Introduction To Conservation Genetics

Introduction toConservation GeneticsRichard Frankham,Macquarie University, SydneyJonathan D. BallouSmithsonian Institution, Washington, DCand David A. BriscoeMacquarie University, SydneyLine drawings byKarina H. MclnnessInkbyte, MelbourneCAMBRIDGEUNIVERSITY PRESS

ContentsPrefaceCopyright acknowledgmentsChapter IIntroductionxiiixx1'The sixth extinction'Why conserve biodiversity?Endangered and extinct speciesWhat is an endangered species?What causes extinctions?Recognition of genetic factors in conservation biologyWhat is conservation genetics?How is genetics used to minimize extinctions?Genetic versus demographic and environmental factors inconservation biologyWhat do we need to know to genetically manage threatenedspecies?Methodology in conservation geneticsIsland t h e m eSources of informationSummaryGeneral bibliographyProblemsPractical exercises: Categorizing e n d a n g e r m e n t of species1618191919202122Chapter 223Genetics and extinctionGenetics and the fate of endangered speciesRelationship between inbreeding and extinctionInbreeding and extinction in the wildRelationship between loss of genetic diversity and extinctionSummaryFurther readingProblemsPractical exercises: Computer projectionsSECTION I223679911162427293639394040EVOLUTIONARY GENETICS OF NATURALPOPULATIONSC h a p t e r 3 i Genetic diversity45Importance of genetic diversityW h a t is genetic diversity?Measuring genetic diversityExtent of genetic diversity46475060

CONTENTSLow genetic diversity in endangered speciesW h a t genetic diversity determines evolutionary potential?Variation over space a n d t i m eW h a t explains differences in levels of genetic diversity?Genetic differences a m o n g speciesSummaryFurther readingProblemsPractical exercise: Measuring genetic diversity usingmicrosatellites6667676868686970Chapter 472Characterizing genetic diversity: single lociDescribing genetic diversityFrequencies of alleles and genotypesHardy-Weinberg equilibriumExpected heterozygosityDeviations from Hardy-Weinberg equilibriumExtensions of the Hardy-Weinberg equilibriumMore t h a n one locus-linkage disequilibriumSummaryFurther readingProblemsChapter 5Characterizing genetic diversity: quantitativevariationImportance of quantitative charactersProperties of quantitative charactersBasis of quantitative genetic variationMethods for detecting quantitative genetic variationPartitioning genetic and environmental variationGenotype X e n v i r o n m e n t interactionThe need for contemporary comparisons and controlpopulationsPartitioning of quantitative genetic variationEvolutionary potential and heritabilitySusceptibility to inbreeding depressionCorrelations between molecular and quantitative geneticvariationOrganization of quantitative genetic variationSummaryFurther 05106108108m120122122123123124C h a p t e r 6 j Evolution in large populations. I. Naturalselection and adaptation126The need to evolveFactors controlling t h e evolution of populations127131

CONTENTSSelectionSelection on quantitative charactersDirectional selectionStabilizing selectionDisruptive selectionSummaryFurther readingProblemsPractical exercises: Computer simulationsChapter 7Evolution in large populations. II. Mutation,migration and their interactions with selection133145146149149150150151152154Factors controlling the evolution of populationsImportance of m u t a t i o n , migration and their interactions w i t hselection in conservationOrigin and regeneration of genetic diversityMutationSelective value of m u t a t i o n sMutation-selection balance and t h e m u t a t i o n loadMigrationMigration-selection equilibria and clinesSummaryFurther readingProblems155C h a p t e r 8 1 Evolution in small populations175Importance of small populations in conservation biologyImpact of small p o p u l a t i o n size: c h a n c e effectsInbreedingMeasuring p o p u l a t i o n sizeSelection in small populationsMutation in small populationsMutation-selection equilibrium in small populationsComputer simulationSummaryFurther readingProblemsPractical exercises: Computer pter 9197Maintenance of genetic diversityConservation of genetic diversityFate of different classes of m u t a t i o n sMaintenance of genetic diversity in large populationsNeutral m u t a t i o n s u n d e r r a n d o m genetic driftSelection intensities vary a m o n g charactersBalancing selectionMaintenance of genetic diversity in small 200203204214

CONTENTSSummaryFurther readingProblemsPractical exercises: Computer simulationsS E C T I O N IIChapter 10221221222223EFFECTS OF POPULATION SIZE REDUCTIONLoss of genetic diversity in small populations227Changes in genetic diversity over timeRelationship between loss of genetic diversity and reducedfitnessEffects of sustained population size restrictions on geneticdiversityRelationship between population size and genetic diversity inwild populationsEffective population sizeMeasuring effective population sizeSummaryFurther readingProblemsPractical exercises: Computer simulations228Chapter I I254Inbreeding22923J235239241251252252253What is inbreeding?Conservation concerns with inbreedingInbreeding coefficient (F)Genetic consequences of inbreedingInbreeding in small populationsPedigreesBreeding systems in natureRegular systems of inbreedingMutation-selection balance with inbreedingInbreeding in polyploidsRelationship between inbreeding, heterozygosity, geneticdiversity and population sizeSummaryFurther readingProblems255256256258263269271271274276C h a p t e r 12Inbreeding depression280Inbreeding depression in naturally outbreeding speciesInbreeding depression in the wildInbreeding depression due to small population sizeInbreeding and extinctionCharacteristics of inbreeding depressionGenetic basis of inbreeding depressionPurging281282285286287290295277278278279

CONTENTSDetecting and measuring inbreeding depressionInbreeding and population viabilityRecovering from inbreeding depressionSummaryFurther readingProblems299302305307307308C h a p t e r 13Population fragmentation309Habitat fragmentationPopulation fragmentationPopulation structureCompletely isolated population fragmentsMeasuring population fragmentation: F statisticsGene flow among population fragmentsMeasuring gene flowImpacts of different population structures on reproductivefitnessSummaryFurther readingProblems310310312314324327330C h a p t e r 14 1 Genetically viable populations336Shortage of space for threatened speciesHow large?Retaining reproductive fitnessRetaining evolutionary potentialHow large are threatened populations?What happens to species with Ne 500?Retaining single locus diversity in the long termTime to regenerate genetic diversityAvoiding accumulation of new deleterious mutationsGenetic goals in the management of wild populationsGenetic goals in m a n a g e m e n t of captive p o p u l a t i o n s a compromiseThe fallacy of small surviving populationsSummaryFurther readingProblems337339339341343344348349349351S E C T I O N III332333334334352356357358358FROM THEORY T O PRACTICEC h a p t e r 15 \ Resolving taxonomic uncertainties and definingmanagement units365Importance of accurate taxonomy in conservation biologyWhat is a species?Sub-speciesHigher taxonomic categories366370371371

CONTENTSHow do species arise?Use of genetic markers in delineation of sympatric speciesUse of genetic markers in delineation of allopatric speciesMeasuring differences between populations: genetic distanceConstructing phylogenetic treesOutbreeding depressionDefining management units within speciesSummaryFurther readingProblemsPractical exercise: Building a phylogenetic tree372375376379382385388392392393394C h a p t e r 16 ' Genetics and the management of wildi populations395Genetic issues in wild populationsResolving taxonomy and m a n a g e m e n t u n i t sIncreasing population sizeDiagnosing genetic problemsRecovering small inbred populations with low genetic diversityGenetic m a n a g e m e n t of fragmented populationsGenetic issues in reserve designIntrogression and hybridizationImpacts of harvestingGenetic m a n a g e m e n t of species t h a t are n o t outbreedingdiploidsSummaryFurther readingProblems396399399401401404410411412Chapter 17419Genetic management of captive populations414416417417Why captive breed?Stages in captive breeding and reintroductionFounding captive populationsGrowth of captive populationsGenetic management of captive populationsCurrent genetic management of captive populationsCaptive management of groupsEx situ conservation of plantsReproductive technology and genome resource banksManaging inherited diseases in endangered speciesSummaryFurther 6446C h a p t e r 18448Genetic management f o r reintroductionReintroductionsGenetic changes in captivity t h a t affect reintroduction success449452

CONTENTSGenetic adaptation to captivityGenetic management of reintroductionsHow successful are reintroductions?Supportive breedingCase studies in captive breeding and reintroductionSummaryFurther readingProblems452459463465466469470470C h a p t e r 19 ! Use of molecular genetics in forensics and t ounderstand species biology471Forensics: detecting illegal hunting and collectingAn understanding of species' biology is critical to itsconservationGene trees and coalescencePopulation size and demographic historyGene flow and population structureReintroduction and translocationReproduction, parentage, founder relationships and sexingDiseaseDietSummaryFurther readingProblemsChapter 20The broader context: population viabilityanalysis (PVA)472474475480485491492498499499500500502What causes endangerment and extinction?Predicting extinction probabilities: population viabilityanalysis (PVA)Recovering threatened populationsHow useful are the predictions of PVA?Lessons learnedMinimum viable population sizes (MVP)SummaryFurther readingProblemsPractical exercises: Population viability analyses503506516520523524526526527527Take home messages from this book529Revision problemsGlossaryAnswers to problemsReferencesIndex531533546567607

Chapter 2 Genetics and extinction 23 Genetics and the fate of endangered species 24 Relationship between inbreeding and extinction 27 Inbreeding and extinction in the wild 29 Relationship between loss of genetic diversity and extinction 36 Summary 39 Further reading 39