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

Species Diversity and Species RichnessBirds on Long BranchesIsland StudiesPhylogenetics and Conservation in New Zealand: The Long and the Short of ItMeasures We Rule OutResampling Multiple Phylogenies: How Stable Are the Results?Data Used and Pre-processingThe Roles of Phylogenetic DiversityPriorities for Conservation of the Evolutionary History of Amphibians in the CerradoResultsNormalized Phylogenetic Similarity MeasuresPhylogenetic DispersionCalculations Using Phylogenetic Distinctiveness Fail to Integrate ComplementarityThe Measure of Split DiversityEvolutionary DistinctnessRelict Species and Present Extinction RisksResultsA Maze of MeasuresComputer SoftwarePDA: Phylogenetic Diversity AnalyzerHow the ED Method Converts PD-Dissimilarities to Estimates of Gains and LossesFirst Case: The Original Ranking Does Not Mean SupportWhat Then, Is a Relict Species?The PD Phylogenetic Diversity Framework: Linking Evolutionary History to Feature Diversity for Biodiversity ConservationSarcolaenaceae as a Model Group for Conservation in MadagascarRepresenting Hotspots of Evolutionary History in Systematic Conservation Planning for European MammalsHierarchical ClusteringSplitsTreeBiodiversity Conservation in MadagascarOn a Reptilian LimbHotspots of Species Richness and Phylogenetic Diversity in the NeotropicsIII ApplicationsThe Value of Phylogenetic DiversityResultsResampling AnalysisMaximization of Complementary Richness (MCR)DiscussionMetapopulation Capacity Meets Evolutionary Distinctness: Spatial Fragmentation Complements Phylogenetic Rarity in PrioritizationAre Relict Species Evolutionarily Frozen?Jack-KnifeIn Phase with Modern Systematics and NGS Methods: The Tree First, Then the SpeciesHuman Emotional Responses to the Natural WorldDiscussionFeature Diversity and Evolutionary Models of Character ChangeAppendixExtensionPhylogenetic Beta-DiversityStudy Groups and PhylogeniesComputational Methods in Conservation PlanningRelictness: A Relative Notion and the Need for Formal AnalysesMethodsThe Role of the Number of Phylogenies on Site ScoresPhylogenetic Diversity as a General Measure of BiodiversityShifting the Balance Towards a Low-Diversity EarthIs There a Geographical or a Climatic Component to the Notion of Relictness?Relicts and Ecosystem FunctioningJack-Knife in ConservationMadagascarSpeciation and Extinction as Two Natural ProcessesAn ExampleII MethodsReconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?Material and MethodsSurrogates of BiodiversityPhylogenetic ExtremitiesPhylogenetics and Phylogenetic DiversityAnthropogenic VariablesWhat a Relict Species Is Not?Instrumental ValueFuture PerspectivesI QuestionsDiscussionMüllerian Mimicry: Patterns of Diversity and Community VulnerabilityExtinction Drivers: Animals Versus PlantsDiscussionCase Study SetupInteger ProgrammingMeasures of Biodiversity and Madagascar's Network of Protected AreasSpecies DistributionResultsAnalysisRelict Species and Conservation Biology: A Final AppraisalDiscussionInfluence of Individual PhylogeniesBiodiversity Optimization ProblemsPhylogenetic Split NetworksData and SamplingOptimal ScenarioPhylogenetic DataGlobal Spatial Analyses of Phylogenetic Conservation Priorities for Aquatic MammalsResultsNext StepsReplication Principle for Phylogenetic Diversity MeasuresHill Numbers and Their Phylogenetic GeneralizationsData AnalysisResultsStudy AreaConservation of Phylogenetic Diversity in Madagascar's Largest Endemic Plant Family, SarcolaenaceaePersistence Versus RepresentativenessMaterial and MethodsSome Considerations About the Sites PrioritizedSimulation MethodsThe Influence of Species Richness on Site ScoresQuantifying the Loss of Evolutionary HistoryThe NeotropicsIsland BiogeographySecond Case: The Support for the Original RankingDiscussionNumber of ReplicatesIntrinsic ValueSarcolaenaceae as a Model GroupThe Importance of Phylogeny in ConservationReserve Selection ProblemsAssessing Hotspots of Evolutionary Distinctiveness in New CaledoniaFunction and MorphologyPhylogenetic Structure in Extinction RisksMaterial and MethodsLong Branches and Their Biological MeaningHill Numbers and the Replication PrincipleLong Branches and Phylogenetic DiversityExtinction TrendsExtinction and the Loss of Evolutionary HistoryThe Rarefaction of Phylogenetic Diversity: Formulation, Extension and ApplicationFuture DirectionsConservation PlanningComplementarity: A Key PD AttributeDigital Distribution Maps of the IUCN Red List of Threatened SpeciesGenetic DiversityIndexes UsedDiscussionMoral Justifications for a General Measure of Biodiversity?Greedy AlgorithmsMeasures and AnalysisFormulationSpatial AnalysisMaterial and MethodsGlossaryQuestionsApplicationsStandardisation of SamplingGEO BONMethodsMimicry ClassificationProperties of the Ferrier et al. formulaCalculations and ComparisonsMetric and Corrections for BiasProposed ProtocolPhylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill NumbersThe Main CandidatesWhat Is the Meaning of Extreme Phylogenetic Diversity? The Case of Phylogenetic Relict SpeciesPhylogenetic EvennessPhylogenetic Hill Numbers and Related MeasuresSpecies, Mimicry and Phylogenetic DiversityTaxon Selection ProblemsGeneralized EntropiesEmpirical ExamplesClassic Measures and Their Phylogenetic GeneralizationsUsing Phylogenetic Dissimilarities Among Sites for Biodiversity Assessments and ConservationPatterns of Species, Phylogenetic and Mimicry Diversity of Clearwing ButterfliesSimple Calculations Based on PDMethods and MaterialsResultsThe Future of Phylogenetic SystematicsSupport in Area Prioritization Using Phylogenetic InformationImpacts on Biodiversity ConservationProspectsSplit Diversity: Measuring and Optimizing Biodiversity Using Phylogenetic Split NetworksA Simple Graphical Description of ED for the Single Gradient CaseApplicationPhylogenetics and Conservation Biology: Drawing a Path into the Diversity of LifeOther AlgorithmsOne of Many BiodiversitiesPhylogenetic Diversity as a Basis for Defining “Planetary Boundaries” for BiodiversityPhylogenetic Generalized EntropiesConsideration of Individual SitesMaterial and MethodsMethodological ConsiderationsDecomposition of Phylogenetic Diversity MeasuresMetapopulation CapacityAssessing Hotspots of Evolutionary History with Data from Multiple Phylogenies:Global Self-Consistent Hierarchical High-Resolution Shoreline Data
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