The objectives of this course are to know and understand methods of phylogenetic reconstructions, and to be able to use trees in the current genomic era

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

  • estimating gene trees and species trees
  • detecting positive selection on coding genes


  • Trees inference, gene trees / species trees estimation and molecular evolution (pdf)
  • R script


  • Maximum Likelihood for gene trees (pdf)
  • Estimating species trees (pdf)
  • Testing positive selection (pdf)
  • summary of the biological context

Report to send

The grades for the course will be based on a report covering the practicals that were done. Here are the main details for the report:

  1. it should be handed over by April 30th in the form of a pdf file sent by email to nicolas [.] salamin [at] unil [.] ch
  2. it should contain all the elements covered during the practicals
  3. it should be concise while containing the main results that you obtained with a short explanation on the main elements found

Books important for the course:

  • Felsenstein, J. 2003. Inferring phylogenies. Sinauer Associates.
  • Page, R. 2003. Tangled trees: Phylogeny, cospeciation, and coevolution. University of Chicago Press.
  • Purvis, A., Gittleman, J.L. and Brooks, T. 2005. Phylogeny and conservation. Cambridge University Press.
  • Swofford, D.L., Olsen, G.K., Waddell, P.J. and Hillis, D.M. 1996. Phylogeny reconstruction. Pages 407-514 In Molecular Systematics (D.M. Hillis, C. Moritz, B.K. Mable, eds.). Sinauer Associates.
  • Yang, Z.H. 2006. Computational Molecular Evolution. Oxford University Press.