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Biodiversity Conservation and Phylogenetic Systematics
Phylogenetics and Conservation Biology: Drawing a Path into the Diversity of Life
Questions
Glossary
Methods
Applications
I Questions
The Value of Phylogenetic Diversity
Introduction
A Maze of Measures
One of Many Biodiversities
Measures We Rule Out
Surrogates of Biodiversity
Anthropogenic Variables
The Main Candidates
Species Diversity and Species Richness
Function and Morphology
Genetic Diversity
Phylogenetics and Phylogenetic Diversity
The Roles of Phylogenetic Diversity
Moral Justifications for a General Measure of Biodiversity?
Intrinsic Value
Human Emotional Responses to the Natural World
Instrumental Value
Phylogenetic Diversity as a General Measure of Biodiversity
Conclusion
References
The PD Phylogenetic Diversity Framework: Linking Evolutionary History to Feature Diversity for Biodiversity Conservation
Introduction
Calculations and Comparisons
Simple Calculations Based on PD
Complementarity: A Key PD Attribute
Calculations Using Phylogenetic Distinctiveness Fail to Integrate Complementarity
Prospects
References
Reconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?
Introduction
Speciation and Extinction as Two Natural Processes
Shifting the Balance Towards a Low-Diversity Earth
Extinction Trends
Extinction Drivers: Animals Versus Plants
The Importance of Phylogeny in Conservation
Extinction and the Loss of Evolutionary History
Phylogenetic Structure in Extinction Risks
Quantifying the Loss of Evolutionary History
Feature Diversity and Evolutionary Models of Character Change
Conclusion
References
Phylogenetics and Conservation in New Zealand: The Long and the Short of It
Introduction
Long Branches and Their Biological Meaning
Birds on Long Branches
On a Reptilian Limb
Long Branches and Phylogenetic Diversity
Phylogenetic Extremities
Conclusions
References
What Is the Meaning of Extreme Phylogenetic Diversity? The Case of Phylogenetic Relict Species
Introduction
What Then, Is a Relict Species?
What a Relict Species Is Not?
Are Relict Species Evolutionarily Frozen?
Is There a Geographical or a Climatic Component to the Notion of Relictness?
Relictness: A Relative Notion and the Need for Formal Analyses
Relicts and Ecosystem Functioning
Relict Species and Present Extinction Risks
Relict Species and Conservation Biology: A Final Appraisal
References
II Methods
Using Phylogenetic Dissimilarities Among Sites for Biodiversity Assessments and Conservation
Introduction
How the ED Method Converts PD-Dissimilarities to Estimates of Gains and Losses
A Simple Graphical Description of ED for the Single Gradient Case
Properties of the Ferrier et al. formula
Maximization of Complementary Richness (MCR)
Discussion
Hierarchical Clustering
Persistence Versus Representativeness
Simulation Methods
GEO BON
References
Phylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers
Introduction
Classic Measures and Their Phylogenetic Generalizations
Generalized Entropies
Phylogenetic Generalized Entropies
Hill Numbers and Their Phylogenetic Generalizations
Hill Numbers and the Replication Principle
Phylogenetic Hill Numbers and Related Measures
Replication Principle for Phylogenetic Diversity Measures
Decomposition of Phylogenetic Diversity Measures
Normalized Phylogenetic Similarity Measures
An Example
Conclusion
References
Split Diversity: Measuring and Optimizing Biodiversity Using Phylogenetic Split Networks
Introduction
Phylogenetic Split Networks
The Measure of Split Diversity
Biodiversity Optimization Problems
Taxon Selection Problems
Reserve Selection Problems
Computational Methods in Conservation Planning
Greedy Algorithms
Integer Programming
Other Algorithms
Computer Software
SplitsTree
PDA: Phylogenetic Diversity Analyzer
Conclusions and Perspectives
Appendix
References
The Rarefaction of Phylogenetic Diversity: Formulation, Extension and Application
Introduction
Formulation
Extension
Application
Standardisation of Sampling
Phylogenetic Evenness
Phylogenetic Beta-Diversity
Phylogenetic Dispersion
Future Directions
Conclusion
References
Support in Area Prioritization Using Phylogenetic Information
Conservation Planning
Indexes Used
Jack-Knife
Jack-Knife in Conservation
Optimal Scenario
Proposed Protocol
Number of Replicates
Empirical Examples
First Case: The Original Ranking Does Not Mean Support
Second Case: The Support for the Original Ranking
References
Assessing Hotspots of Evolutionary History with Data from Multiple Phylogenies:
Introduction
Assessing Hotspots of Evolutionary Distinctiveness in New Caledonia
Material and Methods
Data and Sampling
Metric and Corrections for Bias
Resampling Analysis
Results
The Role of the Number of Phylogenies on Site Scores
The Influence of Species Richness on Site Scores
Influence of Individual Phylogenies
Resampling Multiple Phylogenies: How Stable Are the Results?
Consideration of Individual Sites
Discussion
Methodological Considerations
Some Considerations About the Sites Prioritized
Future Perspectives
References
III Applications
Representing Hotspots of Evolutionary History in Systematic Conservation Planning for European Mammals
Introduction
Material and Methods
Case Study Setup
Results
Discussion and Conclusions
References
Priorities for Conservation of the Evolutionary History of Amphibians in the Cerrado
Introduction
Methods
Study Area
Data Used and Pre-processing
Analysis
Results
Discussion
References
Global Spatial Analyses of Phylogenetic Conservation Priorities for Aquatic Mammals
Introduction
Material and Methods
Results
Discussion
References
Metapopulation Capacity Meets Evolutionary Distinctness: Spatial Fragmentation Complements Phylogenetic Rarity in Prioritization
Introduction
Evolutionary Distinctness
Spatial Analysis
Metapopulation Capacity
Island Biogeography
Methods and Materials
Global Self-Consistent Hierarchical High-Resolution Shoreline Data
Digital Distribution Maps of the IUCN Red List of Threatened Species
Data Analysis
Results
Discussion
Summary
Island Studies
Next Steps
References
Patterns of Species, Phylogenetic and Mimicry Diversity of Clearwing Butterflies
Introduction
Material and Methods
The Neotropics
Study Groups and Phylogenies
Mimicry Classification
Species Distribution
Species, Mimicry and Phylogenetic Diversity
Results
Discussion
Hotspots of Species Richness and Phylogenetic Diversity in the Neotropics
Müllerian Mimicry: Patterns of Diversity and Community Vulnerability
Conclusion
References
Conservation of Phylogenetic Diversity in Madagascar's Largest Endemic Plant Family, Sarcolaenaceae
Introduction
Madagascar
Biodiversity Conservation in Madagascar
Sarcolaenaceae as a Model Group
Material and Methods
Phylogenetic Data
Measures and Analysis
Results
Discussion
Sarcolaenaceae as a Model Group for Conservation in Madagascar
Measures of Biodiversity and Madagascar's Network of Protected Areas
Conclusion
References
The Future of Phylogenetic Systematics
In Phase with Modern Systematics and NGS Methods: The Tree First, Then the Species
Impacts on Biodiversity Conservation
Phylogenetic Diversity as a Basis for Defining “Planetary Boundaries” for Biodiversity
References
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