Zoos in the 21st Century: Catalysts for Conservation ? (Conservation Biology)

It Is Widely Accepted Among Conservation Biologists That Genetics Is, More Than Ever, An Essential And Efficient Tool For Wild And Captive Population Management And Reserve Design. However, A True Synergy Between Population Genetics And Conservation Biology Is Lacking. Following The First International Workshop On Population Genetics For Animal Conservation In 2003, The Scientific Committee Felt That, Given The Global Urgency Of Animal Conservation, It Was Imperative That Discussions At The Conference Were Made Accessible To Graduate Students And Wildlife Managers. This Book Integrates 'the Analytical Methods Approach' With The 'real Problems Approach' In Conservation Genetics. Each Chapter Is An Exhaustive Review Of One Area Of Expertise, And A Special Effort Has Been Made To Explain The Statistical Tools Available For The Analysis Of Molecular Data As Clearly As Possible. The Result Is A Comprehensive Volume Of The State-of-the-art In Conservation Genetics, Illustrating The Power And Utility Of This Synergy. Introduction / Heidi C. Hauffe And Valerio Sbordoni -- Statistical Methods For Identifying Hybrids And Groups / Eric C. Anderson -- How To Use Migrate Or Why Are Markov Chain Monte Carlo Programs Difficult To Use? / Peter Beerli -- Nested Clade Phylogeographic Analysis For Conservation Genetics / Jennifer E. Buhay, Keith A. Crandall And David Posada -- A Comparison Of Methods For Constructing Evolutionary Networks From Intraspecific Dna Sequences / Patrick Mardulyn, Insa Cassens And Michel C. Milinkovitch -- Challenges In Assessing Adaptive Genetic Diversity: Overview Of Methods And Empirical Illustrations / Aurélie Bonin And Louis Bernatchez -- Monitoring And Detecting Translocations Using Genetic Data / Giorgio Bertorelle [and Others] -- Non-invasive Genetic Analysis In Conservation / Benoît Goossens And Michael W. Bruford -- The Role Of Ancient Dna In Conservation Biology / Jon Beadell, Yvonne Chan And Robert Fleischer -- Future-proofing Genetic Units For Conservation: Time's Up For Subspecies As The Debate Gets Out Of Neutral! / Michael W. Bruford -- Genetic Diversity And Fitness Related Traits In Endangered Salmonids / Katriina Tiira And Craig R. Primmer -- Genetics And Conservation On Islands: The Galápagos Giant Tortoise As A Case Study / Claudio Ciofi [and Others] -- Evolution Of Population Genetic Structure In Marine Mammal Species / A. Rus Hoelzel -- Recent Developments In Molecular Tools For Conservation / Cristiano Vernesi And Michael W. Bruford -- Theoretical Outlook / Mark Beaumont. Edited By Giorgio Bertorelle ... [et Al.]. Includes Bibliographical References And Indexes. Cover 1 Half-title 3 Series-title 4 Title 5 Copyright 6 Contents 9 Contributors 11 Foreword 15 Acknowledgements 16 1 Introduction 17 The extinction crisis 17 The synergy between conservation biology and genetics 19 Population Genetics for Animal Conservation (PGAC) workshop 25 Acknowledgements 28 References 28 Statistical approaches, data analysis and inference 39 2 Statistical methods for identifying hybrids and groups 41 Introduction 41 Conceptual models and graphical models 42 Mixture models 44 Bayesian inference 46 A survey of methods 46 The structure model without admixture 47 The structure model with admixture 47 The structure model with admixture and prior population information 49 The NewHybrids model 52 The BayesAss+ model 53 Practical issues 55 Acknowledgements 56 References 56 3 How to use Migrate or why are Markov chain Monte Carlo programs difficult to use? 58 What is 'Markov chain Monte Carlo'? 59 An almost too simple example 60 Migrate – a program for inferring population genetic parameters 61 Coalescence theory 62 Mutation models 63 How are these pieces combined? 64 Running in maximum likelihood mode 65 Running in Bayes inference mode 65 A short explanation of what Migrate does and does not do 66 What happens when the population history violates the assumptions? 67 Example data set 69 Analysis using Migrate 71 Basic analysis – getting familiar with MCMC-based software and data 71 Comparison of effect of gene flow using the Bayesian framework 73 Comparison of Bayesian inference and maximum likelihood 74 How long to run 76 Replication and heating 76 How long to wait 77 Can we trust the support intervals in a MCMC-assisted maximum likelihood analysis? 79 Likelihood ratio tests and related test statistics 79 Comparison of two different migration models 80 Use of the coalescent in conservation genetics 83 Summary 85 Acknowledgements 86 References 86 Appendix Data set 91 Run conditions for specific examples in this chapter 94 4 Nested clade phylogeographic analysis for conservation genetics 96 Introduction 96 Network approaches require thorough sampling 97 How to conduct a Nested Clade Phylogeographic Analysis 100 Network construction 100 Network diagrams illustrate different types of information 100 How to resolve loops and ambiguous connections 102 Building the nesting design 103 From haplotype network to geographical analysis using GeoDis 104 Using the inference key to uncover evolutionary processes and patterns 108 A special case: terrestrial versus riparian species 110 Inferring biogeographic patterns 111 NCPA can be used to delimit species' boundaries 112 Summary 115 Acknowledgements 115 References 115 5 A comparison of methods for constructing evolutionary networks from intraspecific DNA.sequences 120 Network construction methods 122 Minimum spanning network (MSN) 122 Reduced median network (RMN) 122 Median-joining network (MJN) 123 Statistical parsimony network 123 Union of maximum parsimonious trees (UMP) 124 Comparison of methods: simulated sequence data 127 Comparison of methods: Empirical data sets 129 Which method(s) should be used to infer genealogical relationships among intraspecific sequences? 133 Acknowledgements 134 References 135 Molecular approaches and applications 137 6 Challenges in assessing adaptive genetic diversity: overview of methods and empirical illustrations 139 Introduction 139 QST-FST comparison 141 Case study: the QST–FST comparison applied to two different ecotypes of the lake whitefish (Coregonus clupeaformis) 143 Analysis of a candidate gene or mutation 144 Case study: melanism in the rock pocket mouse 145 Genome scan 148 Incorporating population genomics into conservation: the Population Adaptive Index 150 Transcription profiling based on a cDNA microarray 151 Rapid evolutionary changes of gene expression in farmed Atlantic salmon (Salmo salar): relevance for the conservation of wild populations 154 General discussion 155 References 158 7 Monitoring and detecting translocations using genetic data 164 Genetic analyses and monitoring of well-known translocation events 167 Detecting a past translocation event from genetic data 176 References 178 8 Non-invasive genetic analysis in conservation 183 Introduction 183 Why non-invasive genetics? 183 What are the applications? 184 Methods and sample sources 187 Sample sources 187 Storage of samples 188 Hair samples 188 Faecal samples 189 Other samples 191 Extraction kits and methods 191 Recent innovations 192 Molecular markers 193 Technical challenges 195 The need for pilot studies 196 Requirements 197 Analysis 197 Reliability 197 Demographic information 198 Perspective 201 Acknowledgements 201 References 201 9 The role of ancient DNA in conservation biology 218 Introduction 218 Methodological challenges 219 Laboratory 219 Data analysis 221 Conservation applications 222 Evolutionarily significant units 222 Establishing prior range 223 Systematics and forensics 225 Genetic diversity in historical context 232 Response to long-term environmental change 235 Conclusions 237 References 238 From genetic data to practical management: issues and case studies 245 10 Future-proofing genetic units for conservation: time's up for subspecies as the debate gets out of neutral! 247 Introduction 247 Current situation 248 Preble's meadow jumping mouse: an example of the problem 250 Getting out of ‘neutral' 253 Future-proofing 258 References 258 11 Genetic diversity and fitness-related traits in endangered salmonids 261 Introduction 261 Background of the study species 264 Endangered salmonid populations 264 Behaviour of juvenile salmonid fish: the importance of aggression 265 Genetic diversity and competitive ability: Experiment I 266 Methods 267 Estimating offspring genetic diversity 267 Behaviour trials 269 Results and discussion 269 Genetic variation and competitive ability: experiment II 272 Methods 272 Behavioural trials 273 Genetic analysis and statistics 274 Results and discussion 275 Experiments I and II: discussion and conclusions 280 Acknowledgements 282 References 282 12 Genetics and conservation on islands: the Galápagos giant tortoise as a case study 289 Introduction 289 Population divergence and taxonomy 289 Restoration genetics 290 Aim of this chapter 291 Sample collection and genetic methods 291 Genetic divergence and phylogeny of island populations 292 Genetic diversity 293 Phylogeny and taxon designation 294 Patterns of genetic differentiation within islands 296 Santa Cruz 296 Isabela 297 Parentage analysis and genetic assignment 301 The Española captive breeding system 301 Genetic assignment of tortoises of unknown origin 303 Conservation and management implications 307 Acknowledgements 309 References 310 13 Evolution of population genetic structure in marine mammal species 314 Introduction 314 Kin associations 315 Habitat dependence 320 Migratory species and predictable habitats 326 Sex-specific dispersal 328 Conclusions 331 References 332 Future directions in conservation genetics 339 14 Recent developments in molecular tools for conservation 341 Introduction 341 Where we are 344 Minisequencing 344 Real-time polymerase chain reaction (RT-PCR) 346 Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) 348 Amplification fragment length polymorphism (AFLP) PCR 349 Pyrosequencing 351 Microarray technology 352 Maximizing DNA retrieval: whole-genome amplification (WGA) and metagenomics approaches 353 Whole-genome amplification 353 Metagenomics 354 Conclusions and perspective 355 References 357 15 Theoretical outlook 365 Introduction 365 Genealogical modelling and demographic history 366 How feasible is it to recover demographic history from genetic data? 368 Recombination 370 Future developments 372 Approximations 372 Improvements to current methods 373 Species identification 376 Multilocus genotypic methods 377 Relatedness and pedigrees 379 Natural selection and adaptation 381 Conclusions 384 References 385 Software index 394 Species index 396 Species index 399 Subject index 402 Cover......Page 1 Half-title......Page 3 Series-title......Page 4 Title......Page 5 Copyright......Page 6 Contents......Page 9 Contributors......Page 11 Foreword......Page 15 Acknowledgements......Page 16 The extinction crisis......Page 17 The synergy between conservation biology and genetics......Page 19 Population Genetics for Animal Conservation (PGAC) workshop......Page 25 References......Page 28 Statistical approaches, data analysis and inference......Page 39 Introduction......Page 41 Conceptual models and graphical models......Page 42 Mixture models......Page 44 A survey of methods......Page 46 The structure model with admixture......Page 47 The structure model with admixture and prior population information......Page 49 The NewHybrids model......Page 52 The BayesAss+ model......Page 53 Practical issues......Page 55 References......Page 56 3 How to use Migrate or why are Markov chain Monte Carlo programs difficult to use?......Page 58 What is 'Markov chain Monte Carlo'?......Page 59 An almost too simple example......Page 60 Migrate – a program for inferring population genetic parameters......Page 61 Coalescence theory......Page 62 Mutation models......Page 63 How are these pieces combined?......Page 64 Running in Bayes inference mode......Page 65 A short explanation of what Migrate does and does not do......Page 66 What happens when the population history violates the assumptions?......Page 67 Example data set......Page 69 Basic analysis – getting familiar with MCMC-based software and data......Page 71 Comparison of effect of gene flow using the Bayesian framework......Page 73 Comparison of Bayesian inference and maximum likelihood......Page 74 Replication and heating......Page 76 How long to wait......Page 77 Likelihood ratio tests and related test statistics......Page 79 Comparison of two different migration models......Page 80 Use of the coalescent in conservation genetics......Page 83 Summary......Page 85 References......Page 86 Appendix Data set......Page 91 Run conditions for specific examples in this chapter......Page 94 Introduction......Page 96 Network approaches require thorough sampling......Page 97 Network diagrams illustrate different types of information......Page 100 How to resolve loops and ambiguous connections......Page 102 Building the nesting design......Page 103 From haplotype network to geographical analysis using GeoDis......Page 104 Using the inference key to uncover evolutionary processes and patterns......Page 108 A special case: terrestrial versus riparian species......Page 110 Inferring biogeographic patterns......Page 111 NCPA can be used to delimit species' boundaries......Page 112 References......Page 115 5 A comparison of methods for constructing evolutionary networks from intraspecific DNA.sequences......Page 120 Reduced median network (RMN)......Page 122 Statistical parsimony network......Page 123 Union of maximum parsimonious trees (UMP)......Page 124 Comparison of methods: simulated sequence data......Page 127 Comparison of methods: Empirical data sets......Page 129 Which method(s) should be used to infer genealogical relationships among intraspecific sequences?......Page 133 Acknowledgements......Page 134 References......Page 135 Molecular approaches and applications......Page 137 Introduction......Page 139 QST-FST comparison......Page 141 Case study: the QST–FST comparison applied to two different ecotypes of the lake whitefish (Coregonus clupeaformis)......Page 143 Analysis of a candidate gene or mutation......Page 144 Case study: melanism in the rock pocket mouse......Page 145 Genome scan......Page 148 Incorporating population genomics into conservation: the Population Adaptive Index......Page 150 Transcription profiling based on a cDNA microarray......Page 151 Rapid evolutionary changes of gene expression in farmed Atlantic salmon (Salmo salar): relevance for the conservation of wild populations......Page 154 General discussion......Page 155 References......Page 158 7 Monitoring and detecting translocations using genetic data......Page 164 Genetic analyses and monitoring of well-known translocation events......Page 167 Detecting a past translocation event from genetic data......Page 176 References......Page 178 Why non-invasive genetics?......Page 183 What are the applications?......Page 184 Sample sources......Page 187 Hair samples......Page 188 Faecal samples......Page 189 Extraction kits and methods......Page 191 Recent innovations......Page 192 Molecular markers......Page 193 Technical challenges......Page 195 The need for pilot studies......Page 196 Reliability......Page 197 Demographic information......Page 198 References......Page 201 Introduction......Page 218 Laboratory......Page 219 Data analysis......Page 221 Evolutionarily significant units......Page 222 Establishing prior range......Page 223 Systematics and forensics......Page 225 Genetic diversity in historical context......Page 232 Response to long-term environmental change......Page 235 Conclusions......Page 237 References......Page 238 From genetic data to practical management: issues and case studies......Page 245 Introduction......Page 247 Current situation......Page 248 Preble's meadow jumping mouse: an example of the problem......Page 250 Getting out of ‘neutral'......Page 253 References......Page 258 Introduction......Page 261 Endangered salmonid populations......Page 264 Behaviour of juvenile salmonid fish: the importance of aggression......Page 265 Genetic diversity and competitive ability: Experiment I......Page 266 Estimating offspring genetic diversity......Page 267 Results and discussion......Page 269 Methods......Page 272 Behavioural trials......Page 273 Genetic analysis and statistics......Page 274 Results and discussion......Page 275 Experiments I and II: discussion and conclusions......Page 280 References......Page 282 Population divergence and taxonomy......Page 289 Restoration genetics......Page 290 Sample collection and genetic methods......Page 291 Genetic divergence and phylogeny of island populations......Page 292 Genetic diversity......Page 293 Phylogeny and taxon designation......Page 294 Santa Cruz......Page 296 Isabela......Page 297 The Española captive breeding system......Page 301 Genetic assignment of tortoises of unknown origin......Page 303 Conservation and management implications......Page 307 Acknowledgements......Page 309 References......Page 310 Introduction......Page 314 Kin associations......Page 315 Habitat dependence......Page 320 Migratory species and predictable habitats......Page 326 Sex-specific dispersal......Page 328 Conclusions......Page 331 References......Page 332 Future directions in conservation genetics......Page 339 Introduction......Page 341 Minisequencing......Page 344 Real-time polymerase chain reaction (RT-PCR)......Page 346 Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF)......Page 348 Amplification fragment length polymorphism (AFLP) PCR......Page 349 Pyrosequencing......Page 351 Microarray technology......Page 352 Whole-genome amplification......Page 353 Metagenomics......Page 354 Conclusions and perspective......Page 355 References......Page 357 Introduction......Page 365 Genealogical modelling and demographic history......Page 366 How feasible is it to recover demographic history from genetic data?......Page 368 Recombination......Page 370 Approximations......Page 372 Improvements to current methods......Page 373 Species identification......Page 376 Multilocus genotypic methods......Page 377 Relatedness and pedigrees......Page 379 Natural selection and adaptation......Page 381 Conclusions......Page 384 References......Page 385 Software index......Page 394 Species index......Page 396 Species index......Page 399 Subject index......Page 402 Modern zoos and aquaria are playing an increasingly active and important role in protecting and managing global biodiversity. Many zoos include wildlife conservation in their mission and have started changing the focus of their institutions in order to increase even further the benefits of their activities for in situ wildlife conservation. With these developments, the following searching questions are now being asked: What is the true role of zoos in conservation? How can they contribute more significantly to global conservation efforts? What are the unique attributes of zoos that can be applied in the conservation landscape? And should zoos be doing more? In parallel with this voluntary movement, legal requirements for zoos to support conservation in the wild are also becoming more stringent. This book defines a new conservation vision for zoos and aquaria that will be of interest to those working in zoos, alongside practitioners and researchers in conservation. Zimmermann brings together the assessments, analyses, criticisms, reviews, experiences, visions and recommendations of over 40 leading thinkers and zoo practioners. She also defines a new conservation vision for zoos and aquaria that increases their contribution to tackling the ongoing biodiversity crisis