Technologies for the EnvironmentModule LABORATORY OF MOLECULAR PHYLOGENETICS
Academic Year 2023/2024 - Teacher: ANNA MARIA PAPPALARDOExpected Learning Outcomes
The course aims to make the student acquire basic and advanced knowledge on the main laboratory techniques for the study of molecular phylogenetics at different taxonomic levels or of the evolutionary relationships between organisms through the analysis of molecular data and their representation through phylogenetic trees. More specifically, the student will be able to use the main basic techniques such as genomic DNA extraction, PCR amplification, agarose gel electrophoresis, sequencing along with basic notions on the use of bioinformatics software for data analysis.
Course Structure
Lectures and laboratories.
Required Prerequisites
Attendance of Lessons
Detailed Course Content
Introduction to phylogeny. Molecular phylogenetics: orthologous and paralogous genes. Multiple alignments of sequences. Molecular evolution models. Analysis of molecular markers useful for phylogenetic purposes at different taxonomic levels Phylogenetic reconstruction methods: Neighbor-Joining, Maximum Parsimony, Maximum Likelihood. Methods for evaluating phylogenetic accuracy. Main software for phylogenetic analysis. General information on techniques in preparation for laboratory activities: isolation of genomic DNA, PCR amplification, agarose gel electrophoresis, sequencing. Data analysis using bioinformatics tools: analysis and editing of chromatograms of DNA sequences; Genbank database, search for similarity of sequences using Blast; multiple alignment of DNA sequences (ClustalW; MAFFT); case studies of phylogenetic inference.
Textbook Information
1. Stingo et al., Anatomia Comparata. Edi. Ermes
2. Pascarella, Paiardini, Bioinformatica. Zanichelli
3. Graur. Molecular and Genome Evolution. Sinauer Associates, Oxford University Press.
4. Other material (pdf files) provided by the teacher
Course Planning
| Subjects | Text References | |
|---|---|---|
| 1 | 1. Molecular phylogeny: orthologous and paralogous genes | 1. CAP17 - 2. CAP1 |
| 2 | 2. Multiple sequence alignments | 1. CAP17 - 2. CAP6 - 3. CAP3 |
| 3 | 3. Models of molecular evolution | 1. CAP17 - 2. CAP1- 3. CAP3, CAP4 |
| 4 | 4. Molecular markers | 4. |
| 5 | 5. Phylogenetic reconstruction methods | 1. CAP17- 3. CAP5 |
| 6 | 6. Phylogenetic inference software | 4. |
| 7 | 7. Molecular biology techniques for studying phylogeny | 4. |
| 8 | 8. Sequence databases | 2. CAP2 |
| 9 | 9. Sequence similarity search in databases | 2. CAP5 - 4. |
| 10 | 10. Case studies of phylogenetic inference | 4. |
Learning Assessment
Learning Assessment Procedures
The final exam consists of an oral interview on the topics covered in the lectures.The exam is designed to ascertain the degree of learning and understanding and the ability to analyse and synthesis of the topics covered during the course. The assessment consists of a grade in thirtieths, with a minimum mark of 18/30, averaged with the exam grade for the Mycology Module.
Examples of frequently asked questions and / or exercises
What are the main methods of phylogenetic reconstruction?
On what principle is PCR amplification based and how is a reaction mix prepared?
What can the BLAST tool do?