Computational Phylogenetics

Objectives

The objectives of this course are to know and understand methods of phylogenetic reconstructions, and to be able to use tree to test evolution of genes and organisms

Topics covered

Beside discussing what is a phylogenetic tree and how to interpret it, we will introduce the main reconstruction methods available. This will include a thorough description of

• optimization critera and models of evolution
• finding the optimal tree
• Bayesian methods and MCMC
• how to be sure you have the right tree?

Then we will discuss several aspects that uses phylogenetic trees as tool to understand gene and organisms evolution. This includes

• detecting positive seleciton on coding genes
• testing coevolution and cospeciation
• macroevolution: i) dating divergence times; ii) mode and tempo of evolution; iii) testing key innovations
• phylogenetics and conservation

Lectures

• Trees and Inference (pdf)
  
• Model testing (pdf)
  
• Dating trees (pdf)
  
• Comparative methods (pdf)
  
• Tempo of evolution (pdf)
  

Practicals

• File format (pdf)
• Maximum Likelihood and Bayesian (pdf)
• Dating trees (pdf)
• Testing macroevolution with R (pdf)
• Testing positive selection (pdf)