Programme

### 1. Introduction to Molecular Biology Applied to Nature Conservation

- Main threats to biodiversity: habitat loss and fragmentation, climate change, invasive alien species, overexploitation of natural resources, and extinctions.
- Role of genetic and molecular information in biodiversity research and conservation.
- Principles of molecular evolution: mutations, nucleotide substitutions, genetic variability, and sequence divergence.
- Applications of molecular biology to conservation: species identification, biodiversity monitoring, characterisation of genetic variability, and assessment of population status.

### 2. Main Molecular Approaches to Biodiversity Research and Conservation

- DNA barcoding: principles, molecular markers, species identification, and applications.
- DNA metabarcoding: methodological principles and applications to biodiversity monitoring, including the analysis of environmental samples.
- Population genetics: genetic variability, population structure, gene flow, and connectivity.
- Conservation genomics: characterisation of genomic diversity, identification of evolutionarily significant units, and assessment of the adaptive potential of populations.
- Transcriptomics: general principles and applications to the study of organismal responses to environmental changes and stress.

### 3. Main Molecular Biology Techniques

- DNA extraction and purification: principles, methodologies, and the main factors affecting the quality and quantity of extracted DNA.
- Polymerase Chain Reaction (PCR): principles, reaction components, main steps, and applications.
- Agarose gel electrophoresis: principles, gel preparation, and separation and visualisation of DNA fragments.
- Quality control of biological samples and molecular data.

### 4. Practical Laboratory Activities

- DNA extraction from biological samples provided by the instructor.
- Preparation of PCR reactions and amplification of one or more genetic markers.
- Preparation and performance of agarose gel electrophoresis.
- Visualisation and interpretation of amplification products.
- Discussion of the results obtained and the main challenges associated with the experimental procedures.

### 5. Bioinformatics Analysis and Applications of Molecular Data

- Introduction to the main computational tools used for DNA sequence analysis.
- Sequence quality control, cleaning, and assembly.
- Multiple sequence alignment and identification of nucleotide differences.
- DNA barcoding exercises: sequence comparison, sample identification, and interpretation of results.
- Phylogenetic reconstruction exercises: construction and interpretation of phylogenetic trees.
- Phylogeography exercises: interpretation of the geographical distribution of genetic variability and relationships among populations.
- Discussion of the potential and limitations of different molecular methodologies in conservation applications.

Prerequisiti

To adequately follow the course, students are advised (but not required) to have basic knowledge of: - General and cell biology, particularly with regard to the structure and function of nucleic acids. - Genetics, including the concepts of genes, alleles, genetic variability, mutations, and inheritance. - Evolutionary biology, particularly with regard to the processes of molecular evolution, natural selection, genetic drift, and speciation. - Zoology, botany, and ecology, particularly with regard to biological diversity, populations, and the main threats to biodiversity. No prior experience with specific molecular analysis or bioinformatics software is required, as these tools will be introduced and used during the practical sessions.

Core Documentation

Allendorf et al., 2022. Conservation and the genomics of populations. Oxford university press.

The lecturer will provide additional didactic material.

Reference Bibliography

Allendorf et al., 2022. Conservation and the genomics of populations. Oxford university press.

Type of delivery of the course

The course will consist of practical activities in laboratory.

Attendance

The course will be held in person and attendance is strongly recommended.

Type of evaluation

The course includes theoretical lectures, practical laboratory activities, and bioinformatics exercises, aimed at providing students with the knowledge and skills required to apply molecular techniques to biodiversity research and conservation. The theoretical lectures will be supported by multimedia presentations, practical examples, and case studies drawn from the scientific literature. The main principles of molecular biology and molecular evolution will be introduced, highlighting the potential of genetic and genomic approaches in research and conservation activities. The practical activities will involve guided training in some of the main laboratory procedures, including DNA extraction from biological samples, amplification of molecular markers by PCR, and verification of amplification products through gel electrophoresis. These activities will be organised to familiarise students with the different stages of the experimental process, helping them understand the underlying principles and potential challenges. Part of the course will be devoted to the use of software and bioinformatics tools for processing and analysing DNA sequences. Through guided exercises, students will perform basic analyses involving DNA barcoding, phylogenetic reconstruction, phylogeography, and population genetics, using molecular data obtained during the practical activities and/or datasets provided by the instructor. The course will therefore adopt an integrated theoretical and practical approach, combining fundamental knowledge with the direct application of molecular techniques and data analysis tools, while highlighting their contribution to biodiversity research, monitoring, and conservation.