This is the archive repository for the 'Online Practical Materials' for the book of 'Modern Phylogenetic Comparative Methods' (ed. Garamszegi, 2014). The available content here is a usable copy of the material at http://www.mpcm-evolution.com.
How to use MPCMArchive?
The explanations for the online practical materials divided into sections corresponding to the chapters of the book are listed on the Wiki page:
Files referred during the exercises are available in the 'data_files' folder, in the above repository.
Please feel free to let us know if you find any missing information or mistake.
Phylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators.
Table of contents
Foreword by Mark Pagel
Preface by László Zsolt Garamszegi
Part I Introduction
1.- An Introduction to the Phylogenetic Comparative Method.
2.- Working with the Tree of Life in Comparative Studies: How to Build and Tailor Phylogenies to Interspecific Datasets.
3.- An Introduction to Supertree Construction (and Partitioned Phylogenetic Analyses) with a View toward the Distinction between - Gene Trees and Species Trees.
4.- Graphical Methods for Visualizing Comparative Data on Phylogenies.
5.- A Primer on Phylogenetic Generalised Least Squares.
6.- Statistical Issues and Assumptions of Phylogenetic Generalised Least Squares.
Part II Handling Phylogenies in Different Statistical Designs
7.- Uncertainties due to Within-Species Variation in Comparative Studies: Measurement Errors and Statistical Weights.
8.- An Introduction to Phylogenetic Path Analysis.
9.- Phylogenetic Logistic Regression for Binary Dependent Variables.
10.- Keeping Yourself Updated: Bayesian Approaches in Phylogenetic Comparative Methods with a focus on Markov-chain models of Discrete Character Evolution.
11.- General Quantitative Genetic Methods for Comparative Biology.
12.- Multimodel-Inference in Comparative Analyses.
Part III Specific Models for Studying Evolutionary Mechanisms
13.- Simulation of Phylogenetic Data.
14.- Use and Misuse of Comparative Methods in the Study of Adaptation.
15.- Modelling Stabilising Selection: the Attraction of Ornstein-Uhlenbeck Models.
16.- Hidden Markov Models for Studying the Evolution of Binary Morphological Characters.
17.- Detecting Phenotypic Selection by Approximate Bayesian Computation (ABC) in Phylogenetic Comparative Methods.
18.- Phylogenetic Comparative Methods for Studying Clade-Wide Convergence.
19.- Metrics and Models of Community Phylogenetics.
20.- Event-Based Cophylogenetic Comparative Analysis.
21.- Phylogenetic Prediction to Identify “Evolutionary Singularities”.
22.- Preparing Paleontological Datasets for Phylogenetic Comparative Methods.