Advanced Evolutionary Genomics


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





Responsible teacher

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


Weekly - 2

Total - Available soon

Teaching language



Available soon


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

Available soon

Evaluation method

Available soon

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