C9094 - TECNOLOGIE PER LO STUDIO DELLE POPOLAZIONI MARINE E DEGLI STOCK DA PESCA

Learning outcomes

By the end of the course, students will be able to apply technologies, methods and tools for monitoring and analysing marine populations and fish stocks based on bio-ecological characteristics and biomolecular markers, both consciously and critically. Students will acquire the necessary biological, methodological and analytical knowledge to: 1) assess the status of marine resources and contribute to their sustainable exploitation in accordance with European regulations; and 2) identify the evolutionary and environmental factors that influence the biodiversity of marine populations. This involves distinguishing adaptive traits from neutral ones and assessing their functional role in marine ecosystems. Students will be able to: 1) describe the biological aspects that regulate population dynamics; 2) assess the effects of anthropogenic and natural pressures on populations and ecosystems; 3) apply monitoring methods and laboratory analysis techniques; 4) use analytical methodologies for the assessment of biological resources; 5) critically analyse fisheries management strategies from a sustainability perspective; 6) estimate connectivity between populations and understand the genetic structure of marine populations; 7) reconstruct the evolutionary and ecological processes that determine this in spatial and temporal dimensions, as well as the main related demographic parameters; 8) Identify adaptive traits by analysing molecular markers that are potentially under selection in the marine environment.

Course contents

Prerequisites

A basic knowledge of zoology, ecology, evolutionary biology, genetics, molecular biology and statistics is useful for successfully following the course.

Basic computer skills, familiarity with spreadsheets and an understanding of the general principles of data analysis are also recommended. The knowledge required to use the specific software introduced during the practical classes will be provided during the course.

Previous practical experience in molecular genetics methods is not required. Students who have never undertaken molecular laboratory work will be offered an optional introductory activity aimed at providing the necessary basic background.

Course structure

The course addresses the study of marine populations and fishery stocks through the integration of biomolecular and bio-ecological approaches. The two modules are closely interconnected and jointly contribute to the identification and understanding of biological units relevant to the conservation, monitoring and sustainable management of marine resources.

Module 1 – Biomolecular technologies for the study of marine populations

Lecturer: Alessia Cariani – 3 ECTS

Conceptual foundations

• Concepts of population, stock, metapopulation, population structure and connectivity.
• Dispersal and connectivity in marine organisms with high and low dispersal capacity.
• Effects of environmental, ecological, behavioural and reproductive characteristics on genetic variation.
• Main microevolutionary processes: mutation, genetic drift, gene flow and natural selection.
• Differences between neutral, potentially adaptive and functional genetic variation.
• Relationships between demographic population size and effective population size.

Molecular markers and technologies

• Sampling principles for population genetics and population genomics studies.
• Collection, preservation and traceability of biological samples.
• Characteristics, potential applications and limitations of the main molecular markers.
• Sequence-based markers, mitochondrial DNA, microsatellites and single nucleotide polymorphisms.
• Principles of high-throughput sequencing technologies and genome-wide genotyping approaches.
• Quality control of genetic and genomic data.
• Selection of appropriate markers according to the biological or management question being addressed.

Analysis of genetic variation

• Genetic diversity within populations and differentiation among populations.
• Allele and genotype frequencies.
• Hardy–Weinberg equilibrium.
• Fixation indices and estimation of genetic differentiation.
• Analysis of molecular variance.
• Methods for identifying population structure and assigning individuals to populations.
• Reconstruction of phylogeographic patterns and demographic history.
• Analysis of temporal changes in genetic diversity.
• Identification of molecular markers potentially under selection and assessment of relationships between genomic variation and environmental variables.

Applications

• Identification and delimitation of populations and fishery stocks.
• Assessment of connectivity among marine populations.
• Genetic erosion and stock depletion.
• Genetic and genomic monitoring of exploited populations.
• Geographic and individual traceability of seafood products.
• Applications to conservation, fisheries and aquaculture.
• Limitations, uncertainty and critical interpretation of biomolecular results.

Data analysis practical classes – Dry lab

Practical classes will involve the use of genetic and genomic datasets from marine populations. Students will be guided through data organisation and quality control, calculation of the main indices of genetic diversity and differentiation, analysis of population structure, and biological and management-related interpretation of results.

Activities may include the analysis of DNA sequence, microsatellite and SNP data, the use of specialised software, and basic analytical procedures in the R environment.

Optional molecular laboratory activity – Wet lab

Students who have not previously acquired practical experience in basic molecular genetics methods may be offered an optional introductory laboratory activity.

The activity may include:

• tissue sampling and preservation;
• DNA extraction and assessment of DNA quality;
• polymerase chain reaction amplification;
• agarose gel electrophoresis;
• basic principles of sequencing and genotyping.

This activity is intended to provide foundational training. It does not introduce additional compulsory examination content and does not directly contribute to the final grade.

Module 2 – Bio-ecological technologies for the study of fishery stocks

Lecturer: Marco Stagioni – 3 ECTS

Exploited populations and fishery stocks

• Concepts of biological population, fishery stock and management unit.
• Main biological characteristics governing the dynamics of exploited marine populations.
• Effects of fishing and other anthropogenic pressures on marine populations, communities and ecosystems.
• Effects of environmental variability and natural changes on stock productivity.
• Principles of marine biological resource monitoring.
• Relationships among data collection, stock status assessment and management decisions.
• Principles of sustainable fisheries management within the framework of European policies concerning the marine environment and fishery resources.

Fishery sampling and organism identification

• Main types of commercial fishing and the associated fishing gear.
• Characteristics, operation and selectivity of fishing gear.
• Design and organisation of biological sampling.
• Sorting of catches and bycatch.
• Taxonomic identification of fish, crustaceans and molluscs.
• Sorting and identification of the main benthic organisms.
• Collection, recording and quality control of biological data.

Biological analysis of catches

• Biometric measurements and length–weight relationships.
• Sex determination and assessment of sex ratios.
• Macroscopic assessment of sexual maturity.
• Reproductive cycle, fecundity and reproductive potential.
• Somatic and condition indices.
• Length and age structure of populations.
• Principles of age estimation in fish.
• Collection, preparation and reading of otoliths.
• Dissection and analysis of stomach contents.
• Main indicators used to investigate diet and trophic relationships.
• Interpretation of biological data for stock monitoring and management.

Practical activities

Depending on the availability of biological material, practical classes may include:

• identification of fishing gear;
• sorting and taxonomic identification of catches;
• collection of biometric data;
• determination of sex and maturity stage;
• calculation of condition indices;
• collection and analysis of otoliths;
• dissection and analysis of digestive tracts;
• identification of benthic organisms;
• recording, organisation and interpretation of the data collected.

Particular attention will be paid to the standardisation of procedures, data quality, reproducibility of observations and the limitations of the methods applied.

Readings/Bibliography

Compulsory material for examination preparation

The material required to prepare for the examination will be made available on the Virtuale platform and will include:

• lecture presentations;
• handouts and protocols for practical activities;
• selected scientific articles;
• datasets and instructions for practical classes;
• software user guides;
• technical and regulatory documents discussed during the course.

All materials identified as compulsory on Virtuale form an integral part of the examination syllabus.

Students who do not attend classes are advised to consult the platform regularly and to contact the lecturers for clarification regarding the organisation of their independent study.

Recommended further reading

• Allendorf, F.W., Luikart, G.H. and Aitken, S.N. Conservation and the Genetics of Populations. Second edition. Wiley-Blackwell.
• Jennings, S., Kaiser, M.J. and Reynolds, J.D. Marine Fisheries Ecology. Blackwell Science.
• Bombace, G. and Lucchetti, A. Elementi di biologia della pesca. Edagricole.
• Kaiser, M.J., Attrill, M.J., Jennings, S. and Thomas, D.N. Marine Ecology: Processes, Systems, and Impacts. Third edition. Oxford University Press.

The recommended textbooks do not replace the materials provided by the lecturers. Additional readings may be suggested during the course.

Teaching methods

The course includes lectures, presentation and discussion of case studies, data analysis practical classes and laboratory activities.

Lectures will provide the conceptual and methodological foundations required to understand the technologies used to study marine populations and fishery stocks. Case studies drawn from the scientific literature will be used to critically discuss the applicability, advantages, limitations and sources of uncertainty associated with different approaches.

In Module 1, lectures will be complemented by computer-based practical classes carried out individually or in small groups. Students will analyse genetic and genomic datasets and will be guided in selecting appropriate methods, performing analyses and interpreting the results.

The molecular laboratory component of Module 1 will be optional and will be intended primarily for students who have no previous practical experience in basic molecular methods.

In Module 2, lectures will be complemented by practical activities using biological samples. Students will apply protocols for the identification, sampling and analysis of catches and will discuss the relevance of the resulting data to stock monitoring and management.

The practical activities are also intended to develop transferable skills in problem-solving, data organisation, critical evaluation of evidence, teamwork and scientific communication.

Health and safety training

In view of the activities and teaching methods adopted, participation in the laboratory activities requires prior completion of Modules 1 and 2 of the health and safety training programme in e-learning mode, as well as participation in Module 3, which provides specific training on health and safety in study and research environments.

Information on the schedule and procedures for attending Module 3 is available in the relevant section of the Degree Programme website and will also be communicated through Virtuale.

Access to the laboratory activities is subject to completion of the required health and safety training and compliance with the operational procedures and personal protective equipment requirements communicated by the lecturers.

Assessment methods

Learning outcomes will be assessed through an integrated individual oral examination, normally lasting approximately 35–45 minutes and covering the contents of both modules.

The examination will include:

1. one question concerning the conceptual foundations and biomolecular approaches used to study marine populations;
2. one question concerning bio-ecological methods for monitoring and analysing fishery stocks;
3. discussion of a case study, figure, table or simple analytical result, aimed at assessing the student’s ability to critically interpret data and integrate information obtained using different methods.

The examination assesses:

• knowledge of the biological, ecological and evolutionary principles underlying population dynamics;
• knowledge of the technologies and protocols presented during the course;
• ability to select appropriate methods for a specific research or management question;
• ability to interpret bio-ecological, genetic and genomic data;
• ability to evaluate the advantages, limitations and sources of uncertainty of different approaches;
• ability to relate scientific results to monitoring, conservation and sustainable management objectives;
• command of disciplinary terminology and clarity of presentation.

Practical and laboratory activities are not assessed separately. The skills acquired during practical classes will be assessed through the discussion of methods, data and results during the oral examination.

No compulsory interim assessments or assignments to be submitted before the examination are planned.

The final mark is expressed on a scale of 30. The minimum passing grade is 18/30. To pass the examination, students must demonstrate at least sufficient knowledge of the contents of both modules. A single final grade will be awarded, taking into account the student’s overall preparation and ability to integrate the two components of the course.

Grading criteria

• 18–19: limited and mainly descriptive knowledge of the topics; ability to analyse and establish connections emerges primarily with guidance from the lecturers; generally appropriate use of terminology.
• 20–24: adequate knowledge of the fundamental topics; ability to apply methods correctly to standard situations; limited independence in the analysis of more complex problems.
• 25–29: broad and well-organised knowledge; good ability to critically analyse and interpret data and independently select suitable methods; confident use of specialist terminology.
• 30–30 with honours: complete and in-depth preparation; full ability to critically integrate bio-ecological and biomolecular approaches and discuss their assumptions, limitations and implications; excellent independent judgement, clarity and rigour of argument. Honours are awarded for outstanding preparation and a particularly strong ability to develop original and interdisciplinary reasoning.

During the examination, students may not use textbooks, notes, electronic devices, software, calculators or other supporting materials, except for authorised assistive tools.

Students must register for the examination through AlmaEsami by the deadline indicated for each examination session.

Use of generative Artificial Intelligence

The use of generative Artificial Intelligence for the assessment is prohibited. Any use of such tools constitutes a breach of academic integrity.

Students with disabilities or specific learning disorders

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students ) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

Teaching tools

Lectures and practical activities will be supported by:

• presentations and audiovisual materials;
• scientific articles and review papers;
• laboratory protocols and handouts;
• taxonomic identification keys and guides;
• biological samples and reference collections;
• microscopes, stereomicroscopes and instruments for biometric and biological analyses;
• computers and computer laboratory facilities;
• genetic, genomic and bio-ecological datasets;
• spreadsheet software;
• the R environment and specialised software that is freely available or accessible through University facilities;
• the Virtuale platform for teaching materials, announcements and instructions concerning practical activities.

Whenever possible, teaching materials will be provided in accessible formats. Students requiring adjustments to teaching tools or practical activities are advised to contact the relevant University services sufficiently in advance.

Generative Artificial Intelligence may be used during individual study exclusively as a support tool for reorganising notes, generating self-assessment questions or obtaining preliminary simplifications of complex concepts. Any information produced by such tools must be critically verified against course materials and the scientific sources recommended by the lecturers. AI tools must not be regarded as scientific sources and cannot replace students’ independent reasoning.

Office hours

See the website of Alessia Cariani

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