Part I: Introduction
An Introduction to the Phylogenetic Comparative Method
Working with the Tree of Life in Comparative Studies: How to Build and Tailor Phylogenies to Interspecific Datasets
An Introduction to Supertree Construction (and Partitioned Phylogenetic Analyses) with a View toward the Distinction between Gene Trees and Species Trees
Graphical Methods for Visualizing Comparative Data on Phylogenies
A Primer on Phylogenetic Generalised Least Squares
Statistical Issues and Assumptions of Phylogenetic Generalised Least Squares
Part II: Handling Phylogenies in Different Statistical Designs
Uncertainties due to Within-Species Variation in Comparative Studies: Measurement Errors and Statistical Weights
An Introduction to Phylogenetic Path Analysis
Phylogenetic Logistic Regression for Binary Dependent Variables
Keeping Yourself Updated: Bayesian Approaches in Phylogenetic Comparative Methods with a focus on Markov-chain models of Discrete Character Evolution
General Quantitative Genetic Methods for Comparative Biology
Multimodel-Inference in Comparative Analyses
Part III: Specific Models for Studying Evolutionary Mechanisms
Simulation of Phylogenetic Data
Use and Misuse of Comparative Methods in the Study of Adaptation
Modelling Stabilising Selection: the Attraction of Ornstein-Uhlenbeck Models
Hidden Markov Models for Studying the Evolution of Binary Morphological Characters
Detecting Phenotypic Selection by Approximate Bayesian Computation (ABC) in Phylogenetic Comparative Methods
Phylogenetic Comparative Methods for Studying Clade-Wide Convergence
Metrics and Models of Community Phylogenetics
Event-Based Cophylogenetic Comparative Analysis
Phylogenetic Prediction to Identify 'Evolutionary Singularities'
Preparing Paleontological Datasets for Phylogenetic Comparative Methods.