Advanced Evolutionary Genomics

Objectives

This course will provide the students with advance knowledge in the field of Evolutionary Genomics growing from the basic concepts and methodologies that were acquired during the first semester.

The students will be introduced to the theoretical foundations of the mechanisms of molecular evolution and how these processes affect the evolution of genes and genomes.

The students will be also exposed to recent methodological developments in the field as well as applications of Evolutionary Genomics in the study of natural diversity and in biomedical research.

It is intended that the students acquire a critical thinking in evolutionary genomics, that they can recognize signals of the evolutionary process in genomes, and understand the most relevant methodologies of analysis.

General characterization

Code

12498

Credits

3.0

Responsible teacher

José Paulo Nunes de Sousa Sampaio, Patrícia Filipa Homem de Campos Tavares de Brito

Hours

Weekly - 2

Total - Available soon

Teaching language

Português

Prerequisites

N/A

Bibliography

Below is a list of main bibliography. In addition to the books listed the students will be asked to read specific research articles that will be provided during class.

Anisimova, M., Ed. 2012. Evolutionary genomics. Statistical and computational methods, Volume 1 and 2. Springer.   
Lemey, P., Salemi, M., Vandamme, A-M., Eds. The Phylogenetic handbook. A pratical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, 2nd edition. 750pp.

Teaching method

Teaching is organized in 90 min lectures and 3-hour sessions of active learning activities. During the lectures the students are introduced to main concepts, methodologies, and outstanding questions in the field. Although this is mainly expositive teaching the students are always encouraged to participate in classroom discussions. The active learning sessions are dedicated to computer labs with hands-on exercises, tutorials and journal clubs. The aim of these classes is to provide the students with an opportunity to experience the process of data analysis and acquire a critical thinking in evolutionary genomics. Student evaluation is based on class assessment throughout the semester (30%) that includes class preparation, attendance, and participation. The remaining 70% correspond to one final examination that includes knowledge acquired in the lectures and during the active learning sessions.

Evaluation method

Student evaluation is based on class assessment throughout the semester (30%) that includes class preparation, attendance, and participation. The remaining 70% correspond to one final examination that includes knowledge acquired in the lectures and during the active learning sessions.

Subject matter

1. Mechanisms of molecular evolution
2. Evolution of genome structure in Eucaryotes and Prokaryotes
3. Phylogenetic inference from genome-scale data
4. Applied population genomics to phylogeography and speciation   
5. Evolution in infectious diseases from large-scale population structure to transmission studies and within-host evolution.
    5.1. Comparative analysis of microbial genomes and pangenomes
    5.2. Virus evolution and molecular epidemiology    
6. Metagenomics in the analysis of Human microbiota in health and in disease
7. Evolution in cancer: clonal evolution and inference of intratumor diversity