https://www.sciencedirect.com/)  and  also  from  reports  from  FAO  and  the  European 

Commission. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

7 

 
 
 
 
 
 
The list of references used for the preparation of this Task is presented in Table 1. 

Table 1. List of references used in the preparation of the literature review. 

Reference 

Application 

Cajka et al. (2016) 

Book  chapter  dealing  with  all  recent  advances  in  mass 

spectrometry  for  food  authenticity  testing  in  an  omics 

perspective 

Ellis et al. (2016) 

Review study addressing the subject of omics approaches for 

the detection of food fraud 

Mazzeo  and  Siciliano 

Review  study  covering  the  proteomics  methods  for  the 

(2016) 

authentication of fish species 

Mohanty et al. (2019) 

Book chapter dealing with omics technology in fisheries and 

aquaculture 

Ortea et al. (2010) 

Study  on  identification  of  commercial  prawn  and  shrimp 

species of food interest by native isoelectric focusing 

Pinu et al. (2019) 

Review  study  on  systems  biology  and  multi-omics 

integration 

Salla and Murray (2013)  Study  on  matrix-assisted  laser  desorption  ionization  mass 

spectrometry for identification of shrimp 

Sobolev et al. (2017) 

Review  study  dealing  with  molecular  fingerprinting  of  food 

authenticity 

2.1.3.  RESULTS 

This subsection shows the results achieved on the review of the literature regarding the 

main issues that had been previously defined in the literature review index as worthy of 

attention and revision. The following items composed the literature review index: 

1. 

2. 

3. 

4. 

5. 

6. 

Background; 

Alternative methodologies for fish product authenticity; 

DNA-based species assignment; 

Ongoing studies and research projects; 

Emerging technologies; 

Challenges and mitigation; 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

8 

 
 
 
 
 
 
7. 

Future perspectives. 

These sections enabled a thorough revision of the state-of-the-art of molecular analysis 

for the purpose of food authenticity testing with a particular focus on fish products. 

2.1.3.1.  BACKGROUND 

The  challenges  of  the  XXIst  Century  comprise  an  enhanced  pressure  on  resources  in 

order  to  feed  the  ever-increasing  world  population  (FAO,  2018),  which  results  in 

overfishing and expansion of fisheries towards previously unexploited species  (Swartz 

et al., 2010). Illegal, unreported and unregulated (IUU) fishing exacerbate the problems 

derived  from  overfishing  and  mismanagement  (Pauly  and  Zeller,  2016).  Additionally, 

there  has  been  an  increase  level  of  consumer  awareness  of  the  critical  importance  of 

food  quality  and  safety  for  health  and  sustainability  as  species  substitution  not  only 

decrease  food  quality,  but  can  sometimes  be  harmful  (Armani  et  al.,  2015).  Thus, 

authentication of fishery products is a central issue for both, sustainable management of 

resources and human health. Species substitution is a common form of fish fraud, which 

also include the use of undeclared and/or illegal additives, the addition of glaze water to 

frozen products, the mislabeling of ingredients, the use of falsified-brand products, and 

the mislabeling of geographic origin or of production method and/or fishing gear (FAO, 

2018). 

Species substitution is  defined  as the unintentional  or deliberate misidentification of  a 

fish  product.  Accidental  substitutions  may  occur  when  two  species  have  similar 

morphological  features  or  when  ambiguities  with  the  species  nomenclature  exist  and 

deliberate substitutions often involve the replacement of a high value species by a lower 

value  one  for  financial  gain  (Spink  and  Moyer,  2011).  Since  2000,  the  European 

Commission  (Council  Regulation  (EC)  No  104/2000,  1999)  prepared  directives  and 

regulations  regarding  fishery  and  aquaculture  products  determining  what  must  be 

written on the label: fish species, geographical origin, and production method (wild or 

farmed).  Furthermore,  the  European  Food  Safety  Authority  (EFSA)  established  a 

detailed scheme of traceability for food (comprising fishery and aquaculture products) 

and  feed  companies  in  order  to  control  food  safety  throughout  the  processing  and 

distribution chain (Council Regulation (EC) No. 178/2002, 2002). 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

9 

 
 
 
 
 
 
The  identification  of  fish  species  using  morphological  characteristics  is  often  not 

straight forward even for fresh fish because some species are very similar, especially at 

young  age  (e.g.  the  Yellowfin,  Thunnus  albacares,  and  the  bigeye,  T.  obesus,  tuna  or 

the  white,  Lophius  piscatorius,  and  the  black  L.  boudegassa,  anglerfishes),  which 

translates into high misidentification rates (Nakamura and Séret, 2002; Laurenson et al., 

2008).  When  it  comes  to  processed  products  (filleted,  canned,  …)  the  morphological 

identification becomes almost impossible as anatomical and morphological traits (e.g., 

head,  fins,  skin),  of  great  importance  for  fish  species  identification,  are  absent.  Thus, 

analytical  methods  not  relying  on  morphological  characteristics  are  required  for 

ensuring  unambiguous  assignment  of  species  to  fish  product.  Moreover,  in  order  to 

allow  for  the  screening  a  large  number  of  samples,  these  methods  should  be  high-

throughput and scalable. At present, the methods for species recognition that are based 

on  the  use  of  DNA  and  protein  markers  are  considered  the  most  suitable  methods  for 

fish  authentication  (Lavilla  et  al.,  2013).  Nonetheless,  other  methods  based  on 

proteomics, metabolomics, and lipidomics have made important progresses and deserve 

to be mentioned and reviewed. 

In  any  case,  DNA-based  analyses  fulfil  these  requirements  and  have  been  shown 

applicable and affordable for fish authentication. Moreover, as opposed to protein based 

biochemical  analyses  (e.g  isoelectric  focusing,  high  performance  chromatography  or 

immunoassays), which are based on heat-sensitive proteins, DNA based assays can be 

applied to heated or highly processed products as, although DNA can also be degraded 

during  the  food  processing  process,  this  molecule  is  more  thermostable  than  proteins, 

and short  fragments, valid  for  authenticity  tests,  are  generally recoverable  (Chapela  et 

al.,  2007a).  Consequently,  the  development  of  DNA-based  methods  to  identify  fish 

species is a growing field (Hellberg and Morrissey, 2009) that will allow improving at-

sea inspection and surveillance of fisheries products. 

2.1.3.2.  ALTERNATIVE METHODOLOGIES FOR FISH PRODUCT AUTHENTICITY 

The  challenges  of  the  XXIst  Century  comprise  an  enhanced  pressure  on  resources  in 

order  to  feed  an  ever  increasing  world  population  and  higher  levels  of  consumer 

awareness  of  the  critical  importance  of  food  for  health,  being  quality  and  safety  of 

paramount importance. For fishery products, this poses specific problems, since there is 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

10 

 
 
 
 
 
a  clear  pressure  toward  using  undervalued  species  as  other  more  valued  species, 

especially  after  processing,  and  product  authenticity  has  become  a  highly  sensitive 

issue. Precisely, authentication of fishery products is a central issue for the evaluation of 

food  quality  and  safety.  In  the  fishery  market,  the  most  usual  falsification  is  the 

replacement  of  more  valuable  fish  species  by  inferior  ones.  Specifically,  the 

identification  of  processed  products  by  eye  inspection  becomes  very  challenging  as 

anatomical  and  morphological  traits  (e.g.,  head,  fins,  skin),  traditionally  of  great 

importance  for  fish  species  authentication,  are  impossible  to  recover  after  processing. 

These  falsifications  are  constantly  growing  as  a  result  of  market  globalization  and, 

besides affecting product quality, pose also health risks to the consumers (Mazzeo and 

Siciliano, 2016). Since 2000, EU prepared directives and regulations regarding fishery 

and  aquaculture  products  determining  what  must  be  written  on  the  label:  fish  species, 

geographical origin, and production method (wild or farmed) (EC No 104/2000, 1999; 

EC  No  2065/2001,  2001).  Furthermore,  the  European  Food  Safety  Authority  (EFSA) 

established  a  detailed  scheme  of  traceability  for  food  (comprising  fishery  and 

aquaculture products) and feed companies in order to control food safety throughout the 

processing  and  distribution  chain,  as  reported  in  EC  regulation  No  178/2002  (2002). 

Furthermore,  there  have  been  developments  with  the  EU  introducing  a  much  more 

stringent  regulation  (EC  No  1379/2013,  2013).  This  regulation  dealt  with  different 

issues  regarding  the  common  organization  of  the  markets  in  fishery  and  aquaculture 

products. 

In general, genomics, proteomics, metabolomics and lipidomics are four alternative and 

in some cases suppletive systems corresponding to biological approaches that are often 

employed  for  food  fraud  detection  studies  (Ellis  et  al.,  2016).  An  overview  of  these 

different approaches is given in Table 2. The analytical methods for fish authentication 

that  were  first  put  into  use  were  based  on  the  analysis  of  protein  extracts  by 

electrophoretic,  chromatographic,  and  immunological  methods  (Mazzeo  and  Siciliano, 

2016).  More  specifically,  isoelectric  focusing  (IEF)  using  sarcoplasmic  proteins  has 

been able to distinguish different fish (Mazzeo and Siciliano, 2016) and shrimp (Ortea 

et  al.,  2010).  This  methodology  was  considered  validated  for  species  identification  by 

the  Association  of  Official  Analytical  Chemistry  (Mazzeo  and  Siciliano,  2016).  IEF 

profiles  of  sarcoplasmic  proteins  from  various  fish  species  have  been  assembled 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

11 

 
 
 
 
together  in  a  database  by  the  U.S.  Food  and  Drug  Administration  (FDA),  being 

accessible in the internet library Regulatory Fish  Encyclopedia. However, it should be 

stressed that the available databases for proteomics, metabolomics, and lipidomics are 

still not reliable to be used in identification efforts at the species level. 

Table 2. Overview of the main approaches used for food fraud detection. 

Technique 

Description 

Classification 

Cytochrome  b  gene 

Amplification of a 

Genomics 

amplification 

specific 

DNA 

Reference 

Chapela  et 

al. (2007b) 

fragment 

(cytochrome 

b 

gene) 

using 

Polymerase  Chain 

Reaction (PCR) 

mtDNA  control  region 

Amplification of a 

Genomics 

amplification 

specific 

DNA 

Quinteiro  et 

al. (2001) 

fragment (mtDNA 

control 

region) 

using PCR 

12S 

rRNA 

region 

Amplification of a 

Genomics 

amplification 

specific 

DNA 

Zhang  et  al. 

(2006) 

fragment 

(12S 

rRNA 

region) 

using PCR 

Gas  Chromatography 

Molecular 

Lipidomics 

(GC) 

mass 

profiling 

system 

spectrometry 

applied  to  lipids 

Black  et  al. 

(2017) 

using 

a  MS 

technique 

Liquid  chromatography 

Molecular 

Lipidomics 

(LC) mass spectrometry 

profiling 

system 

Black  et  al. 

(2017) 

applied  to  lipids 

using 

a  MS 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

12 

 
 
 
 
technique 

Nuclear 

Magnetic 

Molecular 

Lipidomics 

Resonance 

(NMR) 

profiling 

system 

spectroscopy 

applied  to  lipids 

using 

a  NMR 

technique 

Rapid 

Evaporative 

Molecular 

Lipidomics 

Ionization 

Mass 

profiling 

system 

Spectrometry (REIMS) 

applied  to  lipids 

using 

a  MS 

technique 

Black  et  al. 

(2017) 

Song  et  al. 

(2019) 

Mass 

(MS) 

Spectrometry 

Molecular 

Metabolomics/Lipidomics  Cajka  et  al. 

(2016) 

profiling 

system 

applied  to  lipids 

and 

other 

metabolomes 

using 

a  MS 

technique 

Isoelectric 

focusing 

Method  based  on 

Proteomics 

Mazzeo  and 

(IEF) 

protein 

analysis 

and 

already 

applied 

to 

sarcoplasmic 

proteins 

Isoelectric 

focusing 

Method  based  on 

Proteomics 

(IEF) 

protein 

analysis 

and 

already 

applied 

to 

sarcoplasmic 

proteins 

Siciliano 

(2016) 

Ortea  et  al. 

(2010) 

Ambient 

Mass 

Molecular 

Proteomics/other omics 

Black  et  al. 

Spectrometry (AMS) 

profiling 

system 

(2016) 

applied to proteins 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

13 

 
 
 
and peptides using 

a MS technique 

Desorption 

Molecular 

Proteomics/other omics 

Gerbig et al. 

Electrospray  Ionization 

profiling 

system 

(2017) 

(DESI) 

applied to proteins 

and peptides using 

a MS technique 

Electrospray  Ionization 

Molecular 

Proteomics/other omics 

Gerbig et al. 

(ESI) 

profiling 

system 

applied to proteins 

and peptides using 

a MS technique 

(2017) 

Low 

Temperature 

Molecular 

Proteomics/other omics 

Gerbig et al. 

Plasma 

ionization 

profiling 

system 

(2017) 

(LTP) 

applied to proteins 

and peptides using 

a MS technique 

Matrix-Assisted  Laser 

Molecular 

Proteomics/other omics 

Stahl 

and 

Desorption/Ionization-

profiling 

system 

Time  of  Flight-Mass 

applied to proteins 

Spectrometry (MALDI-

and peptides using 

TOF-MS) 

a MS technique 

Schröder 

(2017) 

Rapid 

Evaporative 

Molecular 

Proteomics/other omics 

Black  et  al. 

Ionization 

Mass 

profiling 

system 

(2017) 

Spectrometry (REIMS) 

applied to proteins 

and peptides using 

a MS technique 

Meanwhile,  DNA-based  methodologies  that  use  the  amplification  of  specific  DNA-

fragments  —cytochrome  b  gene  (Chapela  et  al.,  2007b),  mtDNA  control  region 

(Quinteiro  et  al.,  2001),  and  12S  rRNA  region  (Zhang  et  al.,  2006)  using  Polymerase 

Chain  Reaction  (PCR)—  have  gained  much  acceptance.  In  addition,  DNA-barcoding 

has been also deemed as reliable for fish authentication and the FDA's Regulatory Fish 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

14 

 
 
 
 
Encyclopedia  has  incorporated  DNA  barcode  data  (Khaksar  et  al.,  2015).  These 

methods  have  been  shown  to  be  sensitive  and  specific,  even  when  species  are  closely 

related  (Santaclara  et  al.,  2015).  These  were  tuna  species  (Thunnus  species  and 

Katsuwonus  pelamis)  in  food  products.  However,  processing  of  fishery  products  may 

involve  industrial  operations  that  affect  DNA  integrity  (e.g.  heat  treatment,  acidic 

conditions),  thus  causing  non-specific  identification.  The  difficulties  in  standardizing 

protocols  for  DNA  analyses  are  also  frequently  cited  as  a  potential  cause  of 

inconsistencies in  results  from  different  laboratories (Mazzeo and Siciliano, 2016). Of 

course,  this  could  be  problematic,  leading  to  regulatory  or  legal  repercussions. 

Moreover,  though  DNA  analysis  costs  have  been  falling,  relatively  high  costs  of 

analysis should also be taken into account (Clark, 2015). 

These drawbacks and the necessity of developing high-throughput methodologies have 

stimulated  research  into  unambiguous  biomarkers  of  authenticity  and  to  set  up 

techniques enabling the screening of many samples with minimal expenditure of time. 

Precisely,  in  the  last  years,  within  the  so-called  omics  approach,  proteomics  has 

significantly contributed to investigate authenticity (Mazzeo and Siciliano, 2016). In the 

area of fish authentication, progress has been achieved through the classical proteomics 

that couples two-Dimensional gel Electrophoresis (2-DE) and mass spectrometry. This 

was followed by methods based on the analysis of peptides and intact proteins by  high 

resolution  and  tandem  mass  spectrometry.  These  methods  ushered  in  a  new  phase  in 

biomarkers  discovery  and  were  applied  in  evaluating  identity  of  fish-based  food 

(Tedesco  et  al.,  2014).  What  is  more,  molecular  profiling  schemes  based  on  Matrix-

Assisted  Laser  Desorption/Ionization-Time  of  Flight-Mass  Spectrometry  (MALDI-

TOF-MS)  have  become  an  alternative  tool  to  define  biomarkers  concerning  fish 

authenticity (Salla et al., 2013; Stahl and Schröder, 2017). 

More  recently,  Ambient  Mass  Spectrometry  (AMS)  is  a  new  field  of  analytical 

chemistry and MS, which seems promising at detecting food fraud (Black et al., 2016). 

Rapid  Evaporative  Ionization  Mass  Spectrometry  (REIMS)  is  one  of  the  most  recent 

forms of AMS and it was developed for medical research purposes. It operates using an 

electrosurgical  knife,  bipolar  forceps  or  laser,  thereby  generating  an  aerosol  (smoke) 

when  cutting  into  a  tissue  sample  (Black  et  al.,  2017).  Results  may  be  obtained  near-

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EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

15 

 
 
 
 
 
instantaneously (2–3 s) and the technique appears to yield semi-quantitative results for 

solid samples without requiring any form of sample preparation using a liquid solution. 

Precisely, a very recent study applied REIMS analysis to 478 samples of five different 

white fish species using an electrosurgical knife (Black et al., 2017). The identification 

of  99  validation  samples  provided  a  98.99  %  correct  classification,  being  species 

identification achieved near-instantaneously (≈ 2 s), thereby surpassing any other form 

of  food  fraud  analysis.  Additionally,  Black  et  al.  (2017)  have  shown  that  REIMS  can 

also be applied in differentiating between capture methods of fishery products. Hence, 

REIMS  seems  to  be  an  innovative  technique  to  help  in  the  detection  of  fish  fraud 

(Böhme et al., 2019), being further studies essential. Furthermore, another recent trend 

involves  the  miniaturization  of  the  mass  spectrometer  system  in  combination  with 

different  ambient  ionization  methods.  Indeed,  Gerbig  et  al.  (2017)  tested  for  food 

authentication —chemical fingerprinting of five fish species— three alternative ambient 

ionization  methods:  Electrospray  Ionization  (ESI),  Desorption  Electrospray  Ionization 

(DESI),  and  Low  Temperature  Plasma  ionization  (LTP).  These  authors  reported  a 

classification accuracy of 100 % in the differentiation of fish species. 

All  these  new  methodologies  show  the  large  potential  held  by  proteomics  and  are 

already  delivering  valuable  and  reliable  results.  Therefore,  proteomics  must  be 

considered  as  a serious alternative to  genomics  whenever ascertaining the authenticity 

of fish products is of paramount importance. 

Besides  proteomics,  metabolomics  and  lipidomics  are  two  promising  approaches  that 

could  enable  to  distinguish  between  different  fish  products.  Sometimes  there  is  some 

conceptual overlap between these two omics approaches. Hence, it should be remarked 

that metabolomics is the study of metabolomes, that is, small molecular end products of 

cellular regulatory pathways (Fiehn, 2002). It should be noted that metabolites are much 

smaller than proteins and smaller than most lipids. Though lipids may be classified as a 

subset  of  metabolites,  their  chemistry  is  quite  specific  and  they  must  be  treated 

separately,  for  instance,  requiring  different  solvents.  Therefore,  lipidomics  has 

developed  as  a  particular  and  independent  omics  field,  being  defined  as  the  systems-

level  analysis  of  lipids  and  their  interactions  (Smith  et  al.,  2014).  In  comparison  to 

genomics  and  proteomics,  lipidomics  is  still  in  its  infancy.  Nonetheless,  the  extreme 

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EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

16 

 
 
 
 
 
variety  of  lipid  structures  and  the  correlation  between  this  variety  and  taxonomical 

groupings  mean  that  lipidomics  holds  a  very  promising  potential.  Indeed,  lipids  are 

grouped  into  eight  categories  that  share  common  physical  and  chemical  properties 

(Fahy et al., 2009), being reported more than 38,000 lipid molecules. 

For  food  authenticity  and  fraud  detection,  metabolomics  and  lipidomics  have  been 

usually applied to matrices such as alcohol beverages (beer, wine, spirits), honey, olive 

oil, milk and cheese products, meat, spices, and juices (Cajka et al., 2016). Moreover, in 

comparison  to  proteomics,  only  a  few  metabolomics  or  lipidomics  studies  have  also 

focused on the analysis of large numbers of samples (>100) in order to achieve robust 

statistical  models.  This  means  that  there  is  still  a  huge  knowledge  gap  concerning 

lipidomics  (and  metabolomics)  and  fish  product  authenticity.  Though  it  is  known  that 

the particular lipid profile of a given fish species is very different depending on being 

wild  or  farmed,  much  more  detailed  knowledge  is  needed  to  make  lipidomics  a  valid 

alternative to genomics and proteomics. There is some seminal research work that aims 

to close these knowledge gaps. Namely, the phospholipid profile is increasingly studied 

for fish authenticity (Black et al., 2017) using multiple analytical methodologies, which 

comprise nuclear magnetic resonance (NMR) spectroscopy,  gas chromatography (GC) 

and liquid chromatography (LC) mass spectrometry. 

The  multidimensional  mass  spectrometry-based  short  gun  method  is  one  of  the  main 

analytical  platforms  in  current  lipidomic  studies.  Nonetheless,  the  experimental 

operation  of  such  methods  is  difficult,  laborious,  and  time  consuming.  A  more  recent 

advance  applies  REIMS  with  an  intrinsic  coupled  intelligent  knife  (iKnife).  This 

technology  is  based  on  the  production  of  gaseous  ions,  mostly  from  lipids  and,  in 

particular, from phospholipids. This has already been used in routine clinical trials and 

more recently has been extended to identify food authenticity because it offers real time 

analysis (Black et al., 2017). Recently, a method using the REIMS system with iKnife 

has  been  developed  and  optimized  to  discriminate  between  salmon  and  rainbow  trout 

(Song  et  al.,  2019).  This  efficient  method  promises  to  meet  a  pressing  demand,  since 

there  are  numerous  claims  that  in  China  rainbow  trout  is  often  labeled  as  salmon. 

REIMS  continues  to  be  investigated  and  developed,  given  its  potential  to  be  used  in 

other situations, for instance, in the distinction between line-caught and trawler-caught 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

17 

 
 
 
 
 
seafood.  Therefore,  lipidomics  application  to  fish  product  authenticity  testing  is  an 

underdeveloped field that, as such, requires further study and intensive investment in the 

application of novel analytical methodologies to particular groups of lipid molecules. 

The  current  state  of  affairs  is  characterized  by  a  clear  prominence  of  genomics  and 

proteomics  in  the  application  to  fish  product  authenticity,  since  it  is  buttressed  in 

statistically  robust  studies  comprising  large  number  of  species  and  products  and 

involving  challenging  situations  (taxonomically  closed  species  or  sampling  from 

products  with  substantial degree of processing).  Metabolomics and lipidomics hold  an 

unmistakable potential, but remain quite behind the other omics. 

2.1.3.3.  DNA-BASED SPECIES ASSIGNMENT 

DNA-based  methods  for  species  assignment  consist  on  identifying  variations  in  the 

DNA  sequences  that  are  unique  to  each  species.  These  variations  can  involve  base 

substitutions,  insertions  or  deletions  as  well  as  structural  variants  comprising 

rearrangements,  repetitions  or  insertion/deletions  of  larger  DNA  fragments  (Liu  and 

Cordes, 2004). These variations can be present in the mitochondrial or nuclear genomes 

and  affect  coding  or  non-coding  regions.  The  mitochondrial  genome  presents 

advantages with respect to the nuclear genome, such as being haploid, presenting high 

number of copies per cell, or having a high substitution rate  (Rehbein, 2013). Yet, for 

some  species,  mitochondrial  makers  are  not  suitable  because  of  the  presence  of  past 

introgression  events  from  close  relatives,  such  as  in  tunas  (Diaz-Arce  et  al.,  2016). 

Although insertion/deletions have been useful to distinguish among even closely related 

species  such  as  for  example  Mytilus  edulis,  M.  galloprovincialis,  and  M.  trossulus 

(Inoue  et  al.,  1995),  most  DNA-based  species  assignment  rely  on  nucleotide 

substitutions. 

Almost all DNA-based methods for species assignment rely on a previous amplification 

step  by  Polymerase  Chain  Reaction  (PCR)  to  increase  the  concentration  of  the  DNA 

fragment  that  contains  the  diagnostic  marker(s).  This  PCR  amplification  is  then 

combined  with  a  method  for  screening  the  amplified  diagnostic  markers,  so  that 

different possible techniques exist, the most common being: 

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EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

18 

 
 
 
 
 
 
 
i) 

Amplified Fragment  Length  Polymorphism (AFLP), whereby the amplified 

region  differ  between  target  species,  which  can  be  visualized  in  agarose  or 

acrylamide gel electrophoresis  (e.g. (Inoue et al., 1995)); 

ii) 

Restriction Fragment Length Polymorphism (RFLP), whereby the amplified 

product is digested with restriction enzymes to create DNA profiles that can 

then  be  visualized  in  agarose  or  acrylamide  gels  (e.g.  (Lin  and  Hwang, 

2007)); 

iii) 

Random  Amplified  Polymorphic  DNA  (RAPD),  whereby  the  DNA  is 

amplified using random primers to generate patterns of bands that can then 

visualized through electrophoresis (e.g. (Lakra et al., 2007)); 

iv) 

DNA  barcoding,  whereby  the  amplified  product  is  sequenced,  and  the 

obtained  nucleotide  string  is  compared  against  a  database  that  contains  the 

correspondence  between  species  and  DNA  sequences  (e.g.  (Lockley  and 

Bardsley, 2000)); 

v) 

Real-time  or  quantitative  PCR  (qPCR),  whereby  the  DNA  sequences  are 

amplified  and  quantified  simultaneously  by  measuring  the  fluorescence 

resulting  either  from  the  binding  of  a  binding  dye  to  the  double  stranded 

DNA  or  that  resulting  from  the  binding  of  the  reporter  probe  to  the  target 

DNA (e.g. (Lockley and Bardsley, 2000)); 

vi) 

High resolution melting (HRM), whereby the qPCR amplified DNA product 

is heated until the two strands of DNA separate, which will be sooner or later 

depending  on  the  sequence  and  which  can  be  monitored  by  the  loss  of 

florescence (e.g. (Jin et al., 2014); 

vii)  Microarrays,  whereby  many  fluorophore-labeled  oligonucleotide  probes 

specific  to  the  target  sequences  are  disposed  in  glass  microscope  slides, 

whose signal is measured for species detection (e.g. (Teletchea et al., 2008)). 

The selection of the method of choice will depend on several factors (Teletchea, 2009) 

such as: 

i) 

the prior knowledge of diagnostic markers for a given species: for some 

species,  standard  markers  such  as  the  cytochrome  oxidase  I  gene  are 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

19 

 
 
 
available  in  reference  databases  (eg.  most  tuna  species  (Viñas  and 

Tudela,  2009),  however,  for  others  less  studied  markers  need  to  be 

sequenced to determine their diagnostic capacity; 

ii) 

the  amount  of  samples  to  be  tested:  if  more  than  100  samples  will  be 

analyzed, qPCR or electrophoresis assays are preferred to sequencing as, 

although they require less processing time and result more cost effective 

the more samples are analyzed; 

iii) 

the  expected  presence  of  closely  related  species:  in  these  cases,  the 

genetic marker that unequivocally discriminates among species needs to 

be selected (e.g Armani et al., 2012); 

iv) 

the knowledge of potential intraspecific variation, in which case the use 

of  a  combination  of  different  markers  might  be  necessary  (Liu  et  al., 

2017); 

v) 

the expected DNA quality or quantity to be obtained from the sample. 

AFLP,  RFLP  and  RAPD  are  methods  considered  obsolete  for  the  purpose  of  species 

identification  as  they  rely  on  visual  inspection  of  electrophoretic  gels  and  a  prior 

knowledge of the expected patterns and are very sensitive to DNA degradation (Tabit, 

2016).  Among  the  above  cited  methods,  recently,  the  popular  one  is  DNA-barcoding, 

which relies on sequence variations within a short and standardized region of genome 

(barcode) that  can be amplified using species or group specific primers  (Hebert et  al., 

2003). The method has been used extensively for identification of seafood (Griffiths et 

al.,  2014), including processed products  (Pardo et  al.,  2018).  In  general,  markers used 

for  barcoding  fish  species  are  based  on  mitochondrial  genes  (Cytochrome  oxidase  I  – 

COI,  Cytochrome  b  –  cytb  or  12S  ribosomal RNA  –  12S  rRNA)  which  are  amplified 

using universal primers. DNA barcoding has the advantage of not requiring developing 

species-specific assays and allowing detection of intraspecific variability. This method 

is  particularly  interesting  if  no  prior  knowledge  of  the  target  species.  However,  if  the 

main purpose is to detect if the product belongs to one or two species, the most efficient 

assay are the qPCR and the HRM. Although these methods require a prior investment of 

time in developing the assay and purchasing species specific probes, they become cost-

effective if a large number of samples needs to be assessed. As opposed to sequencing, 

which  requires  a  few  days  before  the  result  can  be  available,  qPCR  and  HRM  results 

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EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

20 

 
 
 
 
can be obtained within hours. Additionally, both methods rely on a short DNA fragment 

and  are  thus  less  sensitive  to  DNA  degradation.  Concerning  microarrays,  these  are 

suitable when several species (hundreds) need to be detected at the same time, which is 

unlikely  in  the  case  of  food  authentication.  Comapred  to  barcoding  and  qPCR/HRM 

methods, microarrays are more sensitive to contamination (Tabit 2016). 

2.1.3.4.  ONGOING STUDIES AND RESEARCH PROJECTS 

DNA-based  analyses  are  currently  being  used  for  food  authenticity  and,  in  particular, 

for fish traceability. Analyses based on DNA barcoding, qPCR and HRM are applied at 

different  steps  of  the  process,  from  vessels,  ports,  markets  (Mariani  et  al.,  2015) 

supermarkets  (Harris  et  al.,  2016)  to  restaurants  (Pardo  et  al.,  2018)  worldwide  in 

support  of  fishing  traceability  and  compliance.  Among  the  projects  that  are  currently 

developing/using DNA technologies for fish traceability are: 

FOODINTEGRITY: https://secure.fera.defra.gov.uk/foodintegrity/ 

LABELFISH: http://www.labelfish.eu/ 

SEATRACES: https://www.seatraces.eu/publications/ 

2.1.3.5.  EMERGING TECHNOLOGIES 

Although  DNA  barcoding  and  qPCR  are  the  most  commonly  used  methods  for 

assigning fish product to species, there are new methodologies that are currently being 

developed and that could become a game-changer in the future: 

-  Portable  high-throughput  sequencing  devices  (e.g.  Oxford  Nanopore  Minion), 

which allow the on-site sequencing of DNA for a quick response; 

o  Advantages:  Small  and  portable;  relatively  inexpensive  (two  orders  of 

magnitude cheaper than a bench sequencer) 

o  Disadvantages: Requires good quality DNA: high error rate 

-  Loop-mediated  isothermal  amplification  (LAMP),  a  method  that  achieves 

amplification of the target sequences without the need of a thermocycler and in 

less than 90 min (Notomi et al., 2015); 

o  Advantages: Rapid, portable; almost no equipment required 

o  Disadvantages:  Still 

incipient  and  developments  needed;  requires 

optimization for each species; can be unspecific  

-  Microfluidics based high-throughput DNA barcoding (Jiang et al., 2016). 

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EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

21 

 
 
 
 
 
o  Rapid; can detect > 20 species simultaneously 

o  Requires costly assay optimization; species detectability is compromised 

by DNA quality 

2.1.3.6.  CHALLENGES AND MITIGATION 

Using  DNA  techniques  for  species  identification  has  inherent  challenges  that  are 

impossible  or  very  difficult 

to  overcome  even  with  advanced 

technological 

developments: 

i) 

It does not allow to determine age of the specimen, meaning that it does not 

allow controlling for catches of young specimens for example; 

ii) 

It  does  not  allow  detecting  origin  of  the  catch  if  no  genetic  differentiation 

among locations exist. 

There are other challenges associated to DNA barcoding that can be mitigated: 

-  Database completeness: for DNA-barcoding to be useful, the DNA sequence of 

the  target  species  should  be  available  in  the  database;  currently,  the  Genbank 

database (https://www.ncbi.nlm.nih.gov/genbank/) is where DNA sequences are 

stored;  however,  there  are  databases  specific  for  some  markers  that  have  been 

curated  by  experts  such  as  BOLD  (http://www.boldsystems.org/)  or  (SILVA 

https://www.arb-silva.de/) which are preferred for barcoding studies; 

-  Universal  primers  used  for  fragment  amplification  are  not  equally  efficient  for 

all species; 

- 

- 

- 

- 

Intraspecific variability might induce errors in the species identification if these 

variants are not known; 

If DNA is too degraded, even short barcodes can be difficult to amplify; 

If contamination have occurred, false positives can be derived; 

If the product is mixed, only the most predominant one will be detected; 

-  Lastly,  this  document  will  identify  potential  practical  problems  directly  related 

to  the  process  of  collecting  and  transporting  the  samples  that  could  undermine 

the  DNA  analysis  and  concomitantly  propose  some  relevant  respective 

mitigation measures; 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

22 

 
 
 
 
 
 
- 

If there are hybrids or species with introgressed DNA in their genomes, species 

identification might fail. 

2.1.3.7. 

FUTURE PERSPECTIVES 

Genomics,  proteomics,  metabolomics,  and  lipidomics  are  research  fields  which  have 

developed tremendously in the last decades, bringing forth new knowledge insights as 

well as various practical applications. The increasing importance of the omics research 

and analysis is buttressed in the increasing sophistication of a large group of analytical 

techniques.  In  spite  of  the  impressive  developments,  there  are  still  large  challenges, 

especially in the achievement of effective and reliable applications. 

Namely, it should be stressed that most of the data generated over the past 25 years by 

the various omics platforms have been qualitative or semi-quantitative in nature. While 

qualitative data can be used to compare similar variables across samples within a single 

lab,  they  do  not  support  comparisons  across  labs  or  across  platforms.  Likewise, 

qualitative measurements do not allow for consistent and accurate integration of multi-

omics data where measurements typically have to be done on multiple platforms, across 

multiple  laboratories,  over  extended  time  periods  (Pinu  et  al.,  2019).  Achieving  fully 

quantified omics data allows much more accurate comparison to reference values, more 

consistent  inter-laboratory  comparisons,  greater reliability, and a more straightforward 

integration of data (Pinu et al., 2019). Moreover, the combination of the various omics 

and  their  data  resources  is  a  challenge  that  could  bring  large  advances  in  the  future. 

Instead of relying on a single field (for instance, proteomics), all omics could be applied 

and  the  generated  data  integrated  in  order  to  minimize  uncertainty  and  enhance 

reliability,  especially  in  the  field  of  food  authenticity.  Of  course,  this  requires  the 

application of overarching bio-informatic algorithms based on applied mathematics and 

computer science (Smith et al., 2014). 

It must also be pointed out that there can be issues and caveats that are specific to each 

of the omics fields, such as the measurement issues associated with molecular and mass 

spectrometry analysis of food matrices (Burns et al., 2016). In particular, food products 

present  themselves  as  complex physical  and biochemical  matrices, the  composition  of 

which can be strongly dependant on a variety of environmental factors such as climate, 

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EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

23 

 
 
 
 
 
 
seasonality, and storage conditions. This reality represents a permanent challenge to the 

detection  of  food  fraud.  For  the  future  perspectives  of  the  omics  application  to  food 

authenticity  testing,  the  creation  and  development  of  MS/NMR/other  techniques 

databases  of  authentic  food  samples  can  be  useful  for  routine  verification  of 

authenticity. Another important point will be the development of widely shared standard 

protocols  for  MS/NMR/other  techniques  metabolite  profiling  of  specific  foodstuffs 

(Sobolev et al., 2017). 

As conclusion, it must be mentioned that the particular omics approaches hold a great 

deal of promise for the detection of food authenticity and integrity, especially so when 

using  an  integrated  omics  approach  (in  tandem  with  future  technological  and 

computational advances). Large benefits could also be accrued from the knowledge and 

expertise  from  a  wide  range  of  sources,  thereby  leading  to  valuable  new  insights  and 

applications,  which,  in  turn,  may  induce  further  technological  leaps.  These  advances 

may  lead  to  beneficial  outcomes  for  an  equally  wide-range  of  areas  with  complex 

intrinsic and extrinsic links to global food systems (Ellis et al., 2016). 

2.2 TASK 2 – MANUAL OF PROCEDURES 

2.2.1.  OBJECTIVES 

The  core  objective  was  to  prepare  an  International  Manual  of  Procedures  (IMP)  to  be 

used  in  the  NAFO  RA  to  guide  the  collection  of  samples  from  fisheries  products  for 

genetic analysis. This  main  goal  was more specifically  threefold leading to  three Sub-

Tasks:  (i)  To  analyse  and  retrieve  valuable  elements  of  the  Portuguese  Manual  of 

Procedures;  (ii)  To  prepare  a  descriptive  analysis  of  the  fishing  fleets;  and  (iii)  To 

elaborate the IMP on the basis of the results of the previous Sub-Tasks results. 

2.2.2.  METHODOLOGY 

This was also mainly a desk-based Task, but differently from the previous one, drawing 

from practical and empirical knowledge of the reality of the fishing fleets operating in 

the  NAFO  RA  and  of  the  template  provided  by  a  Portuguese  Manual  of  Procedures, 

which  already  structured  and  organized  all  the  measures  and  steps  for  a  successful 

sampling  of  fish  products  for  genetic  analysis.  More  specifically,  the  outcome  was 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

24 

 
 
 
 
 
 
based  on  the  collection  of  knowledge  and  experience  during  meetings  with  experts. 

These  were  considered  experts  due  to  their  practical  experience  on  fishing  fleets 

operating  in  the  NAFO  RA  and  on  using  the  template  provided  by  the  Portuguese 

Manual  of  Procedures.  Moreover,  an  additional  effort  of  literature  revision  —yielding 

the  figures  in  the  NAFO  fleet  section  and  based  on  the  NAFO  SC  reports  as  well  as 

others  papers,  which  have  been  added  to  the  reference  list—  and  of  networking  with 

experts  within  the  organization  of  the  Consortium  Partners  enabled  to  deepen  and 

mature the future IMP, ensuring a high level of quality and realistic approach to every 

detail. 

2.2.3.  RESULTS 

2.2.3.1. 

SUB-TASK 2.1 - ANALYSIS OF THE PORTUGUESE MANUAL OF PROCEDURES 

This  Sub-Task  is  divided  in  the  translation  and  adaptation  of  the  current  Portuguese 

Manual of Procedures and in the critical revision of the document with the purpose to 

improve it and make it a truly valuable contribution for the elaboration of the IMP. 

2.2.3.1.1.  TRANSLATED AND REVISED PORTUGUESE MANUAL OF PROCEDURES 

The  Portuguese  Manual  of  Procedures  previously  prepared  by  the  Portuguese 

governmental  department,  DGRM  (Direção-Geral  de  Recursos  Naturais,  Segurança  e 

Serviços  Marítimos  –  General  Division  for  the  Natural  Resources,  Security,  and 

Maritime  Services)  was  duly  translated  to  English  taking  into  account  the  specific 

nomenclature  of  the  discussed  subjects  and  the  need  to  adapt  to  a  slightly  differing 

reality of an international nature. 

This manual was structured along the following main themes: 

- 

- 

- 

- 

I - Introduction and Objectives; 

II - Definitions; 

III - Types of Sample; 

IV - Kit for the Collection of Samples; 

-  V - Procedures for Sampling, Collection, Registration, Transport, and Delivery; 

-  VI - Costs; 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

25 

 
 
 
 
 
 
 
-  VII - Forms; 

-  VIII - Certification of the Fishery Inspectors; 

- 

IX – Versions; 

-  X – Legal References; 

-  XI – Annexes. 

The Portuguese Manual of Procedures, after translation to English, was restructured and 

revised with the final purpose of constituting a valuable contribution to the IMP. 

2.2.3.1.2.  CRITICAL APPRAISAL OF THE PORTUGUESE MANUAL OF PROCEDURES 

The translated Portuguese Manual of procedures was considered a starting point for the 

elaboration  of  the  IMP.  This  had  to  do  with  its  specific  scope  and  novelty  in  the 

Portuguese framework. Indeed, such novelty and absence of previous work entailed that 

many  practice-related  issues  were  not  incorporated  in  the  build  up  of  the  Portuguese 

Manual  of  Procedures.  These  manuals  are  always  improvable  with  the  progressive 

trickle down of field experiences in direct contact with the fishers and fleets. The reality 

forces new adaptations of the manuals and also presents new problems —that were not 

initially  foreseen—  that  lack  solutions,  thereby  leading  to  novel  approaches  and 

modifications of parts or even of whole procedures. 

Among those problems, it should be mentioned: 

-  Adequate random sampling of different lots; 

-  Appropriate sampling dimension for any given lot; 

-  Proper 

training 

in  handling  samples,  especially  avoiding  any  cross-

contamination. 

Hence, all required changes resulted from the intersection of the research of the newest 

technical  reports  and  scientific  studies  with  the  empirical  experience  made  by  the 

Portuguese  inspectors  in  the  application  of  the  Portuguese  Manual  of  Procedures 

(sampled  through  interviews  with  2  Portuguese  inspectors  with  a  large  experience, 

including  in  the  application  of  the  Portuguese  Manual  of  Procedures),  which,  in  turn, 

generated field notes that were collated in internal reports to the competent Portuguese 

Authority  in  the  field  (Direção-Geral  de  Recursos  Naturais,  Segurança  e  Serviços 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

26 

 
 
 
 
 
 
 
Marítimos  –  General  Division  for  the  Natural  Resources,  Security,  and  Maritime 

Services). Whenever a procedure was revealed as empirically inviable, alternative (more 

viable) solutions were put forward on the basis of the most recent literature. 

The  issues  previously  mentioned  led  to  the  importance  of  the  conduction  of  a  critical 

appraisal  of  the  Portuguese  Manual  of  Procedures,  taking  into  account  some  gathered 

information of the application of the Manual to the reality of Portuguese fisheries. There 

are  also  doubtful  issues,  such  as  the  number  of  samples  of  the  lot  to  collect  and  its 

relation to the quantity range of the fishery products’ lot. 

These issues were until the date of delivery of the Draft Final Report debated and some 

solutions were achieved. Namely, a formula for the estimation of the sample dimension 

was  proposed  and  incorporated  in  the  International  Manual  of  Procedures,  thereby 

replacing the Table that correlated sample dimension with the tonnage of the fish lots. 

There were also adaptations of the Manual of Procedures that were specifically done to 

meet  the  kind  of  fisheries  of  the  particular  NAFO  RA,  thus  incorporating  all  the 

information conveyed by the Descriptive Analysis of Fishing Fleets, which is discussed 

below.  Finally,  a  section  comprising  treatment  of  the  samples  and  DNA  analysis 

procedures  was  included  in  order  to  cover  also  aspects  that  are  relevant  for  all 

professionals involved in the fish species identification activity. 

2.2.3.2. 

SUB-TASK  2.2  -  PREPARATION  OF  DESCRIPTIVE  ANALYSIS  OF  FISHING 
FLEETS 

The  Sub-Task  2.2  encompasses  a  detailed  and  thorough  analysis  of  the  fishing  fleets 

operating in the NAFO RA. This will be a major contribution to the preparation of the 

IMP,  since  this  document  will  deliver  the  knowledge  of  the  reality  that  exists  in  the 

sector and in the particular geographical area that are the addressees of the IMP. Indeed, 

this descriptive analysis will guide in the adaptation of general principles to the practical 

realities found in the fishing fleets. 

2.2.3.2.1.  STATUS OF THE SUB-TASK 2.2 

This  subsection  shows  the  progress  achieved  on  the  review  of  the  literature  regarding 

between others, fishing fleets operating in the NAFO RA, type of fishing gear, catches - 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

27 

 
 
 
 
 
 
 
volumes  of  fishing  products  by  species,  legislations  about  as  stowage  plans,  type  of 

processing presentation. Identification of relevant factors to take into account in each of 

those  for  the  designing  of  specific  sampling  schemas  and  other  specific  necessary 

adaptations to each type of fleet. 

1 – Introduction to NAFO; 

2 – NAFO Conservation and Enforcement Measures; 

3  – NAFO Fleets/Fisheries; 

4  Literature. 

This task has been completed, thereby reaching a highly detailed and refined level in the 

description and distribution of species. Furthermore, rules regarding the stowage plans 

have  been  researched  and  included  below.  On  the  other  hand,  it  must  be  emphasized 

that directed fishing at the level of each national fleet/boat is difficult to track and fully 

monitor, being especially prone to changes over time (depending on national quotas). 

2.2.3.2.2.  INTRODUCTION TO NAFO 

NAFO is an intergovernmental fisheries science and management body, to ensure long 

term conservation and sustainable use of the fishery resources in the Convention Area 

and,  in  so  doing,  to  safeguard  the  marine  ecosystems  in  which  these  resources  are 

found. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

28 

 
 
 
 
 
 
Figure  1.  NAFO  Convention  Area  and  NAFO  Regulatory  Area  maps.  ©Northwest 

Atlantic Fisheries Organization (NAFO website: www.nafo.int). 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

29 

 
 
 
     
 
 
Currently NAFO Contracting Parties are: Canada; Cuba; Denmark (in respect of Faroe 

Islands and Greenland - DFG); European Union (EU); France (in respect of St. Pierre et 

Miquelon);  Iceland;  Japan;  Norway;  Republic  of  Korea;  Russian  Federation;  Ukraine 

and United States of America. 

Table 3. Stocks managed by NAFO. 

Fisheries on: 

Species 

Scientific name 

Stock 

Management 

Cod 

Gadus morhua 

Divs. 2J3KL 

Divs. 3NO 

Redfish 

S. mentella; 

Divs. 3LN 

S. fasciatus; 

Div. 3O 

TAC 

TAC 

TAC 

TAC 

American 

Hippoglossoides 

plaice 

platessoides 

Yellowtail 

Limanda 

flounder 

ferruginea 

Divs. 3LNO 

TAC 

Divs. 3LNO 

TAC 

Grand Bank 

Witch flounder 

Glyptocephalus 

Divs. 2J3KL 

cynoglossus 

Divs. 3NO 

TAC 

TAC 

White hake 

Thorny skate 

Capelin 

Shrimp 

Urophycis 

tenuis 

Amblyraja 

radiata 

Mallotus 

villosus 

Pandalus 

borealis 

Divs. 3NOPs 

TAC 

Divs. 3NOPs 

TAC 

Divs. 3NO 

TAC 

Divs. 3LNO 

TAC 

Cod 

Gadus morhua 

Div. 3M 

TAC 

S. mentella; 

Redfish 

S. fasciatus; 

Div. 3M 

TAC 

Flemish Cap 

S. norvegicus 

American 

Hippoglossoides 

plaice 

Shrimp 

platessoides 

Div. 3M 

TAC 

Pandalus 

Div. 3M 

Effort 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

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of samples from fisheries products for genetic analysis" 

30 

 
 
 
 
borealis 

Greenland 

Reinhardtius 

SA  2  +  Divs. 

hippoglossoides 

3KLMNO 

TAC 

S. mentella 

SA  2  +  Divs. 

TAC 

by 

1F+3K 

NEAFC 

Beryx splendens  SA 6 

TAC & Effort 

Widely 

distributed 

stocks 

halibut 

Pelagic 

Redfish 

Splendid 

alfonsino 

Short-finned 

Illex 

Squid 

illecebrosus 

SA 3+4 

TAC 

2.2.3.2.3.  NAFO CONSERVATION AND ENFORCEMENT MEASURES (NAFO, 2019A) 

The  NAFO  Conservation  and  Enforcement  Measures  (NAFO  CEM)  incorporate  all 

NAFO measures  presently in  force  as adopted by  the Commission  in  accordance with 

provisions of Articles VI and XIV of the Convention on Cooperation in the Northwest 

Atlantic  Fisheries.  Every  year  the  NAFO  CEM  is  revised  by  the  Commission.  The 

document  incorporates  amendments  which  were  adopted  at  the  most  recent  NAFO 

Annual Meeting in September (NAFO website). 

Some measures are relevant for this contract, such as: 

Total Allowable Catches (TAC) for each stock in 2020 (NAFO, 2019e) as an example 

of the level of catches of the managed species/stocks, these TACs can change each year. 

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31 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Table 4. 2020 annual quota values (NAFO, 2019e). 

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Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

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33 

 
 
 
  
Mesh Sizes: No vessel shall fish with a net having a mesh size smaller than prescribed 

for each of the following species (NAFO, 2019a): 

(a) 40 mm for shrimps and prawns (PRA); 

(b) 60 mm for short finned squid (SQI); 

(c) 280 mm in the codend and 220 mm in all other parts of the trawl for skate (SKA); 

(d) 130 mm for all other groundfish, as defined in Annex I.C.; 

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34 

 
 
 
 
 
(e) 100 mm for pelagic Sebastes mentella (REB) in Subarea 2 and Divisions 1F and 3K; 

and 

(f) 90 mm for redfish (RED) in the fishery using mid-water trawls in Division 3O, 3M 

and 3LN. Within this fishery mid-water trawl means trawl gear that is designed to fish 

for pelagic species, no portion of which is designed to be or is operated in contact with 

the  bottom  at  any  time.  The  gear  shall  not  include  discs,  bobbins  or  rollers  on  its 

footrope or any other attachments designed to make contact with the bottom. The trawl 

may have chafing gear attached. 

Article 27 - Product Labelling Requirements (NAFO, 2019a) 

When  processed,  all  species  harvested  in  the  RA  shall  be  labelled  in  such  a  way  that 

each  species  and  product  category  is  identifiable.  All  species  must  be  labelled  using 

respectively the following data: 

(a) the name of the capture vessel; 

(b) the 3-Alpha Code for each species as listed in Annex I.C; 

(c) in the case of shrimps the date of capture; 

(d) the Regulatory Area and Division of fishing; and 

(e) the product form presentation code as listed in Annex II.K. 

Labels shall be securely affixed, stamped or written on packaging at the time of stowage 

and be of a size that can be read by inspectors in the normal course of their duties. 

Labels shall be marked in ink on a contrasting background. 

Each package shall contain only: 

(a) one product form category; 

(b) one division of capture; 

(c) one date of capture (in the case of shrimps); and 

(d) one species. 

Table 5. Product form presentation for each 3-Alpha Codes (Annex II.K). 

3-Alpha 

Presentation 

Description 

Code 

CBF 

CLA 

Cod butterfly (“escalado”)  HEA with skin on, spine on, tail on 

Claws 

Claws only 

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35 

 
 
 
 
 
 
DWT 

FIL 

ICCAT code 

Filleted 

Gilled, gutted, part of head off, fins off 

HEA + GUT + TLD + bones off Each fish 

originates two fillets not joined by any part 

FIS 

Filleted and skinned fillets  FIL+SKI    Each  fish  originates  two  fillets 

FSB 

Filleted  with  skin  and 

Filleted with skin and bones on 

not joined by any part 

bones 

FSP 

Filleted 

skinned  with 

Filleted with skin removed and pinbone on 

GHT 

GUG 

GUH 

GUL 

GUS 

GUT 

HEA 

HET 

JAP 

JAT 

LAP 

LVR 

OTH 

ROE 

SAD 

SAL 

SGH 

SGT 

SKI 

SUR 

TAL 

pinbone on 

Gutted headed and tailed 

GUH+TLD 

Gutted and gilled 

Guts and gills removed 

Gutted and headed 

Guts and head removed 

Gutted liver in 

GUT without removing liver parts 

Gutted headed and skinned  GUH+SKI 

Gutted 

Headed 

All guts removed 

Heads off 

Headed and tailed 

Heads and tails off 

Japanese cut 

Transversal  cut  removing  all  parts  from 

Tailed Japanese cut 

Japanese cut with tail removed 

head to belly 

Lappen 

Liver 

Other 

Roe (s) 

Double fillet, HEA, skin + tails + fins ON 

Liver only 

Any other presentation 

Roe(s) only 

Salted dry 

Headed with skin on, spine on, tail on and 

salted dry 

Salted wet light 

CBF + salted 

Salted, gutted and headed  GUH + salted 

Salted gutted 

GUT + salted 

Skinned 

Surimi 

Tail 

Skin off 

Surimi 

Tails only 

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36 

 
 
 
TLD 

TNG 

TUB 

WHL 

WNG 

Tailed 

Tongue 

Tube only 

Whole 

Wings 

Tail off 

Tongue only 

Tube only (Squid) 

No processing 

Wings only 

Article 28 – Monitoring of Catch (NAFO, 2019a) 

Recording of Catch and Stowage: For the purposes of monitoring catch, each fishing 

vessel  shall  utilize  a  fishing  logbook,  a  production  logbook  and  a  stowage  plan  as 

defined below, to record fishing activities in the RA: 

Fishing Logbook: Each fishing vessel shall maintain a fishing logbook consistent with 

Annex II.A that: 

(a) accurately records catch of each tow/set related to the smallest geographical area for 

which a quota has been allocated; 

(b) indicates the disposition of the catch of each tow/set, including the amount (in kg, 

live weight) of each stock that is retained on board, discarded, offloaded, or transhipped 

during the current fishing trip; and 

(c) is retained on board for at least 12 months. 

Production Logbook: Each fishing vessel shall maintain a production logbook that: 

(a) accurately records the daily cumulative production for each species and product type 

in kg for the preceding day from 00:01 UTC until 24:00 UTC; 

(b) relates the production of each species and product type to the smallest geographical 

area for which a quota has been allocated; 

(c) lists the conversion factors used to convert production weight of each product type 

into live weight when recorded in the fishing logbook; 

(d) labels each entry in accordance with Article 27; and 

(e) is retained on board for at least 12 months. 

Stowage  of  Catch:  Each  vessel  shall,  with  due  regard  for  safety  and  navigational 

responsibilities of the master, stow all catch taken in the NAFO RA separately from all 

catch  taken  outside  the  NAFO  RA,  and  ensure  that  such  separation  is  clearly 

demarcated using plastic, plywood or netting; 

Each fishing vessel shall maintain a stowage plan that: 

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37 

 
 
 
 
 
(a) clearly shows: 

(i) the location and quantity, expressed as product weight in kg, of each species within 

each fish hold; 

(ii)  the  location  in  each  hold  of  shrimp  taken  in  Division  3L  and  in  Division  3M  that 

includes the quantity of shrimp in kg, by Division; 

(iii) the top view of product within each fish hold; 

(b) is updated daily for the preceding day from 00:01 to 24:00 UTC; and 

(c)  is  retained  on  board  for  each  day  fished  until  the  vessel  has  been  unloaded 

completely. 

In this context, it is worth mentioning that there is a potential problem because the level 

of  reporting  catches  is  not  at  the  level  of  the  Product  Labelling  Requirements  or  the 

stowage plan. 

2.2.3.2.4.  NAFO FLEETS/FISHERIES 

The term fleet can be interpreted in different ways: a set of vessels of the same tonnage; 

a set of vessels using the same gear; set of vessels owned by the same flag State; set of 

vessels directed to the same species and others combinations. 

The term fishery can be associated with the gear used, depth, the target species, etc. 

Fisheries  in  the  NAFO  RA/Fishing  effort  by  gear  type  (NAFO,  2018a:  STATIC 

Report) 

NAFO  traditionally  identifies  three  main  fisheries  in  its  RA:  the  groundfish  (GRO  - 

primarily in Div. 3LMNO), shrimp (PRA - primarily in Div. 3LM) and pelagic redfish 

fisheries  (REB  -  primarily  in  Div.  1F  and  2J).  The  PRA  and  the  REB  fisheries  have 

been under moratoria. In 2017, fisheries in the NAFO RA were limited to GRO. There 

were  112  trips  by  45  fishing  vessels  spending  a  total  of  3,872  days  in  the  NAFO  RA 

(Table 6). Additionally, a single vessel (class size 5) spent 14 days, as part of its fishing 

trip,  in  Division  6G  catching  alfonsinos.  According  to  the  observer  report,  the  fishing 

gear used was a mid-water trawl. 

Smaller vessels (<500 GT) tend to  fish in Divisions 3NO using mainly longlines. The 

vast majority of the effort comes from larger vessels (> 500 GT) which account for 96 

%  of  fishing  effort  in  terms  of  days.  The  larger  vessels  use  bottom  trawl  and  fish  in 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

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of samples from fisheries products for genetic analysis" 

38 

 
 
 
 
 
 
Divisions 3LMNO. The major species caught by the bottom trawlers are cod, Greenland 

halibut, redfish, and thorny skate (Table 6). 

Table 6. Fishing effort in the NAFO RA for trips that ended in 2017. 

Vessel 

# 

of 

# 

of 

Main 

f = Days 

Fishing 

Main 

Fishing Area 

Class 

fishing 

fishing 

Gear 

present 

Trip 

Species 

vessels 

trips 

in 

the 

Range 

NRA 

(days) 

Class  3-4 

7 

17 

Longline  205 

vessels 

(less than 

500 mt) 

Class  5 

10 

31 

Bottom 

1051 

Trawl 

vessels 

(500-

1000 

MT) 

1-18 

days 

Cod, 

Flemish  Cap 

Yellowtail 

(for  cod);  Tail 

flounder 

of  the  Grand 

Banks 

(for 

yellowtail 

flounder) 

9-71 

days 

Cod, 

Flemish  Cap; 

Greenland 

Tail  and  Nose 

halibut, 

of  the  Grand 

redfish, 

Banks 

skates 

Class  6 

26 

60 

Bottom 

2435 

2-100 

Cod, 

Flemish  Cap; 

vessels 

(1000-

2000 

MT) 

Trawl 

days 

Greenland 

Tail  and  Nose 

halibut, 

of  the  Grand 

redfish, 

Banks 

skates 

Class  7 

2 

4 

Bottom 

181 

28-57 

Cod, 

Flemish  Cap; 

vessels 

(>  2000 

MT) 

Trawl 

days 

Greenland 

Tail  and  Nose 

halibut, 

of  the  Grand 

redfish, 

Banks 

skates 

Total 

45 

112 

3,872 

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39 

 
 
 
 
 
 
 
 
 
 
Fisheries  in  the  NAFO  RA/Effort  Distribution  by  depth  of  GRO  vessel  (NAFO, 

2018a: STATIC Report) 

The requirement of providing the speed and course information in the position reports 

of  Vessel  Monitoring  System  (VMS)  is  satisfied.  Hourly  positions  are  required  to  be 

transmitted. Speeds between 0.5 and 5 knots were assumed to be fishing speeds in this 

analysis.  In  Figure  2,  the  distribution  of  fishing  effort  in  hours  of  GRO  vessels  is 

presented. It shows that about half of all GRO effort is at depths 400 meters and below 

(skates, redfish and cod). Figure 2 also shows a concentration of fishing effort around 

1000 meters and this can be attributed to the Greenland halibut fishery. 

Figure  2.  Distribution  of  fishing  effort  (in  hours)  by  depth  (m)  in  the  NAFO  RA  in 

2017. Vessels are assumed to be fishing at speed in the range of 0.5-5.0 kt. 

Fisheries in the NAFO RA/Catch totals (NAFO, 2018a: STATIC Report) 

In  2017,  a  grand  total  of  59,533  t  of  fish  (58,141  t  retained  +  1,392  t  rejected)  were 

caught by NAFO-registered vessels (as reported in the daily CATs) authorized to fish in 

the  RA  (Tables  7  and  8).  In  terms  of  quantities  caught,  the  stocks  3M  Cod,  3LMNO 

Greenland  halibut,  3M  Redfish,  3LN  Redfish,  3O  Redfish,  3LNO  Yellowtail  flounder 

and 3NO Skates constitute the major GRO fishery in the NAFO RA. 

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40 

 
 
 
 
 
 
 
 
 
 
Table 7. Total reported retained catches (in tonnes) of species (in FAO 3-alpha code) by 

Division for trips that ended in 2017 (Source: CA field of CAT Reports). 

Table 8. Total reported rejected catches (in tonnes) of species (in FAO 3-alpha code) by 

Division for trips that ended in 2017 (Source: RJ field of CAT Reports). 

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41 

 
 
 
 
 
 
 
 
 
Main  Commercial  Species 

in  NAFO  Regulatory  Area  (NRA):  Description; 

distribution and fishery 

Cod (Gadus morhua) 

Description 

The Atlantic cod (Gadus morhua) is one of 59 species of the family gadidae. The cod 

family  is  the  most  numerous  and  best  represented  of  fishes  in  the  Canadian  area.  A 

marine fish which occurs mainly in cool waters in northern seas, the cod is soft-rayed, 

has three dorsal fins on its back and two anal fins behind its whitish-coloured belly, and 

generally has an elongated hair-like projection called a barbel on its chin (Figure 3). It is 

generally grey or green but may be brown or reddish, depending upon the habitat into 

which  its  colour  will  generally  blend.  The  scales  are  small  and  smooth.  The  mouth  is 

large with a projecting upper jaw and the gill openings are wide. The lateral line of the 

cod is pale, and the tail is slightly concave, almost square. Generally, cod average 2 to 3 

kg in  weight  and about  60 to  70 cm  in length.  They usually do not  exceed 30 kg, but 

there is one record of a cod that weighed about 96 kg and was more than 180 cm long 

(Lear, 1993). 

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42 

 
 
 
 
 
 
Figure 3. Illustration representing cod (Gadus morhua). 

Distribution 

Figure 4. Geographical distribution of cod (Gadus morhua) (Lear, 1993). 

Similar  species  in  NAFO:  Hakes  (Urophycis  spp.),  cod,  haddock  (Melanogrammus 

aeglefinus), Pollock (Pollachius virens) and others round fishes. 

Most common product presentation: CBF (cod butterfly - escalado), GUG  (Guts 

and 

gills removed), GUT (All guts removed), GUH (Guts and head removed), SAL (CBF + 

salted), SGH (GUH + salted), SGT (GUT + salted) and all kind of fillets. 

Fishery 

Both stocks, Divs. 2J3KL; Div. 3NO, are under moratoria since the first half of the 90s. 

In  the  NAFO  RA,  the  catches  are  bycatches  of  others  directed  fisheries  (primarily 

caught in the redfish, yellowtail flounder and skate fisheries - NAFO Website). Canada 

by  other  hand  has  a  sentinel  fishery  and  a  stewardship  fishery,  on  the  stock  Divs. 

2J3KL, inside of its exclusive economic zone (EEZ). 

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Divisions 3NO 

A moratorium was implemented in 1994. Catches since that time are by-catch in other 

fisheries. 

Last  assessment  June  2018  (NAFO,  2018b)  -  Stock  status:  The  spawning  biomass 

increased  noticeably  between  2010  and  2015  but  has  subsequently  declined  and  the 

2018 estimate of 18,537 t represents only 31% of Blim (60,000 t). The 2006 year class 

remains  relatively  strong  and  at  age  12  in  2018  makes  up  more  than  half  of  the 

estimated SSB. Subsequent year classes are much weaker, suggesting that the medium-

term prospects for the stock are not good. Fishing mortality values over the past decade 

have been low and well below Flim (0.3). 

Figure  5.  3NO  Cod:  Catches  and  TACs;  Biomass;  Fishing  mortality  and  Recruitment 

(NAFO, 2018b). 

Division 3M 

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44 

 
 
 
 
 
 
 
 
The  cod  fishery  on  the  Flemish  Cap  has  traditionally  been  a  directed  fishery  by 

Portuguese  trawlers  and  gillnetters,  Spanish  pair-trawlers  and  Faroese  longliners.  Cod 

has  also  been  taken  as  bycatch  in  the  directed  redfish  fishery  by  Portuguese  trawlers. 

Estimated bycatch in shrimp fisheries is low. Large numbers of small fish were caught 

by  the  trawl  fishery  in  the  past,  particularly  during  1992-1994.  Total  annual  catches 

from 1996 to 2010 were very small compared with previous years. From the reopening 

of the fishery in 2010, catches increased until 2013 to the TAC value, and remained at 

this level since (NAFO, 2019b). In recent years eight countries fished cod in Div. 3M, 

trawlers  from  EU-Estonia,  EU-Portugal,  EU-Spain,  Japan,  Norway  and  Russia  and 

longliners from Norway, Faroe Islands and USA. 

The Div. 3M stock is open and the TAC is set at 8,531 tonnes for 2020. 

Last assessment June 2019 (NAFO, 2019b) - Stock status: Current SSB is estimated to 

be well above Blim (15,177 t) although it is expected to decline rapidly in the near future 

due  to  poor  recruitment  since  2015.  F  increased  in  2010  with  the  re-opening  of  the 

fishery but it has remained below Flim (0.167). 

Figure  6.  3M  Cod:  Catches  and  TACs;  Biomass;  Fishing  mortality  and  Recruitment. 

Dashed lines represents the 80% probability (NAFO, 2019b). 

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45 

 
 
 
 
 
 
Redfish (Sebastes spp.) 

Description 

Redfish  catches  include  three  species  of  the  genus  Sebastes:  Sebastes  mentella  and 

Sebastes fasciatus, known as "beaked redfish", and Sebastes norvegicus (= S. marinus). 

Swimming  in  the  deep  waters  at  the  edge  of  the  great  fishing  banks  and  in  deep 

channels  carved  in  the  ocean  floor,  redfish  are  mainly  noted  for  the  brilliant  scarlet 

colour from which they take their name. Aside from its deep colour, which ranges from 

orange  to  flame-red,  sometimes  with  a  brownish  cast,  the  beaked  redfish  is 

distinguished from other spiny-rayed fish by a bony protrusion on the lower jaw, by a 

fan  of  bony  spines  that  radiate  out  from  around  the  gill  cover,  and  by  its  large  eyes 

(Figure  5).  Three  types  of  redfish  are  known  in  the  Northwest  Atlantic,  Sebastes 

mentella  being  the  more  common.  It  is  found  at  depths  of  greater  than  200  m,  has  a 

bright  red  colour,  a  relatively  large  eye  and  a  long,  well  developed  beak.  The  S. 

marinus, usually found at depths of less than 240 m, is orange in colour rather than red, 

has a smaller eye and a small, blunt beak that is relatively weak. It generally grows to a 

much  larger  size  than  its  close  cousins.  As  far  as  the  commercial  fishery  or  fisheries 

management is concerned, the two (or three) species are managed together as a single 

unit. 

Figure 7. Illustration representing redfish (Sebastes spp.). 

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46 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Distribution 

Figure  8.  Geographical  distribution  of  redfish  (Sebastes  spp.)  (McKone  and  LeGrow, 

1991). 

Similar species in NAFO: redfish, alfonsino (B. splendens). 

Most common product presentation: JAP (Transversal cut removing all parts from head 

to belly), GUH (Guts and head removed) and GHT (Guts, head and tail removed). 

Fishery 

All three stocks, Divs. 3LN, 3M and Div. 3O, are open. Canada, Russia and Portugal are 

the main countries in this fishery. 

In NAFO 2015 (WGESA report): The redfish fishery, in Divs. 3LNO, is conducted with 

130 mm mesh size trawl bottom trawls with the primary areas being the slope area of 

Div.  3O,  the  east-central  area  of  Div.  3N  and  the  southeast  area  of  Div.  3L  near  the 

border  with  Div.  3N  in  depths  <600  m.  Redfish  comprise  90  %  of  the  catch  and  the 

main  by-catch  species  were  American  plaice  (2  %),  cod  (2  %),  silver  hake  (2  %)  and 

Atlantic  halibut  (2  %)  based  on  2015  logbook  information.  Although  mid-water 

trawling  has  comprised  a  significant  percentage  of  redfish  fisheries  for  principal 

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47 

 
 
 
 
 
 
 
 
Russian fleet in the past, its use has diminished in recent years and only bottom trawls 

were deployed in 2013-14. 

Divisions 3LN 

There are two species of redfish in Divisions 3L and 3N, the deep-sea redfish (Sebastes 

mentella)  and  the  Acadian  redfish  (Sebastes  fasciatus)  that  have  been  commercially 

fished and reported collectively as redfish in fishery statistics. 

A management strategy  has been adopted for this stock based on a stepwise rule with 

biennial catch increases over the years 2015 to 2020. The TAC is set for 2020 at 18,100 

t. 

Last assessment June 2018 (NAFO, 2018b) - Stock status: The stock is currently in the 

safe zone of the NAFO precautionary approach framework and is estimated to be at 1.5 

x Bmsy. There is a very low risk of the stock being below Blim. Fishing mortality is well 

below Fmsy  (0.36 x Fmsy), and the probability of being above Flim (= Fmsy) is very low. 

Recent recruitment appears to be low. 

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"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

48 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Figure  9.  3LN  Redfish:  Catches  and  TACs;  Biomass;  Fishing  mortality  (NAFO, 

2018b). 

Division 3O 

Redfish  are  caught  primarily  in  bottom  trawl  fisheries,  but  in  the  past,  some  landings 

were reported from mid-water trawl fisheries. In directed redfish fisheries, Atlantic cod, 

American plaice, witch flounder and other species are landed as bycatch. In turn, redfish 

are also caught as bycatch in fisheries directing for other species.  

The fishery in NAFO division 3O is regulated by minimal mesh size and quota. 

The TAC is set for 2020 at 20,000 t. 

Last assessment June 2019 (NAFO, 2019b) -  Stock status: Survey index values for the 

past  three  years  were  generally  at  or  below  their  time-series  average  compared  to 

relatively high values observed in  2010 to  2012.  Current  fishing mortality is  low, and 

recent recruitment is unknown. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

49 

 
 
 
 
 
 
 
 
 
Figure  10.  3O  redfish:  Catches  and  TACs;  Fishing  mortality  and  Survey  Biomass 

indices (NAFO, 2019b). 

Division 3M 

Redfish is caught in directed bottom trawl fisheries at intermediate depths (300-700m), 

but  also  as bycatch in  fisheries directed for cod  and Greenland halibut.  The fishery in 

NAFO Div. 3M is regulated by minimum mesh size and quota. 

The TAC is set at 8,591 tonnes for 2020. 

Last assessment June 2019 (NAFO, 2019b) - Stock status: The stock is declining after a 

marked  recovery  that  started  in  2002-2003.  High  levels  of  biomass  were  maintained 

until 2014, supported by low fishing mortalities and individual growth of survivors, but 

could  not  be  sustained.  The  decline  in  abundance  is  more  pronounced,  with  no 

perspective  to  stop  in  the  short  term  since  year  classes  at  recruitment  continue  to  be 

extremely weak. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

50 

 
 
 
 
 
 
 
Figure 11. 3M redfish: Catches and TACs; Biomass; Recruitment and Fishing mortality 

(NAFO, 2019b). 

American plaice (Hippoglossoides platessoides) 

Description 

American plaice (Hippoglossoides platessoides) belongs to the flatfish group of fishes, 

whose members are strongly compressed laterally and lie and swim on one side (Figure 

7). When the young fish hatch from the egg, at or near the surface, they have the normal 

fish  form.  During  development,  as  they  settle  to  the  bottom  of  the  ocean,  a  change 

occurs in the body structure. The head becomes twisted so that the fish now swims and 

lies  on  its  side.  The  upper  side  (which  now  has  both  eyes)  is  normally  pigmented  as 

compared  to  the  lower  side  which  lacks  pigmentation.  Plaice  almost  invariably  have 

their eyes on the right side of the body. The fish has a large mouth that extends at least 

below the middle of the eye. The body is covered with relatively small scales, the tail 

fin  is  rounded,  and  the  line  that  runs  along  the  side  of  the  body  (the  lateral  line)  is 

slightly curved just behind the gill openings. The colour is normally reddish to greyish 

brown on the upper pigmented side and white on the lower side. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

51 

 
 
 
 
 
 
Figure 12. Illustrationrepresenting American plaice (Hippoglossoides platessoides). 

Distribution 

Figure  13.  Geographical  distribution  of  American  plaice 

(Hippoglossoides 

platessoides) (Pitt, 1989). 

Similar  species  in  NAFO:  Other  flatfishes:  yellowtail  flounder,  witch  flounder, 

Greenland halibut etc. 

Most common product presentation: GUH (Guts and head removed), GHT (Guts, head 

and tail removed) and all kind of fillets. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

52 

 
 
 
 
 
 
 
 
 
 
 
 
Fishery 

Divisions 3LNO 

The stock has been under moratorium (no directed fishery) since 1995. American plaice 

in  recent  years  is  caught  as  bycatch  mainly  in  otter  trawl  fisheries  of  Yellowtail 

Flounder,  skate,  Greenland  Halibut  and  redfish.  A  Conservation  Plan  and  Rebuilding 

Strategy for 3LNO American plaice was created in 2011. 

Last  assessment  was  in  June  2018  (NAFO,  2018b)  -  Stock  status:  The  stock  remains 

low compared to historic levels  and is presently at 34% of the Blim level. Recruitment 

has been low since the late 1980s, but Canadian surveys indicate a large number of pre-

recruits in Div. 3L in recent years. Current estimates of fishing mortality are very low. 

Figure 14. 3NO American plaice: Catches and TACs; Spawning Biomass; Recruitment 

and Fishing mortality (NAFO, 2018b). 

Division 3M  

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

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of samples from fisheries products for genetic analysis" 

53 

 
 
 
 
 
 
American plaice is caught as bycatch in otter trawl fisheries, mainly the cod and redfish 

fisheries. From 1979 to 1993 a TAC of 2,000 t was in effect for this stock. A reduction 

to 1,000 t was agreed for 1994 and 1995 and a moratorium was agreed to thereafter. 

Last assessment was in June 2017 (NAFO, 2017) - Stock status: The stock has increased 

slightly in  recent  years due to  improved recruitment.  Although the catches since 1996 

have been low, this stock remains at a relatively low level. 

Figure 15. 3M American plaice: Catches and TACs; Recruitment; Spawning Biomass 

and Fishing mortality indices (NAFO, 2017). 

Yellowtail flounder (Limanda ferruginea) 

Description 

The  yellowtail  flounder  (Limanda  ferruginea)  has  a  remarkable  adaptability  to  the 

colour  of  the  bottom  of  the  ocean  on  which  it  lies,  and  easily  blends  into  the 

environment  to  become  practically  invisible.  This  is  a  trait  shared  with  some  other 

members  of  the  flatfish  family.  In  the  early  larval  form,  it  is  indistinguishable  from 

other bony fish with respect to its body shape, but as development proceeds in the upper 

water layers, a change occurs in the body structure. The head becomes twisted and the 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

54 

 
 
 
 
 
 
 
fish  now  lies  and  swims  on  its  side  (Figure  9).  The  upper  side,  which  now  has  both 

eyes,  is  pigmented,  while  the  lower  side  lacks  pigmentation.  Adult  yellowtail  fish 

almost  always  have  eyes  on  the  right  side  of  their  bodies.  Yellowtail  fish  have  small 

mouths, and the mouth region is turned up to give the appearance of a "snout". The line 

running along the sides of the body (the lateral line) is distinctly arched just behind the 

gill  openings,  and  the  tail  is  rounded.  The  upper  side  is  usually  brownish  green,  with 

many irregularly shaped rusty reddish spots, and white on the underside with yellowish 

colouration just in front of the tail fin. 

Figure 16. Illustration representing yellowtail flounder (Limanda ferruginea). 

Distribution 

Figure 17. Geographical distribution of yellowtail flounder (Limanda ferruginea) (Pitt, 

1993). 

Similar species in NAFO: Other flatfishes: American place, witch flounder, Greenland 

halibut etc. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

55 

 
 
 
 
 
 
 
 
 
Most common product presentation: GUH (Guts and head removed), GHT (Guts, head 

and tail removed) and all kind of fillets. 

Fishery 

Yellowtail  flounder  are  distributed  within  Divisions  3LNO  and  managed  as  a  single 

stock. 

The  Div.  3LNO  stock,  is  open  with  TACs  for  2020  of  17,000  t.  Canada,  France  St. 

Pierre  et  Miquelon,  United  States  of  America  and  more  recently  Japan  are  the  main 

countries in this fishery. 

Yellowtail flounder is caught in a directed trawl fishery and as by-catch in other trawl 

fisheries.  The  fishery  is  regulated  by  quota  and  minimum  size  restrictions.  Catches  in 

recent years have been low due to industry-related factors. American plaice and cod are 

taken  as  by-catch  in  the  yellowtail  fishery.  There  is  a  15%  by-catch  restriction  on 

American plaice and a 4% limit on cod (NAFO, 2018b). 

Last  assessment  was  in  June  2018  (NAFO,  2018b)  -  Stock  status:  The  stock  size  has 

steadily increased since 1994 and is presently 1.5 times Bmsy (Bmsy=87.63 Kt). There is 

very  low  (<1%)  risk  of  the  stock  being  below  Bmsy  or  F  being  above  Fmsy.  Recent 

recruitment appears higher than average. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

56 

 
 
 
 
 
 
 
 
Figure 18. 3LNO Yellowtail flounder: Catches and TACs; Biomass; Fishing mortality 

and Recruitment. Biomass and fishing mortality with 90% confidence intervals (NAFO, 

2018b). 

Witch flounder (Glyptocephalus cynoglossus) 

Description 

Witch  flounder  (Glyptocephalus  cynoglossus)  or  "greysole",  as  it  is  also  commonly 

known, is a flatfish like American plaice, yellowtail flounder and Greenland halibut. It 

lies  on  its  left  side  with  the  stomach  and  other  visceral  contents  on  the  right.  This 

species  has  several  characteristics  which  make  it  easily  distinguishable  from  other 

flatfishes (Figure 11). The body is relatively narrow compared to other flatfishes, with a 

very small head. On the blind side of the head are about a dozen large open mucous pits 

which are very noticeable. Its body is oval and very thin with the head occupying only 

about one fifth of the total body length. It has a very small mouth not unlike that of the 

yellowtail flounder. The body is covered by smooth scales which make it very slippery 

and extremely difficult to hold. The body colour of witch flounder is less variable than 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

57 

 
 
 
 
 
 
most other flatfishes, with the eyed side a dark greyish brown and the under side white 

with minute dark points all over it, giving it a light grey appearance. lt can grow as large 

as 78 cm in length, with a weight of 3.5-4.0 kg, although witch flounder beyond 60 cm 

in length and 2.5 kg in weight are uncommon. 

Figure 19. Illustration representing witch flounder (Glyptocephalus cynoglossus). 

Distribution 

Figure  20.  Geographical  distribution  of  witch  flounder  (Glyptocephalus  cynoglossus) 

(Bowering, 1990). 

Similar  species  in  NAFO:  Other  flatfishes:  American  plaice,  yellowtail  flounder, 

Greenland halibut etc. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

58 

 
 
 
 
 
 
 
 
 
 
Most common product presentation: GUH (Guts and head removed), GHT (Guts, head 

and tail removed) and all kind of fillets. 

Fishery 

Witch flounder are distributed within and managed as two separate stocks in Divisions 

3NO and 2J3KL, though a TAC is only assigned for 3L. 

Division 3L  

A  moratorium  was  implemented  in  1995  following  drastic  declines  in  catch  from  the 

mid-70s,  and  catches  and  catches  since  then  have  been  low  levels  of  bycatch  in  other 

fisheries (e.g. Greenland halibut and redfish fisheries). 

A moratorium (no directed fishery) has remained in place since it was declared in 2004. 

Last assessment June 2016 (NAFO, 2016) - Stock status: The stock remains below Blim. 

(The probability of biomass being below Blim = 0.66). Recruitment during 2013 to 2015 

was above average and fishing mortality is current low. 

Figure  21.  2J+3KL  Witch  flounder:  Catches  and  TACs;  Biomass  index  with  95% 

confidence limits; Fishing mortality and Recruitment indices (NAFO, 2016). 

Divisions 3NO  

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EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

59 

 
 
 
 
 
 
 
The  fishery  was  reopened  to  directed  fishing  in  2015  and  is  exploited  by  otter  trawl. 

Prior to the reopening, witch flounder was caught primarily as bycatch in bottom otter 

trawl  fisheries  for  yellowtail  flounder,  redfish,  skate  and  Greenland  halibut  (NAFO, 

2019b). 

The TAC is set at 1,175 tonnes for 2020. 

Last  assessment  was  in  June  2019  (NAFO,  2019b)  -  Stock  status:  The  stock  size 

increased from 1994 to 2013 and then declined from 2013-2015 and has since increased 

slightly. In 2019 the stock is at 41% Bmsy (60,000t). There is 20% risk of the stock being 

below  Blim  and  a  2%  risk  of  F  being  above  Flim  (0.063).  Except  for  the  growth  of  the 

stock following improved recruitment in the late 1990s, it is unclear if the recruitment 

index is representative. 

Figure 22. 3NO Witch flounder: Catches and TACs; Biomass; Recruitment and Fishing 

mortality index. Dashed lines represents the 90% credible intervals (NAFO, 2019b). 

Greenland halibut (Reinhardtius hippoglossoides) 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

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of samples from fisheries products for genetic analysis" 

60 

 
 
 
 
 
 
 
 
Description 

The  Reinhardtius  hippoglossoides  belongs  to  an  order  of  flat,  bilaterally  symmetrical 

fish,  the  Pleuronectiformes,  comprising  some  seven  families  and  117  species.  The 

members of this order undergo an amazing transformation during the larval stage. They 

begin life swimming with the dorsal fin upwards, like any salmon or trout. Gradually, 

however, one eye migrates across the top of the larva's skull to position itself close to 

the eye on the other side of the head (Figure 13). There are corresponding modifications 

to  the  skull  bones,  nerves  and  muscles.  The  eyeless  side,  for  example,  becomes  flat 

while  the  other  side  grows  slightly  rounded.  Then,  the  developing  fish  turns  over  and 

swims  on  its  flat,  eyeless  side.  A  few  features  distinguish  the  Greenland  halibut  from 

other flatfish. Normally, the eyes of flatfish are located on the top, coloured side of the 

body, and the blind side is  white. Most  such fish in  the north Atlantic are right-sided. 

That means that individuals of the species lie on the left side as the eye migrates from 

the left  to the right  during larval  development.  In the Greenland halibut,  however, the 

left eye has not completely migrated to the right side but is located on the upper edge of 

the forehead. Moreover, the blind side is not white, but dark grey, while the other side is 

nearly black. Furthermore, the fish is not perfectly symmetrical so that some members 

of  the  species,  those  smaller  fish  that  tend  to  swim  in  the  middle  levels  of  the  ocean 

rather  than  along  the  seabed,  have  been  known  to  swim  with  the  dorsal  fin  upwards. 

These  special  characteristics  make  the  Greenland  halibut  unusually  mobile,  and  the 

position  of  the  left  eye  allows  it  a  greater  field  of  vision  than  is  possessed  by  most 

flatfish. 

Figure 23. Illustration representing Greenland halibut (Reinhardtius hippoglossoides). 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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61 

 
 
 
 
 
 
 
 
 
 
Distribution 

Figure  24.  Geographical  distribution  of  Greenland  halibut 

(Reinhardtius 

hippoglossoides) (Bowering, 1993). 

Similar  species in  NAFO: Other  flatfishes:  American place, witch  flounder,  yellowtail 

flounder etc. 

Most common product presentation: GUH (Guts and head removed), GHT (Guts, head 

and tail removed) and all kind of fillets. 

Fishery 

Divisions 3LMNO  

Fisheries Commission implemented a harvest control rule (FC Doc. 10/12) to generate 

annual TACs.  The TAC is set at 12,542 tonnes for 2020. The most recent assessment 

occurred in 2017 when a new Management Strategy was adopted which shall be in force 

from 2018 to 2023, inclusive. 

Subarea 2 and Div. 3K 

Due to overlap with the Canadian EEZ no TAC is set at this time. 

White hake (Urophycis tenuis) 

Description 

White  hake  is  a  groundfish  species  belonging  to  the  gadoid  or  cod  family  of  fishes. 

They  have  characteristics  in  common  with  cod,  but  in  general  they  are  more  slender, 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

62 

 
 
 
 
 
 
 
 
 
soft-bodied fish with a slender caudal peduncle and weak tail (Figure 15). Their eyes are 

larger than the cod's but the chin barbel is smaller. They also have two dorsal fins, one 

anal fin and long narrow feeler-like ventral fins. The first dorsal fin has one ray which is 

filamentous  and  is  as  long  as  the  fin  proper  is  high.  White  hake  show  considerable 

variation in colour but are usually muddy or purple brown above with sides sometimes 

bronzed and the belly a white or yellowish white peppered with small black spots. The 

dorsal and anal fins are edged with black and the pelvic fins are pale like the belly, but 

are  usually  tinged  with  yellow.  The  white  hake  has  many  characteristics  in  common 

with another hake called the red or squirrel hake (U. chuss). The two differ in terms of 

numbers of rows of scales, the length of the filamentous ray on the dorsal fin, the length 

of  the  pelvic  fins,  the  gillraker  count  and  the  position  of  the  posterior  angle  of  the 

mouth. There is considerable overlap and variation in some of these characteristics, but 

there is sufficient difference to consider the two as separate species. It would appear that 

the white hake is the more numerous of the two species. 

Figure 25. Illustration representing white hake (Urophycis tenuis). 

Distribution 

Figure 26. Geographical distribution of white hake (Urophycis tenuis) (Bishop, 1993). 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

63 

 
 
 
 
 
 
 
Similar  species  in  NAFO:  Red  hake  (Urophycis  chuss),  Longfin  hake  (Urophycis 

chesteri),  cod,  haddock  (Melanogrammus  aeglefinus),  Pollock  (Pollachius  virens)  and 

others round fishes. 

Most  common  product  presentation:  GUT  (All  guts  removed),  GUH  (Guts  and  head 

removed), all kind of fillets. 

Fishery 

White hake are distributed through Divisions 3NO and Subdivision 3Ps though quota is 

only assigned for Divs. 3NO. Previous studies indicate that fish younger than 1 year, 2+ 

juveniles,  and  mature  adults  distribute  at  different  locations  within  Div.  3NO  and 

Subdiv.  3Ps  so  information from  the subdivision is  factored into assessments  of Divs. 

3NO. 

Divisions 3NO  

White hake is caught in directed gillnet, trawl and long-line fisheries. In directed white 

hake  fisheries,  Atlantic  cod,  black  dogfish,  monkfish  and  other  species  are  landed  as 

bycatch.  In  turn,  white  hake  are  also  caught  as  bycatch  in  gillnet,  trawl  and  long-line 

fisheries directing for other species. The fishery in NAFO division 3NO is regulated by 

NAFO  and  in  subdivision  3Ps,  by  Canada  (quota  initially  established  in  2018).  The 

fishery  is  opportunistic  when  favorable  ecosystem  conditions  allow  good  recruitment 

(NAFO, 2019b). 

The TAC is set at 1,000 tonnes for 2020. 

Last  assessment  was  in  June  2019  (NAFO,  2019b)  -  Stock  status:  The  assessment  is 

considered data limited and is associated with a relatively high uncertainty. Biomass of 

this stock increased in  1999 and 2000, generated by the large recruitment observed in 

those years. Subsequently, the biomass index decreased and has since remained variable 

but  lower.  No  large  recruitments  have  been  observed  since  2000.  Fishing  mortality  is 

low. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
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of samples from fisheries products for genetic analysis" 

64 

 
 
 
 
 
 
 
 
 
 
Figure 27.  3NO White hake:  Catches and TACs;  Recruitment; Survey  Biomass  index 

and Fishing mortality index (NAFO, 2019b). 

Thorny skate (Amblyraja radiata) 

Description 

Commercial catches of skates comprise a mix of skate species (Raja radiata, Bathyraja 

spinicauda, Raja hyperborean, Raja senta, etc). Thus the catch of skate refers to Raja 

spp. However, thorny skate dominates, comprising about 95 % of the skate taken in the 

catches. 

The  bodies  of  skates  are  strongly  flattened  dorsoventrally  (generally  disc-like),  with  a 

well-developed tail which usually has two small dorsal (upper) fins (Figure 17). These 

are either separated by a very narrow gap or joined at their bases. The mouth is situated 

on the ventral (lower) surface. The highly developed pectoral (front) fins are attached to 

the  sides  of  the  head,  lending  them  a  wing-like  appearance.  A  pair  of  well-developed 

spiracles (breathing holes) are usually present, located on top of the head. Breathing is 

accomplished  by  inhaling  through  the  spiracles  and  expelling  the  water  through  the 

gills. The males, when mature, usually have a well developed pair of claspers, or mating 

organs, which are situated at the apex of the pelvic (rear) fins and tail. Depending on the 

species, these claspers can be rather long and slender, or relatively short and sturdy with 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

65 

 
 
 
 
 
 
a  club-like  thickening  (as  in  thorny  skate).  The  claspers  have  a  cartilaginous  hatched 

(covered) blade-shaped structure called a "knife" which is mostly hidden underneath in 

the posterior ventral (rear) lobe opening. This knife can be very sharp and care should 

be taken in handling. The males also develop several rows of alar (spawning) spines on 

the dorsal  surface of the pectoral  fins. These spines, when mature, are very sharp and 

hook-like at the tip. Depending on size or stage of maturity of the skate, there may be 2 

to 5 rows with 4 to 10 spines per row. These spines develop during the maturing period 

and are used to hold the female during mating. The thorny skate (Raja radiata) can be 

distinguished  by  a  row  of  large  thorns  on  the  dorsal  (upper)  surface  along  the  spine 

extending from  the scapular (front shoulder) region behind  the first  dorsal  fin  — with 

one sometimes between the first and second dorsal fin. There are not more than a total 

of  19  thorns,  or  a  total  of  10  behind  the  axils  of  pelvic  fins.  In  addition,  there  are 

generally two or three large thorns on each shoulder; one thorn in front and one behind 

each eye; and one close to the inner end of each breathing hole. Some smaller thorns are 

scattered on the snout (nose), pectoral fins and tail. The base of the thorns on the dorsal 

surface is usually star - shaped. The thorny skate is usually brown on the dorsal surface 

with  some  darker  spots;  the  under  surface  is  generally  white  or  slightly  sooty.  It  may 

grow to approximately 100 to 110 cm. 

Figure 28. Illustration representing thorny skate (Amblyraja radiata). 

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66 

 
 
 
 
 
 
 
 
 
 
 
 
Distribution 

Figure 29. Geographical distribution of thorny skate (Amblyraja radiata) (McKone and 

LeGrow, 1983). 

Similar  species  in  NAFO:  Other  skates  (Raja  radiata,  Bathyraja  spinicauda,  Raja 

hyperborean, Raja senta, etc). However, thorny skate dominates, comprising about 95 

% of the skate taken in the catches. 

Most common product presentation:  WNG (Wings only), and wings without skin. 

Fishery 

Thorny skate are distributed within Divisions 3LNO and Subdivision 3Ps. Skates in all 

divisions  are  managed  as  a  single  stock.  Subdivision  3Ps  is  presently  managed  as  a 

separate unit by Canada and France in their respective EEZ’s while 3LNO is managed 

by NAFO. As bycatch, it is primarily caught in the cod and redfish fisheries. 

Divisions 3LNO  

Thorny  Skate  is  caught  in  directed  gillnet,  trawl  and  long-line  fisheries.  In  directed 

Thorny Skate fisheries, Atlantic Cod, Monkfish, American Plaice and other species are 

landed as bycatch. In turn, Thorny Skate are also caught as bycatch in gillnet, trawl and 

long-line  fisheries directing  for other species. The fishery in  NAFO division  3LNO is 

regulated by quota and mesh size (280mm). 

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67 

 
 
 
 
 
 
 
 
 
The TAC is set at 7,000 tonnes for 2020. 

Last assessment was in June 2018 (NAFO, 2018b) - Stock status: The stock is currently 

above Blim. The probability that the current biomass is above Blim is >95%. Total survey 

biomass  in  Divs  3LNOPs  has  remained  stable  since  2007.  Recruitment  in  2017  was 

above average. Fishing mortality is currently low. 

Figure 30. 3NO Thorny skate: Catches and TACs; Recruitment; Biomass; and Fishing 

mortality (NAFO, 2018b). 

Capelin (Mallotus villosus) 

Description 

Once  thought  to  be  different  species,  the  Atlantic  and  Pacific  capelin  are  now 

considered to be the same species, Mallotus villosus. The specific name comes from the 

Latin, "hairy", and it is interesting to note that the common name of capelin in Norway 

is "lodde" from the word lodden, meaning hairy. This name may have derived from the 

spawning ridges of the male. During spawning, two pairs of ridges develop, a prominent 

dorsal  pair  running  the  length  of  the  body  above  the  lateral  line  and  a  smaller  ventral 

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68 

 
 
 
 
 
 
 
pair extending from the pectoral fin back to the pelvic fin (Figure 19). These ridges are 

formed  from  elongation  of  scales  that  project  outward  to  form  soft  (hairy)  ridges. 

Besides  the  spawning  ridges,  the  males  also  have  larger  fins  which  project  from  the 

body at this time. Males are larger than females at sexual maturity and this together with 

the larger fins and spawning ridges gives the males a distinctly more robust appearance. 

These external sexual characteristics in the males begin to develop at least four to five 

weeks  before  the  spawning  season.  During  the  rest  of  the  year  the  sexes  are  almost 

indistinguishable. Mature specimens are relatively small, approximately 13-20 cm. The 

colour ranges from olive to bottle green above the lateral line and silver below. The fish 

are  elongate  and  slender  and  there  are  two  fins  on  the  back,  a  larger  dorsal  fin  in  the 

middle and a smaller adipose fin just in front of the tail (Carscadden, 1981). 

Figure 31. Illustration representing capelin (Mallotus villosus). 

Distribution 

Figure 32. Geographical distribution of capelin (Mallotus villosus) (Carscadden, 1981). 

Similar  species  in  NAFO:  Sand  lances/eels  (Ammodytes),  American  smelt  (Osmerus 

mordax) 

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69 

 
 
 
 
 
 
 
 
 
Most common product presentation: No reference is found 

Fishery 

Divisions 3NO  

Capelin  was  caught  in  a  directed  trawl  fishery.  There  is  low  bycatch  in  other  trawl 

fisheries.  The  directed  fishery  was  closed  in  1992  and  the  closure  has  continued.  No 

catches have been reported for this stock from 1993 except 1 t of Spanish catch in 2014 

and 5 t Estonian catch in 2016. In 2017, 11 t of discards were reported (NAFO, 2018b). 

No  directed  fishing  was  advised  through  2019-  2021.  Unless  an  acoustic  survey  is 

available, the Scientific Council will be unable to produce more specific advice. 

Last  assessment  was  in  June  2018  (NAFO,  2018b)  -  Stock  status:  Acoustic  surveys 

series  terminated  in  1994  indicated  a  stock  at  a  low  level.  Although  biomass  indices 

have  increased  in  recent  years,  bottom  trawl  surveys  are  not  considered  a  satisfactory 

basis for a stock assessment of a pelagic species. 

Figure  33.  3NO  Capelin:  Biomass  index;  Fishing  mortality  and  mean  catch  from 

Canadian spring surveys (NAFO, 2018b). 

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70 

 
 
 
 
 
 
 
 
 
 
Shrimp (Pandalus borealis) 

Description 

Shrimp belong to a class of animals known as the crustaceans which includes lobsters, 

crabs, and crayfish. They possess a hard outer shell (exoskeleton), have jointed legs and, 

since  most  are  aquatic,  breath  through  gills  (Figure  21).  The  northern  shrimp  is  pale 

scarlet, has a pair of large compound eyes and attains total lengths of 15 to 16 cm. The 

shell covering the head and thorax (carapace) is modified into a long, curved, sabre-like 

structure called a rostrum which has numerous spines on both edges.  

Many shrimps, including the northern shrimp, are good swimmers. Appendages on the 

tail  (abdomen), called pleapods, act  like paddles and enable the animals  to  move with 

remarkable agility, both horizontally and vertically, over considerable distances. Sudden 

flexing  of  the  tail  also  allows  rapid  movement  over  short  distances  as  an  emergency 

mechanism of escape. 

Figure 34. Illustration representing shrimp (Pandalus borealis). 

Similar species in NAFO: other shrimps. 

Most common product presentation:  WHL (No processing). 

Fishery  

Directed fishing for Northern shrimp must follow the guidance of Article 9, Article 13 

(mesh size 40mm) and Annex IIB (Authorized Topside Chafers/Shrimp Toggle Chains) 

of the NAFO Conservation and Enforcement Measures. 

Divisions 3LNO  

The  fishery,  until  2014,  was  a  directed  bottom  trawl  fishery  and  there  is  little  or  no 

bycatch  of  shrimp  in  other  trawl  fisheries.  A  moratorium  (no  directed  fishery)  has 

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71 

 
 
 
 
 
 
 
 
 
 
remained in place since it was declared in 2015. The fishery in Div. 3LNO is regulated 

by quota. 

Last  assessment  was  in  September  2019  (NAFO,  2019c)  -  Stock  status:  Currently  the 

risk  of  the  stock  being  below  Blim  is  greater  than  95%.  There  is  no  indication  of 

improved recruitment. 

Figure  35.  3LNO  Shrimp:  Catches  and  TACs;  Survey  Female  Biomass,  Exploitation 

rate and Recruitment indices. Error 

bars indicate 95% confidence intervals (NAFO, 2019c). 

Division 3M  

This fishery is effort-regulated. The effort allocations were reduced by 50% in 2010 and 

a moratorium was imposed in 2011, this fishery will reopen in 2020. Bycatches are not 

quantified but is known that small redfish is caught in this fishery when the recruitment 

of redfish is high. 

The TAC is set for 2020 at 2,640 days (109 vessels). 

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72 

 
 
 
 
 
 
 
 
Last  assessment was in  September 2019 (NAFO, 2019c)  - Stock status: The stock has 

shown  signs  of  improvement  since  2014,  and  in  2019,  the  stock  has  a  very  low 

probability of being below Blim. Although recruitment has been weak in the last decade, 

the recruitment index (age 2) has been increasing since the lowest observed in 2014. 

The Scientific Council advised that the catch in 2020 should not exceed the 2009 level 

(5,448 tonnes). 

Figure 36. 3M Shrimp: Catches and TACs; Survey Female Biomass, Exploitation rate 

and Recruitment indices. Error 

bars indicate 2 std. err (NAFO, 2019c). 

Splendid alfonsino (Beryx splendens) 

Description 

The Berycidae (alfonsinos) family are a member of the order Beryciformes. The family 

includes  ten  species  in  two  genera,  Beryx  and  Centroberyx.  Generally,  the  common 

name “alfonsino” is used to refer to splendid alfonsino, Beryx splendens (Lowe 1934). 

There  is  also  another  species  of  alfonsino  that,  in  some  regions,  is  important  in  the 

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73 

 
 
 
 
 
 
 
fisheries and is variously referred to as longfinned beryx, red bream or broad alfonsino, 

B. decadactylus. 

Anon  (2009)  reports  alfonsino  to  have  4  dorsal  spines,  13–16  soft  dorsal  rays,  4  anal 

spines,  and  26-30  soft  anal  rays  (Figure  22).  The  first  infraorbital  bone  has  a  spine 

projecting laterally on its anterior end and the lateral line extends to caudal fin. In young 

fishes, the second dorsal ray is elongated. 

Beryx splendens can be distinguished from B. decadactylus in having a shallower body 

and fewer dorsal-fin soft rays (13–15 dorsal–fin soft rays for B. splendens versus 16–20 

for B. decadactylus). B. splendens is distinguished from other redfishes and the closely 

related roughies (Trachichthyidae) by having only four dorsal-fin spines. 

Figure 37. Illustration representing splendid alfonsino (Berix splendens). 

Distribution 

Alfonsino  (B. splendens) is  widely distributed and can be found in  the deep waters  of 

the Atlantic, Indian and Pacific oceans. In the North Atlantic, Alfonsino is an oceanic 

demersal  species  which  form  distinct  aggregations,  at  300–950  m  depth,  on  top  of 

seamounts.    Alfonsino  is  distributed  over  a  wide  area  which  may  be  composed  of 

several  populations.  Stock  structure  is  unknown.  Until  more  complete  data  on  stock 

structure is obtained it is considered that separate populations live on each seamount. 

Similar species in NAFO: redfishes (Sebastes spp.)  

Most common product presentation: JAP (Transversal cut removing all parts from head to 
belly), GUH (Guts and head removed), WHL (No processing) 

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Fishery 

Division 6G 

Commercial  aggregations  of  alfonsino  on  the  Corner  Rise  have  been  found  on  three 

seamounts. Two of them named “Kükenthal” (known also as “Perspektivnaya”) and “С-

3”  (“Vybornaya”)  are  located  in  the  NAFO  Regulatory  Area.  One  more  bank  named 

“Milne  Edwards”  (“Rezervnaya”)  is  located  in  the  Central  Western  Atlantic.  Russian 

vessels  fished  in  this  area  in  different  periods  between  1976  and  1999  using  pelagic 

trawls. There is no statistics on the Russian fishery on separate seamounts. Based on the 

information  collected  in  the  2004  Spanish  experimental  survey  in  Corner  Rise,  a 

directed commercial fishery had been conducted since 2005 by Spanish vessels. Since 

2006 virtually all the effort has been made in the Kükenthal seamount with pelagic trawl 

gear (NAFO, 2019b). 

No  analytical  or  survey  based  assessment  were  possible.  The  only  data  available  at 

present  are  the  catch  and  effort  time  series.  Despite  the  difficulties  of  interpreting  the 

CPUE  as  an  indicator  of  stock  status  and  knowing  that  this  species  is  easily 

overexploited and can only sustain low rates of exploitation, the sharp decline in CPUE 

to the lowest observed (92% lower than in 2017) and catches in the last year indicate an 

apparent  overfishing  situation  and  that  the  stock  may  be  depleted.  The  SC  advises  in 

June  2019  to  close  the  fishery  until  biomass  increases  to  exploitable  levels  (NAFO, 

2019c). 

The fishery was closed in 2020. 

Last  assessment  was  in  June  2019  (NAFO,  2019b)  -  Stock  status:  Appears  to  be 

depleted. 

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75 

 
 
 
 
 
 
 
Figure 38. 6G Splendid alfonsino: Catch and CPUE (NAFO, 2019b). 

Short-finned Squid (Illex illecebrosus) 

Description 

Squid  belong  to  the  Class  Cephalopoda  of  the  Phylum  Mollusca.  There  are 

approximately 650 recognized species of cephalopods alive today and more than 10,000 

fossil  forms.  Cephalopod  translates  literally  into  "head  footed"  which  explains  why 

squid, as well as the nautilus, cuttlefish and octopus among others, with their arms and 

tentacles attached directly to their heads, are so named. 

People are often surprised to learn that the rapidly-swimming squid (Figure 23), with no 

external  shell,  is  related  to  molluscs  such  as  clams,  oysters  and  snails.  In  fact,  squid 

have a small internal shell called a pen which extends along the back of the body and 

acts as a support to the soft, muscular body. 

Short-finned  squid  reach  a  body  or  "mantle"  length  of  more  than  30  cm  and  a  total 

length  of more than 60  cm.  The cigar-shaped body has two triangular fins at  the rear, 

and  a  funnel  and  distinct  head  with  eight  sucker-equipped  arms  and  two  tentacles,  on 

the other end. They have large, well-developed eyes and a strong parrot-like beak. Squid 

use their fins for swimming in much the same way fish do, and the funnel for extremely 

rapid  "jet"  propulsion  forward  or  backward.  The  squid's  capacity  for  sustained 

swimming  allows  it  to  migrate  long  distances  as  well  as  to  move  vertically  through 

hundreds of metres of water in its daily feeding. 

The short-finned squid generally has a mixed, iridescent coloration of milky white and 

rusty  brown.  The  colour  changes  rapidly  as  the  squid  expands  or  contracts  the  colour 

cells in its skin as a camouflage or in response to attack (Rowell, 1989). 

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76 

 
 
 
 
 
 
 
Figure 39. Illustration representing short-finned squid (Illex illecebrosus). 

Distribution 

Figure 40. Geographical distribution of short-finned squid (Illex illecebrosus) (Rowell, 

1989). 

Similar species in NAFO: Other Cephalopods. 

Most common product presentation:  TUB (Tube only), WHL (No processing). 

Fishery 

Subareas 3 + 4 

Prior to the mid-1980s, international bottom trawl and midwater trawl fleets participated 

in  directed fisheries in  Subareas 3, 4  and 5+6. Since 1999, there has been no directed 

fishery  in  Subarea  4,  but  some  squid  is  taken  as  bycatch  in  the  Canadian  small-mesh 

bottom trawl fishery for silver hake. Directed fisheries currently consist of a Canadian 

inshore jig fishery in Subarea 3 and a small-mesh bottom trawl fishery in Subareas 5+6. 

In  2018,  at  least  one  vessel  conducted  a  directed  trawl  fishery  in  3O.  There  is  no 

bycatch  in  the  jig  fishery.  There  are  separate  management  regulations  applied  by 

NAFO, USA and Canada (NAFO, 2019d). 

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77 

 
 
 
 
 
 
 
 
 
 
Fishing may not occur from 1 January to 30 June in Subareas 3 +4 in accordance with 

Article 11, NAFO CEM. 

The TAC is set at 34,000 tonnes for 2020. 

Last  assessment  was  in  September  2019  (NAFO,  2019d)  -  Stock  status:  Trends  in 

fishery and research vessel survey data indicate that a period of high productivity (1976-

1981) occurred in Subareas 3+4 between two low productivity periods (1970-1975 and 

1982-2017).  During  2018,  the  Div.  4VWX  survey  was  not  completed.  However,  the 

Div. 4VWX biomass index and mean body size during 2019 indicate that the stock may 

be moving towards a high productivity period. 

Figure  41.  SA  3  +  4  Short-finned  Squid:  Catches  and  TACs;  Biomass;  Mean  Body 

Weight and Fishing mortality (NAFO, 2019d). 

This  thorough  description  helped  in  the  understanding  of  the  specific  reality  of  the 

fisheries and fleets operating in the targeted NAFO RA. 

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78 

 
 
 
 
 
 
 
 
 
 
2.2.4.  SUB-TASK 2.3 – ELABORATION OF MANUAL OF PROCEDURES 

The Sub-Task 2.3, entitled “Elaboration of Manual of Procedures”, was initiated in mid-

August  after  the  delivery  of  the  Interim  Report.  The  timely  accomplishment  of  the 

chronologically  previous  Sub-Tasks  (2.1  and  2.2)  was  a  decisive  contribution  for  the 

accomplishment of Sub-Task 2.3. Indeed, the structure and several main key pillars of 

the  IMP  have  already  been  brought  to  a  state  of  development  that  makes  possible  the 

successful fulfilment of this Sub-Task’s objectives within the stipulated timeframe. 

The IMP structure can already be sketched to be built along the following main themes: 

- 

- 

- 

- 

I - Introduction and Objectives; 

II - Definitions; 

III - Types of Sample; 

IV - Kit for the Collection of Samples; 

-  V - Procedures for Sampling, Collection, Registration, Transport, and Delivery; 

-  VI – Laboratory Analysis; 

-  VII - Costs; 

-  VIII - Forms; 

- 

IX - Certification of the Fishery Inspectors; 

-  X – Versions; 

-  XI – Legal References; 

-  XII – Annexes. 

In  the  section  I  –  Introduction  and  Objectives,  the  regulatory  framework  that 

encompasses  the  development  and  establishment  of  an  International  Manual  of 

Procedures  is  presented.  Within  the  frame  of  NAFO,  the  European  regulatory 

framework was used as the reference in structuring the aims and scope of the document. 

Moreover,  on  the  basis  of  the  performed  Literature  Review  (Task  1)  as  explained  in 

section 2.1.3., genomics and DNA analyses were concluded to be preferential methods 

of molecular analysis reaching a quality standard that enables their application in food 

authenticity  testing.  In  particular,  it  is  mentioned  in  section  I  of  IMP  that  the  DNA 

sequences present in the individuals of each species, although different from each other, 

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79 

 
 
 
 
 
 
 
share  patterns  that  allow,  without  ambiguity,  to  distinguish  each  of  the  individuals 

belonging  to  it  from  any  representatives  of  other  species.  This  makes  possible  the 

specific  classification  of  any  individual  through  the  analysis  of  the  respective  DNA 

sequences, the study of which is viable in almost any biological vestige that belongs to 

it, since the same DNA is found in all its organic parts. Hence, several methods of DNA 

analysis  shall  be  possible,  including  DNA  barcoding,  that  is,  to  identify  a  species  by 

extracting a short DNA sequence from a specific gene or genes and comparing it with a 

reference library of such DNA sequences. 

Moreover, it was considered that the European Fisheries Control Agency (EFCA) is the 

most adequate entity for providing suitable training to the Inspectors, comprising overall 

approach  to  fishing  vessels  operating  in  NAFO  RA,  random  selection  of  lots,  and 

sampling  procedures  and  techniques.  Since  EFCA  organizes  training  workshops  for 

NAFO  Inspectors  on  a  yearly  basis,  it  was  also  advised  that  the  updated  IMP  version 

should be distributed among them and feed-back on the IMP should be expected every 

year. In addition, EFCA was deemed to be a better (or at least complementary) forum to 

discuss potential refinements of the IMP, as results of ongoing genetic analyses can be 

shared with EFCA on a practical routine basis. 

The  scope  and  main  goals  of  the  IMP  are  also  presented  and  briefly  discussed.  The 

addressees  of  the  IMP  are  also  mentioned.  Likewise,  the  concept  of  the  Chain  of 

Custody and its procedures are outlined and appraised. 

In  the  section  II  –  Definitions,  the  concepts  necessary  for  the  scope  of  the  IMP  are 

defined.  Namely,  definitions  are  given  for:  Box;  Chain  of  Custody;  Fishery  Products; 

Lot; Presentation/Product Presentation; Shipment; and Transformation. The definitions 

were revised and trimmed to their core concepts. 

Regarding  section  III  –  Types  of  Sample,  it  is  emphasized  that  to  carry  out  a  test  by 

DNA analysis requires sample collection of biological material by removing biological 

material  from  part  of  the  fishery  product  and  that  this  part  may  be  fins,  teeth,  scales, 

muscle,  skin,  blood  or  viscera.  Moreover,  it  was  added  a  detailed  list  of  possible  fish 

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80 

 
 
 
 
 
 
 
species that may be sampled in the NAFO RA, which, in turn, was built on the basis of 

the Descriptive Analysis of the Fishing Fleets operating in the NAFO RA. 

Concerning  section  IV  –  Kit  for  the  Collection  of  Samples,  it  is  explained  in  what 

consists the kit for muscle sampling, being also mentioned further items beyond the kit 

itself. The kit items comprise: a numbered safety casing; three bottles; one non-reusable 

ampoule  containing  ethanol;  disposable  tip  forceps;  disposable  scalpel;  two  pairs  of 

non-powdered  disposable  vinyl  gloves;  absorbent  cloth/tissue;  and  a  15  cm  x  10  cm 

disposable  polypropylene  board.  It  is  also  mentioned  that  each  kit  is  used  for  the 

collection  of  a  single  sample  and  that  each  EU  member  country  as  well  as  extra-EU 

countries (being EU and the extra-EU countries NAFO contracting parties) will engage 

the respective Unity of Inspection and Control for the management of the Kits. 

With  respect  to  section  V  -  Procedures  for  Sampling,  Collection,  Registration, 

Transport,  and  Delivery,  a  detailed  array  of  procedures  is  given  for  the  various  main 

steps of the global action. 

For  sampling,  the  number  of  samples  of  the  lot  to  collect  is  given  as  a  function  of  a 

formula  that  uses  as  input  the  probability  of  species  variability  in  a  given  fishery 

products’ lot, which, in turn, is a function of the fisheries knowledge in the NAFO RA, 

as  seen  in  section  2.2.3.2.  (Sub-Task  2.2  –  Preparation  of  a  Descriptive  Analysis  of 

Fishing  Fleets).  For  a  clearer  understanding  of  the  formula,  its  application  was 

exemplified. 

n0 = Z2 × p × q/e2 

Where, 

n0 – Sampling dimension; 

Z2  -  Abscissa  of  the  normal  curve  that  cuts  off  an  area  a  at  the  tail  (1  -    equals  the 
desired confidence level, for instance, 95 %); 

e - Intended level of precision; 

p  -  Estimated  proportion  of  an  attribute  that  is  present  in  the  population  (species 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

81 

 
 
 
 
 
 
 
 
identity); 

q – Corresponds to 1-p. 

The  value  for  Z  is  found  in  statistical  tables  which  contain  the  area  under  the  normal 

curve. On the other hand, the value of p may be estimated on the basis of the probability 

of finding a fish box from a different species in the fish lot of a given targeted species. 

On the basis of previous knowledge of the fish species and fishing fleets highlighted in 

the Descriptive Analysis of the Fishing Fleets operating in the NAFO RA, it is possible 

to assess p to be in a wide range (particular case-studies for different  fish species and 

taking into account fish preparation processes, for instance, in fillets, are being prepared 

for inclusion in the IMP). 

However, Inspectors should adjust p to the empirical experience as they feed-back the 

species  identification  results  into  the  formula,  thereby  calculating  specific  sampling 

dimensions  for  each  species.  For  instance,  if  it  is  observed  a  probability  of  1:275  of 

finding a fish box from a different species in the fish lot of a given targeted species, that 

is, p is 0.00364, for a confidence level of 95 % and e of 0.05, n0 is approximately 6. 

For the case when the size of the population to be sampled is not large (< 10,000 boxes) 

and  in  accordance  to  STECF  suggestion,  minimum  sampling  size  (n0)  was  adjusted 

with the finite population correction as follows: 

n0corrected = N × n0/(n0 + N -1) 

where N denotes the population size (i.e. number of boxes in a lot). 

Moreover,  whenever  minimum  sampling  size  is  estimated  to  be  less  than  3  boxes,  a 

minimum sample of size equal to 3 boxes was established. 

Finally,  the  consortium  agreed  that  representative  genetic  sampling  throughout  the 

whole NAFO RA was out of the scope of this contract, as inspectors have their own risk 

assessments that define the inspection strategies to target specific lots. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

82 

 
 
 
 
 
 
 
 
 
In the case of collection, the minimum portion required for DNA analysis is given. It is 

also  referred  that  if  the  size  or  characteristics  of  the  product  to  be  sampled  are  not 

sufficient  to  make  up  the  recommended  portion,  in  particular  for  bivalve  molluscs  or 

crustaceans,  whole  specimens  or  parts  of  specimens,  such  as  crab  legs,  should  be 

collected.  Moreover,  a  list  of  special  aspects  that  must  be  taken  into  account  in  the 

collection step are expressed and described. 

The registration of collection is also the object of a detailed description. Indeed, in order 

to  ensure  the  chain  of  custody,  the  entire  process  must  be  documented  through  the 

collection  record  and  the  identity  of  the  individuals  who  had  access  or  handled  the 

sample(s), promoting trustworthiness, integrity, and sample (evidence) traceability until 

use of the sample as evidence. The specific regulatory framework is presented. 

A new sub-section entitled “Preventing Cross-Contamination of Samples” was added. It 

lists a set of good practices that minimize the risk of sample cross-contamination. 

Likewise,  the  transport  and  delivery  are  associated  to  a  specific  set  of  procedures. 

Namely, the maximum period for delivery of the sample in the laboratory must be five 

working days after sample collection. The Form of transport and delivery of the sample 

must always be filled out  at  the time of delivery  of the collection in  the laboratory or 

whenever the evidence(s) (sample(s)) is handled or transported by a person other than 

the  Inspector  who  made  the  collection.  In  the  case  that  it  is  necessary  to  carry  the 

sample  through  transport  companies,  a  copy  of  the  transport  documents  must  be 

attached to the Form of transport and delivery of the sample. 

In a new section VI – Laboratory Analysis, a detailed description of the possible DNA 

analysis methods that may be applied to fish samples is presented. This is largely based 

on  the  Literature  Review  (Task  1).  It  presents  the  most  usual  DNA  analysis 

methodologies, their advantages and drawbacks as well as which criteria must be used 

to choose a particular methodology. 

Afterwards, a detailed description of DNA analysis procedures is given. It comprises the 

procedures for the sample pre-treatment, the sample preparation and extraction (both for 

genomic  and  mitochondrial  DNA),  and  the  DNA  amplification  by  Polymerase  Chain 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

83 

 
 
 
 
 
 
 
Reaction.  The  procedures  for  performing  DNA  barcoding  and  other  identification 

approaches through DNA after PCR are presented in the IMP (Deliverable D2.1). 

Moreover,  in  future,  it  would  be  useful  to  develop  reliable,  real  time  barcoding  and 

species identification applications (e.g. on  smartphones) that could  allow pre-scanning 

of  samples  by  inspectors  ,  so  as  to  reduce  the  number  of  final  genetic  analyses  to  be 

conducted in labs. 

In section VII – Costs, the calculation of the cost of the whole procedure is explained. 

For section VIII – Forms, it is highlighted that the models of the Forms for collection of 

samples of the fishery products and for the transport and delivery of samples of fishery 

products are an integral part of the IMP and are presented in the section XII – Annexes. 

Concerning  section  IX  -  Certification  of  the  Fishery  Inspectors,  the  institutional  and 

regulatory aspects that encompass this subject are presented. 

Regarding section X – Versions, the rules and nomenclature of the various versions of 

the IMP are defined. 

For  section  XI  –  Legal  References,  it  is  emphasized  that  the  references  to  the  legal 

diplomas  of  the  NAFO  contracting  parties  (in  the  case  of  EU,  commissioning  each 

member state) are done in the respective updated versions. 

Finally,  in  section  XII  –  Annexes,  the  case-studies  regarding  estimation  of  sample 

dimension  (number  of  boxes  to  be  sampled  per  lot),  the  statistical  tables  for  the 

calculation of sample dimension, the Form for the collection of samples of the fishery 

products, and the Form for the transport and delivery of samples of the fishery products 

are fully presented. 

The  IMP  document  has  been  completed  and  has  reached  its  definite  version,  being 

deliverable D2.1. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

84 

 
 
 
 
 
 
 
 
 
 
 
 
3. 

TIMETABLE FOR THE IMPLEMENTATION 

The schedule of the work to be developed during the project is detailed in Table 9 and 
follows  the  tender  specifications  with  exception  of  the  extension  of  Task  1  deadline. 
The  contract  started  on  12th  June  2019  and  its  planned  duration  is  5  months,  i.e.,  22 
weeks. Its end will be on the 12th November 2019. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

85 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Table 9. Tasks and activities chronogram. 

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection of samples from fisheries products for genetic analysis" 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

86 

 
 
 
 
 
 
 
4. 

LIST OF DELIVERABLES 

Table  10  provides  a  summary  and  the  timing  of  the  deliverables  to  be  submitted  to 
EASME and DG-MARE during the course of this project. There was no alteration in the 
Deliverables list. 

Table 10. Deliverables list, dissemination level and due date. 

Deliverable no. 

Deliverable name 

Dissemination 
level 

D.01 

D.02 

D0.3 

D0.4 

D1.1 

D2.1 

Inception Report 

Interim Report  

Draft Final Report 

Final Report and Executive 
Summary 

Review Document 

Manual of procedures 

EASME/DG 
MARE 

EASME/DG 
MARE 

EASME/DG 
MARE 

EASME/DG 
MARE 

EASME/DG 
MARE 

EASME/DG 
MARE 

Del. date 

26th June 2019 

11th August 2019 

23rd October 2019 

12th November 2019 

11th August 2019 

12th November 2019 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

87 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
5. 

LIST OF MEETINGS 

Table 11 shows the list  of meetings that are  envisaged during the study.  Likewise, no 
departure from planning. 

Table 11. Meetings list, location, participants and tentative dates. 

Meeting   Meeting name 

Location 

Participation 

Date 

M0.1 

Kick off meeting 

Brussels 

M0.2 

for 

Meeting 
standardization 
of  EU  manual 
protocols1 

M0.3 

Interim meeting 

Skype 
meeting 

Skype 
meeting 

M0.3 

Final meeting 

Brussels 

EASME/DG MARE + Project 
Coordinator (IPMA) + FWC 
Coordinator (AZTI)  

4th July 2019 

IPMA + AZTI + IEO 

14th August 2019 

EASME/DG MARE + Project 
Coordinator (IPMA) + FWC 
Coordinator 

28th August 2019 

EASME/DG MARE + Project 
Coordinator (IPMA) + FWC 
Coordinator (AZTI)  

12th November 
2019 

1 Proposed additional meeting. Not specifically requested in the ToRs.   

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection 
of samples from fisheries products for genetic analysis" 

88 

 
 
 
 
 
 
 
 
                                                 
6. 

LIST OF MILESTONES 

The detailed list of Project Milestones is listed in Table 12. 

Table 12. List of milestones, nature, due date and mean of verification. 

Mil. 
no. 

MS 1.1 

MS 1.2 

MS 2.1 

MS 2.2 

MS 2.3 

MS 2.4 

MS 2.5 

Milestone name 

Establishment  of  the  guidelines  and  criteria  to 
assist in the conduction of the literature review 

Review of the data and information gleaned from 
the literature review 
Review  of  significant  precedents  (Portuguese 
manual of procedures) 

Establishment  of  guidelines  for  the  descriptive 
analysis of the fishing fleets 

Critical  review  and  assessment  of  existing  data 
collected under current protocols against previous 
DCF and SFPA requirements 

Assessment of potentially needed changes to data 
reporting  protocols  under  latest  DCF  and  SFPA 
requirements 

Based on MS 2.1 to 2.4, summary of inputs to be 
considered  for  the  development  of  manual  of 
procedures in Sub-Task 2.3 

MS 2.6 

Establishment of the guidelines to be followed in 
the elaboration of the manual of procedures 

MS 2.7  Preparation of a draft of the manual of procedures 

MS 2.8 

the  collection  of 
Manual  of  procedures  for 
samples  from  fisheries  products  for  genetic 
analysis 

Tas
k 
no. 

Nature2 

Exp. date 

Means of 
verification3 

1 

1 

2 

2 

2 

2 

2 

3 

3 

2 

R 

R 

R 

R 

R  

R 

R 

O 
(manual) 

O 
(manual) 

O 
(manual) 

19th June 
2019 
7th August 
2019 
31st July 
2019 
14th August 
2019 
14th August 
2019 

14th August 
2019 

14th August 
2019 

21st August 
2019 
25th 
September 
2019 
12th 
November 
2019 

Inception 
Report4 
Progress 
Report 
Progress 
Report 

Progress 
Report 

Progress 
Report 

Progress 
Report 

Progress 
Report 

Draft Final 
Report5 

Draft Final 
Report 

Draft Final 
Report 

1 Nature of the Deliverable/Milestone: M = meeting; R = Report, O = Other (specify) 

3 Refer to indicators as appropriate. 

4 First Interim draft Report should be submitted on Week 9. 

5 Draft Final Report should be submitted on Week 16. 

Executive Agency for Small and Medium-sized Enterprises (EASME); European Maritime and Fisheries Fund (EMFF)                                                                                                                  

EASME/EMFF/2016/008 Provision of Scientific Advice for fisheries beyond EU Waters 
"Study to produce an International Manual of Procedures (IMP) to be used in the NAFO Regulatory Area to guide the collection of 
samples from fisheries products for genetic analysis" 

 
 
 
 
 
 
 
                                                 
7. 

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