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A short course of lectures
«Biodiversity Conservation and Phylogenetic Systematics»





Material and MethodsResultsMeasures We Rule OutHill Numbers and the Replication PrincipleAn ExampleThe Rarefaction of Phylogenetic Diversity: Formulation, Extension and ApplicationA Maze of MeasuresFuture PerspectivesQuestionsExtinction TrendsThe Main CandidatesReconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?ResultsAssessing Hotspots of Evolutionary History with Data from Multiple Phylogenies:In Phase with Modern Systematics and NGS Methods: The Tree First, Then the SpeciesMetric and Corrections for BiasFuture DirectionsGeneralized EntropiesMaximization of Complementary Richness (MCR)Feature Diversity and Evolutionary Models of Character ChangeSplit Diversity: Measuring and Optimizing Biodiversity Using Phylogenetic Split NetworksSpecies DistributionCalculations Using Phylogenetic Distinctiveness Fail to Integrate ComplementarityPhylogenetic DataSpatial AnalysisMaterial and MethodsMethodsInstrumental ValueSupport in Area Prioritization Using Phylogenetic InformationMethodological ConsiderationsPhylogenetic Diversity as a Basis for Defining “Planetary Boundaries” for BiodiversityCase Study SetupFirst Case: The Original Ranking Does Not Mean SupportOn a Reptilian LimbRelict Species and Present Extinction RisksDiscussionGenetic DiversityConservation PlanningEvolutionary DistinctnessData and SamplingBiodiversity Conservation in MadagascarResultsComplementarity: A Key PD AttributeBirds on Long BranchesExtinction and the Loss of Evolutionary HistoryPhylogenetic Beta-DiversityConsideration of Individual SitesPhylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill NumbersInteger ProgrammingThe NeotropicsAnthropogenic VariablesSarcolaenaceae as a Model Group for Conservation in MadagascarGlobal Self-Consistent Hierarchical High-Resolution Shoreline DataMüllerian Mimicry: Patterns of Diversity and Community VulnerabilityLong Branches and Their Biological MeaningWhat Is the Meaning of Extreme Phylogenetic Diversity? The Case of Phylogenetic Relict SpeciesStandardisation of SamplingAnalysisApplicationThe Roles of Phylogenetic DiversityFunction and MorphologyDiscussionApplicationsHierarchical ClusteringCalculations and ComparisonsData AnalysisThe Value of Phylogenetic DiversityData Used and Pre-processingNext StepsPhylogenetic Hill Numbers and Related MeasuresPhylogenetic DispersionMoral Justifications for a General Measure of Biodiversity?Properties of the Ferrier et al. formulaIsland StudiesConservation of Phylogenetic Diversity in Madagascar's Largest Endemic Plant Family, SarcolaenaceaeLong Branches and Phylogenetic DiversityIsland BiogeographyQuantifying the Loss of Evolutionary HistoryResultsNormalized Phylogenetic Similarity MeasuresReserve Selection ProblemsResultsPatterns of Species, Phylogenetic and Mimicry Diversity of Clearwing ButterfliesThe Influence of Species Richness on Site ScoresResampling AnalysisGEO BONThe Importance of Phylogeny in ConservationSpecies Diversity and Species RichnessClassic Measures and Their Phylogenetic GeneralizationsPhylogenetic Split NetworksIntrinsic ValueSimple Calculations Based on PDPhylogenetics and Phylogenetic DiversityOther AlgorithmsResultsThe Measure of Split DiversityPhylogenetics and Conservation in New Zealand: The Long and the Short of ItTaxon Selection ProblemsPriorities for Conservation of the Evolutionary History of Amphibians in the CerradoDiscussionMaterial and MethodsSarcolaenaceae as a Model GroupDiscussionThe PD Phylogenetic Diversity Framework: Linking Evolutionary History to Feature Diversity for Biodiversity ConservationSecond Case: The Support for the Original RankingDecomposition of Phylogenetic Diversity MeasuresDiscussionOptimal ScenarioSpeciation and Extinction as Two Natural ProcessesPDA: Phylogenetic Diversity AnalyzerPhylogenetic Generalized EntropiesJack-Knife in ConservationReplication Principle for Phylogenetic Diversity MeasuresSome Considerations About the Sites PrioritizedIndexes UsedWhat a Relict Species Is Not?Phylogenetics and Conservation Biology: Drawing a Path into the Diversity of LifePersistence Versus RepresentativenessAssessing Hotspots of Evolutionary Distinctiveness in New CaledoniaHow the ED Method Converts PD-Dissimilarities to Estimates of Gains and LossesComputational Methods in Conservation PlanningPhylogenetic Structure in Extinction RisksGlobal Spatial Analyses of Phylogenetic Conservation Priorities for Aquatic MammalsPhylogenetic ExtremitiesDiscussionMetapopulation Capacity Meets Evolutionary Distinctness: Spatial Fragmentation Complements Phylogenetic Rarity in PrioritizationSimulation MethodsThe Role of the Number of Phylogenies on Site ScoresWhat Then, Is a Relict Species?Material and MethodsII MethodsShifting the Balance Towards a Low-Diversity EarthComputer SoftwareMetapopulation CapacityAppendixInfluence of Individual PhylogeniesA Simple Graphical Description of ED for the Single Gradient CaseProposed ProtocolMaterial and MethodsIs There a Geographical or a Climatic Component to the Notion of Relictness?Phylogenetic Diversity as a General Measure of BiodiversityOne of Many BiodiversitiesSpecies, Mimicry and Phylogenetic DiversityExtinction Drivers: Animals Versus PlantsMethods and MaterialsRelicts and Ecosystem FunctioningHill Numbers and Their Phylogenetic GeneralizationsHotspots of Species Richness and Phylogenetic Diversity in the NeotropicsRepresenting Hotspots of Evolutionary History in Systematic Conservation Planning for European MammalsImpacts on Biodiversity ConservationMadagascarAre Relict Species Evolutionarily Frozen?DiscussionUsing Phylogenetic Dissimilarities Among Sites for Biodiversity Assessments and ConservationStudy AreaFormulationEmpirical ExamplesNumber of ReplicatesBiodiversity Optimization ProblemsHuman Emotional Responses to the Natural WorldProspectsI QuestionsExtensionIII ApplicationsStudy Groups and PhylogeniesThe Future of Phylogenetic SystematicsMeasures and AnalysisSurrogates of BiodiversityJack-KnifeRelictness: A Relative Notion and the Need for Formal AnalysesRelict Species and Conservation Biology: A Final AppraisalMimicry ClassificationMeasures of Biodiversity and Madagascar's Network of Protected AreasResampling Multiple Phylogenies: How Stable Are the Results?MethodsGlossarySplitsTreeDigital Distribution Maps of the IUCN Red List of Threatened SpeciesGreedy AlgorithmsPhylogenetic EvennessResults
 
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