Phylogenies in Ecology: A Guide to Concepts and Methods

by Marc W. Cadotte, T. Jonathan Davies

Overview

Phylogenies in Ecology is the first book to critically review the application of phylogenetic methods in ecology, and it serves as a primer to working ecologists and students of ecology wishing to understand these methods. This book demonstrates how phylogenetic information is transforming ecology by offering fresh ways to estimate the similarities and differences among species, and by providing deeper, evolutionary-based insights on species distributions, coexistence, and niche partitioning. Marc Cadotte and Jonathan Davies examine this emerging area's explosive growth, allowing for this new body of hypotheses testing.

Cadotte and Davies systematically look at all the main areas of current ecophylogenetic methodology, testing, and inference. Each chapter of their book covers a unique topic, emphasizes key assumptions, and introduces the appropriate statistical methods and null models required for testing phylogenetically informed hypotheses. The applications presented throughout are supported and connected by examples relying on real-world data that have been analyzed using the open-source programming language, R.

Showing how phylogenetic methods are shedding light on fundamental ecological questions related to species coexistence, conservation, and global change, Phylogenies in Ecology will interest anyone who thinks that evolution might be important in their data.

Product Details

ISBN-13:	9780691157689
Publisher:	Princeton University Press
Publication date:	08/09/2016
Pages:	264
Product dimensions:	7.10(w) x 10.10(h) x 0.80(d)

About the Author

Marc W. Cadotte is associate professor of biology at the University of Toronto, Scarborough. T. Jonathan Davies is assistant professor of biology at McGill University.

Table of Contents

Preface ix

CHAPTER 1 An Entangled Bank: Evolutionary Relationships and Ecological Patterns 1

1.1. Systematics and the Diversity of Life 2

1.2. The Origins 3

1.3. “Correcting” Ecological Comparisons 6

1.4. The Emergence of Ecophylogenetics 7

1.5. The Goal of This Book 8

CHAPTER 2 Building and Using Phylogenies 10

2.1. Handling Phylogenies in R 11

2.2. Building Trees 19

2.3. Finding and Adapting Available Trees 31

2.4. Tree Scaling and Rate Smoothing 33

2.5. Conclusion 40

CHAPTER 3 Phylogenetic Patterns within Communities: Inferring Mechanisms of Ecological Assembly Using Phylogenetic Distances 41

3.1. Phylogenetic Distances and Community Assembly 44

3.2. Calculating Community Diversity Metrics 55

3.3. A Note about Phylodiversity Measures—Moving from the Causes to the Consequences of Diversity 65

3.4. Conclusion 66

CHAPTER 4 Randomizations, Null Distributions, and Hypothesis Testing 67

4.1. A Brief History of Randomization Tests in Ecology (or the Simberloffian Shift in Ecology) 72

4.2. How to Build Null Communities 76

4.3. Randomizing Phylogenetic Data 83

4.4. Taking the Pool Seriously 96

4.5. Conclusion 99

CHAPTER 5 Detecting Patterns of Trait Evolution 100

5.1. Phylogenetic Signal 101

5.2. Alternative Models of Trait Evolution 108

5.3. Reconstructing Ancestral States 115

5.4. Conclusion 120

CHAPTER 6 The Geography of Speciation and Character Displacement 121

6.1. Character Divergence and Geographic Overlap 122

6.2. Community-Wide Trait Dispersion 133

6.3. Conclusion 141

CHAPTER 7 Phylogenetic Diversity across Space and Time 143

7.1. Phylobetadiversity: Measuring Phylogenetic Turnover 145

7.2. The Influence of Spatial Scale on Phylogenetic Patterns 161

7.3. Conclusion 170

CHAPTER 8 Speciation, Extinction, and the Distribution of Phylogenetic Diversity 172

8.1. Conservation of the Tree of Life 172

8.2. Macroevolution: Diversification 181

8.3. Conclusion 194

CHAPTER 9 Using Phylogenetic Information to Make Better Conservation Decisions 196

9.1. Why Preserve Evolutionary History? 197

9.2. Quantifying Evolutionary History 201

9.3. Prioritizing Species Based on Evolutionary Distinctiveness 204

9.4. Prioritizing Hotspots of Evolutionary Distinctiveness 207

9.5. Applying Conservation Metrics 208

CHAPTER 10 Conclusion: Where To From Here? 209

10.1. Predicting Ecology from Evolutionary Patterns 210

10.2. Combining Trait and Phylogenetic Information 212

10.3. Phylogenetic Insights into a Changing World 213

10.4. Where To Go from Here? 216

10.5. Heralding the Ecology-Evolution Synthesis? 221

Glossary 223

References 225

Index 249

What People are Saying About This

From the Publisher

"A history lesson, textbook, and lab manual all in one, this terrific book explores the concepts and methods at the intersection of ecology and phylogenetics, from community ecology to conservation. Perfect for experienced researchers and students new to the field."—David Ackerly, University of California, Berkeley

"This how-to manual is a comprehensive review and an important, encouraging, and evenhanded critique of ecophylogenetics. Cadotte and Davies give examples of the full range of ecophylogenetic analyses, which a reader can easily execute, learn from, and then use to create new ways for incorporating phylogenetic information to better understand the workings of organismal assemblages. A super book."—Campbell Webb, Harvard University

"With scope and rigor, this book makes a compelling case that there are indeed ways to gain insights into important ecological questions using phylogenetic methods. A significant contribution to the field, the book presents new conceptions of how community assembly and evolutionary history interact, as well as new interpretations of data. This work provides a clear blueprint for moving the field ahead and will greatly catalyze future work."—Mathew Leibold, University of Texas, Austin

Editorial Reviews

"Ecophylogenetics overlays knowledge of the origin of species with contemporary patterns found in the study of biological communities. To enhance understanding of this new synthesis, the authors provide not only data, but also the programming code (in the R language) so readers can test their comprehension. . . . With 101 figures, 285 snippets of R language programming code, and a 43-entry glossary, this book is as much a how to guide as it is an introduction to this new approach."

Choice

"A history lesson, textbook, and lab manual all in one, this terrific book explores the concepts and methods at the intersection of ecology and phylogenetics, from community ecology to conservation. Perfect for experienced researchers and students new to the field."—David Ackerly, University of California, Berkeley


"This how-to manual is a comprehensive review and an important, encouraging, and evenhanded critique of ecophylogenetics. Cadotte and Davies give examples of the full range of ecophylogenetic analyses, which a reader can easily execute, learn from, and then use to create new ways for incorporating phylogenetic information to better understand the workings of organismal assemblages. A super book."—Campbell Webb, Harvard University


"With scope and rigor, this book makes a compelling case that there are indeed ways to gain insights into important ecological questions using phylogenetic methods. A significant contribution to the field, the book presents new conceptions of how community assembly and evolutionary history interact, as well as new interpretations of data. This work provides a clear blueprint for moving the field ahead and will greatly catalyze future work."—Mathew Leibold, University of Texas, Austin

From the Publisher