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Cover -- Title -- Copyright -- Dedication -- CONTENTS -- Preface -- CHAPTER 1 An Entangled Bank: Evolutionary Relationships and Ecological Patterns -- 1.1. Systematics and the Diversity of Life -- 1.2. The Origins -- 1.3. "Correcting" Ecological Comparisons -- 1.4. The Emergence of Ecophylogenetics -- 1.5. The Goal of This Book -- CHAPTER 2 Building and Using Phylogenies -- 2.1. Handling Phylogenies in R -- 2.2. Building Trees -- 2.3. Finding and Adapting Available Trees -- 2.4. Tree Scaling and Rate Smoothing -- 2.5. Conclusion
CHAPTER 3 Phylogenetic Patterns within Communities: Inferring Mechanisms of Ecological Assembly Using Phylogenetic Distances -- 3.1. Phylogenetic Distances and Community Assembly -- 3.2. Calculating Community Diversity Metrics -- 3.3. A Note about Phylodiversity Measures-Moving from the Causes to the Consequences of Diversity -- 3.4. Conclusion -- CHAPTER 4 Randomizations, Null Distributions, and Hypothesis Testing
4.1. A Brief History of Randomization Tests in Ecology (or the Simberloffian Shift in Ecology) -- 4.2. How to Build Null Communities -- 4.3. Randomizing Phylogenetic Data -- 4.4. Taking the Pool Seriously -- 4.5. Conclusion -- CHAPTER 5 Detecting Patterns of Trait Evolution -- 5.1. Phylogenetic Signal -- 5.2. Alternative Models of Trait Evolution -- 5.3. Reconstructing Ancestral States -- 5.4. Conclusion -- CHAPTER 6 The Geography of Speciation and Character Displacement -- 6.1. Character Divergence and Geographic Overlap
6.2. Community-Wide Trait Dispersion -- 6.3. Conclusion -- CHAPTER 7 Phylogenetic Diversity across Space and Time -- 7.1. Phylobetadiversity: Measuring Phylogenetic Turnover -- 7.2. The Influence of Spatial Scale on Phylogenetic Patterns -- 7.3. Conclusion -- CHAPTER 8 Speciation, Extinction, and the Distribution of Phylogenetic Diversity -- 8.1. Conservation of the Tree of Life -- 8.2. Macroevolution: Diversification -- 8.3. Conclusion
CHAPTER 9 Using Phylogenetic Information to Make Better Conservation Decisions -- 9.1. Why Preserve Evolutionary History? -- 9.2. Quantifying Evolutionary History -- 9.3. Prioritizing Species Based on Evolutionary Distinctiveness -- 9.4. Prioritizing Hotspots of Evolutionary Distinctiveness -- 9.5. Applying Conservation Metrics -- CHAPTER 10 Conclusion: Where To From Here? -- 10.1. Predicting Ecology from Evolutionary Patterns -- 10.2. Combining Trait and Phylogenetic Information -- 10.3. Phylogenetic Insights into a Changing World
10.4. Where To Go from Here?
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