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 Maximum Parsimony (pdf)
• Searching for the best tree (pdf)
• Maximum Likelihood (pdf)
• Bayesian method (pdf)
• Comparative methods (pdf)

Practicals

• Maximum Parsimony (pdf)
• Maximum Likelihood and Bayesian (pdf)
• Dating trees with BEAST (pdf)
• Testing macroevolution with R (pdf)

Papers to Present

1. Model Misspecication and Probabilistic Tests of Topology: Evidence from Empirical Data Sets; pdf
2. Novel Versus Unsupported Clades: Assessing the Qualitative Support for Clades in MRP Supertrees; pdf
3. A Bayesian Framework for the Analysis of Cospeciation; pdf
4. Potential Applications and Pitfalls of Bayesian Inference of Phylogeny; pdf
5. Stochastic Mapping of Morphological Characters; pdf
6. Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models; pdf
7. Heterotachy and Tree Building: A Case Study with Plastids and Eubacteria; pdf
8. A General Comparison of Relaxed Molecular Clock Models; pdf
9. The Importance of Proper Model Assumption in Bayesian Phylogenetics; pdf
10. Estimating a Binary Character’s Effect on Speciation and Extinction; pdf
11. Performance-Based Selection of Likelihood Models for Phylogeny Estimation; pdf
12. Bayesian Phylogenetic Analysis of Combined Data; pdf
13. Statistical Analysis of Diversification with Species Traits; pdf
14. Strange bayes indeed: uniform topological priors imply non-uniform clade priors; pdf
15. Combining Multiple Data Sets in a Likelihood Analysis: Which Models are the Best?; pdf
16. Detecting the Historical Signature of Key Innovations Using Stochastic Models of Character Evolution and Cladogenesis; pdf
17. A Likelihood Framework for Inferring the Evolution of Geographic Range on Phylogenetic Trees; pdf
18. Distribution Modelling and Statistical Phylogeography: An Integrative Framework for Generating and Testing Alternative Biogeographical Hypotheses; pdf
19. Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees; pdf
20. Branch-Length Prior Influences Bayesian Posterior Probability of Phylogeny; pdf
21. The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies; pdf
22. Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?; pdf
23. Analysis of Comparative Data Using Generalized Estimating Equations; pdf
24. Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information Into the Analysis of Interspecific Data; pdf
25. Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution; pdf
26. Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods; pdf
27. Detecting Correlated Evolution on Phylogenies: A General Method for the Comparative Analysis of Discrete Characters; pdf
28. On the Best Evolutionary Rate for Phylogenetic Analysis; pdf