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