Phylogeny and Comparative Methods


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

  • dating phylogenetic trees
  • detecting positive selection on coding genes
  • macroevolution: i) dating divergence times; ii) mode and tempo of evolution; iii) testing key innovations

Lectures (pdfs for lectures and practicals are available on the course page on

  • Trees and Inference
  • Gene trees / species tree estimation and molecular evolution
  • Dating trees
  • Comparative methods


  • File format (pdf)
  • biological context of the data
  • tree reconstruction — phyml output
  • gene trees / species tree estimation — *beast output
  • Testing positive selection — paml output
  • Dating trees — beast output
  • Testing macroevolution with R

Books important for the course:

  • Felsenstein, J. 2003. Inferring phylogenies. Sinauer Associates.
  • Lemey, P., Salemi, M. and Vandamme, A.-M. 2009. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. Cambridge University Press.
  • 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. 2014. Molecular Evolution: A Statistical Approach. Oxford University Press.