- Introduction of instructors & students.
- Introduction to the phylogenetic comparative method. [PDF]
- Exercise 1: Introduction the basics of the R statistical computing environment. [URL]
- Exercise 2: Introduction to reading, writing, manipulating, and visualizing phylogenies and comparative data in R. [URL]
- Brownian motion and phylogenetically independent contrasts. [PDF]
- Exercise 3: Brownian motion & phylogenetically independent contrasts in R. [1, 2]
- Challenge problem 1: Challenge problem on contrasts regression. [solution]
- Excerise 4: Phylogenetic generalized least squares regression. [URL]
- Challenge problem 2: PGLS. [solution]

- Other models of continuous character evolution on trees. [PDF]
- Exercise 5: Fitting models of continuous character evolution. [1, 2]
- Challenge problem 3: Continuous character models. [solution]
- Discrete character evolution on phylogenies. [PDF]
- Exercise 6: Fitting discrete character evolution models to phylogenetic data in R. [URL]
- Challenge problem 4: Discrete character evolution. [solution]
- Ancestral state reconstruction for discrete & continuous characters. [PDF]
- Exercise 7: Ancestral state reconstruction for continuous characters. [URL]
- Exercise 8: Ancestral state reconstruction for discrete characters. [URL]
- Challenge problem 5: Stochastic mapping discrete characters on a phylogeny. [solution]

- Pagel’s model for correlated binary trait evolution. [PDF]
- Exercise 9: Pagel’s model for studying the evolutionary correlation of discrete characters. [URL]
- Challenge problem 6: Examining the limitations of Pagel’s (1994) method. [solution]
- Introduction to multi-rate and multi-regime models of continuous character evolution. [PDF]
- Exercise 10: Multi-rate, multi-regime, and multivariate models for continuous trait evolution. [URL]
- Challenge problem 7: Multi-rate phenotypic evolution. [solution]
- Using reconstructed phylogenies to study the dynamics of species diversification. [PDF]
- Exercies 11: Introduction to studying diversification on phylogenies: LTT plots & γ. [URL]

- Measuring speciation and extinction rates on trees. [PDF]
- Exercise 12: Estimating speciation & extinction rates on phylogenies in R using ape and diversitree. [URL]
- Challenge problem 8: Exploring diversification models in R. [solution]
- State dependent diversification models. [PDF]
- Exercise 13: Fitting state-dependent diversification models in R using diversitree. [URL]
- Complex models of diversification. [PDF]
- Exercise 14: Fitting complex diversification models in R. [URL]
- Course evaluation survey. [URL]
- Exercise 15: Visualizing phylogenies and comparative data in R. [URL]
- Wrap-up and optional additional exercise or lecture.

*Course co-taught by Michael Alfaro, Ricardo Betancur, Luke Harmon, & Liam Revell. 28 June - 1 July 2016.*

Co-organized by Ricardo Betancur (University of Puerto Rico - Río Piedras) and Liam Revell (University of Massachusetts Boston), and funded by the National Science Foundation.