1. Chapter 2 – Working with the Tree of Life in Comparative Studies: How to Build and Tailor Phylogenies to Interspecific Datasets
2. Chapter 4 – Graphical Methods for Visualizing Comparative Data on Phylogenies 
3. Chapter 5  – A Primer on Phylogenetic Generalised Least Squares
4. Chapter 6 – Statistical Issues and Assumptions of Phylogenetic Generalized Least Squares
5. Chapter 7 – Uncertainties due to Within-Species Variation in Comparative Studies: Measurement Errors and Statistical Weights. 
6. Chapter 8 – An Introduction to Phylogenetic Path Analysis
7. Chapter 10 – Keeping Yourself Updated: Bayesian Approaches in Phylogenetic Comparative Methods with a Focus on Markov Chain Models of Discrete Character Evolution
8. Chapter 11 – General Quantitative Genetic Methods for Comparative Biology
9. Chapter 12 – Multimodel-Inference in Comparative Analyses
10. Chapter 13 – Simulation of Phylogenetic Data
11. Chapter 17 – Detecting Phenotypic Selection by Approximate Bayesian Computation in Phylogenetic Comparative Methods
12. Chapter 19 – Metrics and Models of Community Phylogenetics.
13. Chapter 21 – Phylogenetic Prediction to Identify “Evolutionary Singularities”
14. Chapter 22 – Preparing Paleontological Datasets for Phylogenetic Comparative Methods