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
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
- File format (pdf)
- Maximum Likelihood and Bayesian (pdf) — phyml output
- Testing positive selection (pdf) — paml output
- Estimating species trees (pdf) — *BEAST output, summary of the biological context
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.