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Biodiversity Conservation and Phylogenetic Systematics - Roseli Pellens

Year 2016


Phylogenetics and Conservation Biology: Drawing a Path into the Diversity of LifeQuestionsGlossaryMethodsApplicationsReferencesPart I QuestionsThe Value of Phylogenetic DiversityIntroductionA Maze of MeasuresOne of Many BiodiversitiesMeasures We Rule OutSurrogates of BiodiversityAnthropogenic VariablesThe Main CandidatesSpecies Diversity and Species RichnessFunction and MorphologyGenetic DiversityPhylogenetics and Phylogenetic DiversityThe Roles of Phylogenetic DiversityMoral Justifications for a General Measure of Biodiversity?Intrinsic ValueHuman Emotional Responses to the Natural WorldInstrumental ValuePhylogenetic Diversity as a General Measure of BiodiversityConclusionReferencesThe PD Phylogenetic Diversity Framework: Linking Evolutionary History to Feature Diversity for Biodiversity ConservationIntroductionCalculations and ComparisonsSimple Calculations Based on PDComplementarity: A Key PD AttributeCalculations Using Phylogenetic Distinctiveness Fail to Integrate ComplementarityProspectsReferencesReconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?IntroductionSpeciation and Extinction as Two Natural ProcessesShifting the Balance Towards a Low-Diversity EarthExtinction TrendsExtinction Drivers: Animals Versus PlantsThe Importance of Phylogeny in ConservationExtinction and the Loss of Evolutionary HistoryPhylogenetic Structure in Extinction RisksQuantifying the Loss of Evolutionary HistoryFeature Diversity and Evolutionary Models of Character ChangeConclusionReferencesPhylogenetics and Conservation in New Zealand: The Long and the Short of ItIntroductionLong Branches and Their Biological MeaningBirds on Long BranchesOn a Reptilian LimbLong Branches and Phylogenetic DiversityPhylogenetic ExtremitiesConclusionsReferencesWhat Is the Meaning of Extreme Phylogenetic Diversity? The Case of Phylogenetic Relict SpeciesIntroductionWhat 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 AnalysesRelicts and Ecosystem FunctioningRelict Species and Present Extinction RisksRelict Species and Conservation Biology: A Final AppraisalReferencesPart II MethodsUsing Phylogenetic Dissimilarities Among Sites for Biodiversity Assessments and ConservationIntroductionHow the ED Method Converts PD-Dissimilarities to Estimates of Gains and LossesA Simple Graphical Description of ED for the Single Gradient CaseProperties of the Ferrier et al. formulaMaximization of Complementary Richness (MCR)DiscussionHierarchical ClusteringPersistence Versus RepresentativenessSimulation MethodsGEO BONReferencesPhylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill NumbersIntroductionClassic Measures and Their Phylogenetic GeneralizationsGeneralized EntropiesPhylogenetic Generalized EntropiesHill Numbers and Their Phylogenetic GeneralizationsHill Numbers and the Replication PrinciplePhylogenetic Hill Numbers and Related MeasuresReplication Principle for Phylogenetic Diversity MeasuresDecomposition of Phylogenetic Diversity MeasuresNormalized Phylogenetic Similarity MeasuresAn ExampleConclusionReferencesSplit Diversity: Measuring and Optimizing Biodiversity Using Phylogenetic Split NetworksIntroductionPhylogenetic Split NetworksThe Measure of Split DiversityBiodiversity Optimization ProblemsTaxon Selection ProblemsReserve Selection ProblemsComputational Methods in Conservation PlanningGreedy AlgorithmsInteger ProgrammingOther AlgorithmsComputer SoftwareSplitsTreePDA: Phylogenetic Diversity AnalyzerConclusions and PerspectivesAppendixReferencesThe Rarefaction of Phylogenetic Diversity: Formulation, Extension and ApplicationIntroductionFormulationExtensionApplicationStandardisation of SamplingPhylogenetic EvennessPhylogenetic Beta-DiversityPhylogenetic DispersionFuture DirectionsConclusionReferencesSupport in Area Prioritization Using Phylogenetic InformationConservation PlanningIndexes UsedJack-KnifeJack-Knife in ConservationOptimal ScenarioProposed ProtocolNumber of ReplicatesEmpirical ExamplesFirst Case: The Original Ranking Does Not Mean SupportSecond Case: The Support for the Original RankingReferencesAssessing Hotspots of Evolutionary History with Data from Multiple Phylogenies:IntroductionAssessing Hotspots of Evolutionary Distinctiveness in New CaledoniaMaterial and MethodsData and SamplingMetric and Corrections for BiasResampling AnalysisResultsThe Role of the Number of Phylogenies on Site ScoresThe Influence of Species Richness on Site ScoresInfluence of Individual PhylogeniesResampling Multiple Phylogenies: How Stable Are the Results?Consideration of Individual SitesDiscussionMethodological ConsiderationsSome Considerations About the Sites PrioritizedFuture PerspectivesReferencesPart III ApplicationsRepresenting Hotspots of Evolutionary History in Systematic Conservation Planning for European MammalsIntroductionMaterial and MethodsCase Study SetupResultsDiscussion and ConclusionsReferencesPriorities for Conservation of the Evolutionary History of Amphibians in the CerradoIntroductionMethodsStudy AreaData Used and Pre-processingAnalysisResultsDiscussionReferencesGlobal Spatial Analyses of Phylogenetic Conservation Priorities for Aquatic MammalsIntroductionMaterial and MethodsResultsDiscussionReferencesMetapopulation Capacity Meets Evolutionary Distinctness: Spatial Fragmentation Complements Phylogenetic Rarity in PrioritizationIntroductionEvolutionary DistinctnessSpatial AnalysisMetapopulation CapacityIsland BiogeographyMethods and MaterialsGlobal Self-Consistent Hierarchical High-Resolution Shoreline DataDigital Distribution Maps of the IUCN Red List of Threatened SpeciesData AnalysisResultsDiscussionSummaryIsland StudiesNext StepsReferencesPatterns of Species, Phylogenetic and Mimicry Diversity of Clearwing ButterfliesIntroductionMaterial and MethodsThe NeotropicsStudy Groups and PhylogeniesMimicry ClassificationSpecies DistributionSpecies, Mimicry and Phylogenetic DiversityResultsDiscussionHotspots of Species Richness and Phylogenetic Diversity in the NeotropicsMüllerian Mimicry: Patterns of Diversity and Community VulnerabilityConclusionReferencesConservation of Phylogenetic Diversity in Madagascar's Largest Endemic Plant Family, SarcolaenaceaeIntroductionMadagascarBiodiversity Conservation in MadagascarSarcolaenaceae as a Model GroupMaterial and MethodsPhylogenetic DataMeasures and AnalysisResultsDiscussionSarcolaenaceae as a Model Group for Conservation in MadagascarMeasures of Biodiversity and Madagascar's Network of Protected AreasConclusionReferencesThe Future of Phylogenetic SystematicsIn Phase with Modern Systematics and NGS Methods: The Tree First, Then the SpeciesImpacts on Biodiversity ConservationPhylogenetic Diversity as a Basis for Defining “Planetary Boundaries” for BiodiversityReferences
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