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