Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice

✍ Scribed by László Zsolt Garamszegi (eds.)

• Publisher: Springer-Verlag Berlin Heidelberg
• Year: 2014
• Tongue: English
• Leaves: 553
• Edition: 1
• Category: Library

✦ Synopsis

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

Front Matter....Pages i-xv
Front Matter....Pages 1-1
An Introduction to the Phylogenetic Comparative Method....Pages 3-18
Working with the Tree of Life in Comparative Studies: How to Build and Tailor Phylogenies to Interspecific Datasets....Pages 19-48
An Introduction to Supertree Construction (and Partitioned Phylogenetic Analyses) with a View Toward the Distinction Between Gene Trees and Species Trees....Pages 49-76
Graphical Methods for Visualizing Comparative Data on Phylogenies....Pages 77-103
A Primer on Phylogenetic Generalised Least Squares....Pages 105-130
Statistical Issues and Assumptions of Phylogenetic Generalized Least Squares....Pages 131-153
Front Matter....Pages 155-155
Uncertainties Due to Within-Species Variation in Comparative Studies: Measurement Errors and Statistical Weights....Pages 157-199
An Introduction to Phylogenetic Path Analysis....Pages 201-229
Phylogenetic Regression for Binary Dependent Variables....Pages 231-261
Keeping Yourself Updated: Bayesian Approaches in Phylogenetic Comparative Methods with a Focus on Markov Chain Models of Discrete Character Evolution....Pages 263-286
General Quantitative Genetic Methods for Comparative Biology....Pages 287-303
Multimodel-Inference in Comparative Analyses....Pages 305-331
Front Matter....Pages 333-333
Simulation of Phylogenetic Data....Pages 335-350
Use and Misuse of Comparative Methods in the Study of Adaptation....Pages 351-379
Modelling Stabilizing Selection: The Attraction of Ornstein–Uhlenbeck Models....Pages 381-393
Hidden Markov Models for Studying the Evolution of Binary Morphological Characters....Pages 395-408
Detecting Phenotypic Selection by Approximate Bayesian Computation in Phylogenetic Comparative Methods....Pages 409-424
Phylogenetic Comparative Methods for Studying Clade-Wide Convergence....Pages 425-450
Metrics and Models of Community Phylogenetics....Pages 451-464
Event-Based Cophylogenetic Comparative Analysis....Pages 465-480
Front Matter....Pages 333-333
Phylogenetic Prediction to Identify “Evolutionary Singularities”....Pages 481-514
Preparing Paleontological Datasets for Phylogenetic Comparative Methods....Pages 515-544
Back Matter....Pages 545-552

✦ Subjects

Evolutionary Biology; Life Sciences, general; Ecology; Biodiversity; Molecular Ecology; Theoretical Ecology/Statistics