Conservation Genetics in the Neotropics

This book explores how genetics and the new technologies in genomics have been used for conservation of plants and animals in the Neotropics. It shows the new perspective for conservation genetics beyond the use of theoretical and methods in genetics at species level and presents how genetics and genomics can be used for assessing communities. Conservation genetics and genomics are presented as a helpful field of study for resolving taxonomic uncertainties and hidden biodiversity, understanding populations and extinction risk, genetic management, wildlife forensic genetics, assessing biology and molecular ecology, assessing communities, conservation genomics and the use of conservation biology and genetics in science learning, highlighting case studies in the Neotropics. Applications of conservation genetics for management or policy, decision making, planning, and implementation of conservation practice in the Neotropics are addressed across chapters. This book will interest to researchers and students in conservation genetics and biology conservation interested in the Neotropics. Stakeholders and decision makers in conservation biology may also find this book useful. Preface Acknowledgements Contents Part I: Introduction Chapter 1: A Fresh Look at Conservation Genetics in the Neotropics 1.1 Introduction 1.2 Conservation Genetics at the Species Level 1.3 Genetics for Studying Communities and Ecosystems 1.3.1 Phylogenetic Diversity 1.3.2 Comparative Phylogeography 1.3.3 Environmental DNA and Invertebrate-Derived DNA and Conservation 1.4 Conservation Genomics in Neotropics 1.5 Final Considerations References Part II: Species and Conservation Chapter 2: DNA Barcoding for Assessing Biodiversity 2.1 Introduction 2.2 DNA Barcoding, a Tool for Biological Identification 2.2.1 Molecular Markers 2.2.2 The Distance Approach and the DNA Barcoding Gap 2.2.3 Worldwide Initiatives 2.3 DNA Barcoding Methodologies 2.3.1 BOLD System 2.3.2 Voucher and Collection Data 2.3.3 Biological Preservation Methods 2.3.4 DNA Extraction Methods 2.3.5 PCR and Primers Commonly Used 2.3.6 Uploading Data to BOLD 2.4 Single-Gene Species Delimitation Methods 2.4.1 Molecular Operational Taxonomic Units 2.4.2 Distance vs Coalescent Species Delimitation Approaches 2.4.3 Barcode Index Number 2.4.4 Comparing Methods 2.5 DNA Barcoding in Neotropics 2.5.1 Using DNA Barcoding to Assess Biodiversity in Birds 2.5.2 Using DNA Barcoding to Assess Fish Biodiversity 2.5.3 Using DNA Barcoding to Assess Biodiversity in Marine Realm 2.5.4 Using DNA Barcoding to Assess Biodiversity in Insects 2.5.5 Using DNA Barcoding to Assess Biodiversity in Plants 2.6 Final Considerations References Chapter 3: Genetic Tools for the Conservation of Bats 3.1 Introduction 3.2 Literature Review of Genetic Techniques Applied in Bat Conservation 3.3 Issues and Timeline Overview 3.4 Molecular Identification and Taxonomy 3.5 Demographic History, Biogeography, Life History and Genetic Diversity 3.6 Lessons from Population Genetics 3.6.1 Impacts of Geographical Barriers and Distance on Gene Flow 3.6.2 Genetic Structure of Populations 3.6.3 Bats in Islands 3.6.4 Effect of Fragmentation and Other Anthropogenic Effects on Genetic Diversity 3.6.5 Bat Adaptations 3.7 Final Considerations References Chapter 4: Status Quo and Orchid Conservation Challenges in the Neotropical Region 4.1 Introduction 4.2 Genetic Conservation in Orchidaceae 4.3 Neotropical Orchids 4.4 Phylogenetic Relationships 4.5 Population Genetics 4.6 Final Considerations References Chapter 5: Population Differentiation with Introgression 5.1 Introduction 5.2 Population Differentiation and Speciation Genomics 5.3 Balance of Gene Flow and Drift Shape Population Structure 5.4 Population Structure and Secondary Contact 5.5 Patterns of Introgression Across the Genome 5.6 Balance Between Gene Flow and Selection and Population Structure 5.7 Anthropogenic Impact on Introgression 5.8 Differentiation with Gene Flow in the Neotropics 5.9 Final Remarks References Part III: Assessing and Managing Populations Chapter 6: Phylogeography for Neotropical Species Conservation: Lineages Through Time and Space 6.1 Introduction 6.2 The Origins and Drivers of Neotropical Diversity 6.2.1 Terrestrial Organisms 6.2.1.1 Refuge Hypothesis 6.2.1.2 Disturbance-Vicariance Hypothesis 6.2.1.3 Riverine Barrier Hypothesis 6.2.1.4 Marine-Incursions Hypothesis 6.2.1.5 Gradient Hypothesis 6.2.2 Freshwater Organisms 6.3 Evaluating Neotropical Biodiversity at Multiple Scales 6.3.1 Intraspecific Scale 6.3.2 Interspecific Scale 6.3.3 Community Scale 6.4 Assessing Old Phylogeographical Questions with Modern Tools 6.4.1 Species Distribution Modeling 6.4.2 Inference of Demographic Scenarios 6.4.3 Machine Learning for Demographic Inference and Predictive Phylogeography 6.4.4 Phylogeography as a Bridge to Connect Multiple Evolutionary Scales 6.5 Final Considerations References Chapter 7: Landscape Genetics in the Neotropics 7.1 Introduction 7.2 Integrating Genetic and Landscape Data to Elucidate Microevolutionary Processes 7.3 Adaptive Genetic Diversity 7.4 Landscape Genetics in the Neotropics 7.5 Approaches in Neotropical Studies 7.6 Challenges for Neotropical Landscape Genetics 7.7 Opportunities for Neotropical Landscape Genetics 7.8 Final Remarks References Chapter 8: Integrative Cytogenetics, A Conservation Approach in Atlantic Fish: Concepts, Estimates, and Uses 8.1 Introduction 8.2 Marine Environment and Fish Chromosome Diversification 8.3 Chromosomes Under the Aegis of Evolutionary Factors 8.4 Karyotype Evolutionary Processes 8.5 Population Cytogenetics 8.5.1 Supernumerary Chromosomes 8.5.2 Chromosome Inversion Systems 8.5.3 Chromosome Translocation 8.5.4 Microstructural Variations in Repetitive Sequences 8.6 Final Considerations References Chapter 9: In Situ, Ex Situ and On Farm Conservation of Plant Genetic Resources in Neotropics 9.1 Introduction 9.2 The Genetic Erosion in Plant Resources 9.3 Genetics as a Framework for Ex Situ and In Situ Plant Conservation 9.4 Global Strategy and Local Actions to Safeguard the Valuable Genetic Inheritance of Food Plants 9.5 Final Considerations References Chapter 10: Genetic Management Applied to Conservation of Reduced and Fragmented Wild Populations 10.1 Introduction 10.2 When Genetic Management Is a Viable Conservation Strategy and Limitations for In Situ Genetic Management in Neotropical Landscapes 10.3 Planning for Genetic Conservation Management 10.3.1 Pedigree Versus Molecular Analysis: What Genetics Can and Cannot Do 10.3.2 Reintroduction Versus Translocation Strategies 10.3.3 Neotropical Landscape Management Applied to Genetic Conservation 10.4 The Genetic Management Importance to Cope with Climate Change in Neotropical Regions 10.5 Case Studies: What Have We Learned? 10.5.1 Golden Lion Tamarin 10.5.2 Spix’s Macaws 10.5.3 Eugenia Dysenterica: A Tree Species from Brazilian Cerrado 10.6 Recommendations for the Management of Neotropical Populations References Chapter 11: Chromosome Variability of Manatees (Trichechus spp.) from Brazil: The State of the Art, Challenges and Perspectives for Management and Conservation 11.1 Introduction 11.1.1 Genomic Tools for Conservation in the Manatees – Comparative Cytogenetics from the Hybrid Zone Between South American Manatees 11.1.2 The State of Art: Genetic Variability and Possible Hybridization in Trichechus Species 11.1.3 Chromosomal Variability in Trichechus Species 11.1.4 Poque, the First Described Hybrid 11.1.5 Conservation Genetics Foster Manatee (Trichechus spp.) Management in Brazil 11.2 Material and Methods 11.2.1 Sample Collection 11.2.2 Samples 11.2.3 Chromosome Obtention 11.2.4 Cytogenetic Analyses 11.3 Results 11.3.1 Diploid Number and Karyotype Description 11.3.2 G-Banding Comparison 11.4 Discussion 11.4.1 Chromosomal Variation 11.4.2 Chromosomes and Hybridization 11.4.3 Conservation Issues References Chapter 12: Supplemental Technologies for Freshwater Fish Conservation 12.1 Introduction 12.2 Habitat Manipulation to Favor the Reproduction and Recruitment of Specific Populations 12.2.1 Spawning and Recruitment 12.2.2 Migratory Routes 12.2.3 Water Level Regulation: Upstream and Downstream Impacts 12.2.4 Riparian Deforestation 12.3 Unsustainability of Populations Caused by Alteration in the Trophic Chain of the Fish Assembly 12.3.1 Effect of Damming on Riverine Food Webs 12.3.2 Non-native Fish Species 12.3.3 Removing Dams 12.4 Replenish the Environment With Fish Stocking and/or Potential Breeders in Specific Habitats 12.5 Special Breeding Techniques to Promote the Most Genetically Favorable Breeding for Stocking 12.5.1 Genetic Variability Implications 12.5.2 Performance of Captive-Bred Fish to Survive in the Wild 12.6 New Findings on Induced Spawning and Larviculture 12.7 Cloning Gametes to Improve Reproductive Success for Threatened Species 12.7.1 Cryopreservation 12.7.2 Cloning 12.8 Germ Cell Transplantation Technology 12.8.1 Blastula Cell Transplantation 12.8.2 Primordial Germ Cell Transplantation 12.8.3 Gonadal Germ Cell Transplantation Into the Peritoneal Cavity of Larvae or Into the Genital Pore of Adult Recipients 12.9 Technologies to Minimize the Impacts of Aquaculture on Native Fish Species 12.9.1 Triploidy 12.9.2 Interspecific Hybridization 12.9.3 Genome Editing by CRISPR/Cas9 12.10 Some Recommendations 12.10.1 Mitigating Harmful Habitat Changes 12.10.2 Mitigating Impacts of Non-native Species Introduction 12.10.3 Fish Stocking Guidelines 12.11 Limitations and Future Perspectives of Fish Biotechnology References Part IV: Wildlife Forensic Genetics, Ecotoxicology and Conservation Chapter 13: Giving Names to the Characters: Identifying, Tracing and Estimating the Multiple Use of Aquatic Wildlife in Brazil 13.1 Introduction 13.2 Data Collection and Analysis 13.2.1 Field Work 13.2.2 Previous Forensic Identification 13.2.3 Tooth Morphology and Aging 13.3 Results 13.3.1 Molecular Analysis 13.3.2 Age 13.4 Discussion 13.4.1 Trade of Dolphins’ Products in Brazil 13.4.2 Tooth Morphology and Age 13.4.3 Forensic Analyses 13.4.4 Natural Products Derived from Aquatic Wildlife 13.5 Conclusions/Final Remarks References Chapter 14: Wildlife Forensic Genetics: A Tool for Resolving Wildlife Crimes and Support Species Conservation 14.1 Introduction 14.2 An Overview on the Contributions of Forensic Genetics for Animal Wildlife Conservation 14.3 Taxonomic Groups and Species Affected 14.4 Typologies of the Crimes 14.4.1 Examples in Costa Rica 14.5 Molecular Techniques Employed to Solve the Crimes 14.6 A Case Study in the Neotropical Bird Sicalis flaveola (Linnaeus, 1766) 14.7 Lessons for Conservation 14.8 Final Considerations References Chapter 15: Environmental Ecogenotoxicity and Conservation 15.1 Introduction 15.2 Native Fish as Biomonitors, Bioindicators and Test Organisms 15.3 Biomarkers of Genotoxicity and Mutagenicity 15.3.1 Piscean Micronucleus Test (Giemsa and Acridine Orange) 15.3.2 Comet Assay 15.4 Genotoxicological Responses: Native Fish Versus Exotic Fish 15.5 Final Considerations References Part V: Assessing Molecular Ecology and Communities Chapter 16: Molecular Ecology in Neotropical Mammals: Key Aspects for Conservation 16.1 Introduction 16.2 Molecular Species Identification 16.2.1 Molecular Markers for Species Identification 16.2.2 Biodiversity Monitoring Through Molecular Species Identification 16.2.3 Molecular Identification of Prey and Diet 16.3 Sample Individualization and Molecular Sex Identification 16.3.1 Molecular Markers Used in Sample Individualization 16.3.2 Applicability of Individualization in Ecological Studies 16.3.3 Molecular Sexing 16.4 Behavioral Ecology 16.4.1 Relatedness and Mating Systems 16.4.2 Dispersal and Philopatry 16.5 Concluding Remarks References Chapter 17: Molecular Tools to Analyze the Effects of Roads on Wildlife in the Neotropics 17.1 Introduction 17.2 Road Impacts on Wildlife 17.3 Molecular Road Ecology in the Neotropics 17.3.1 Molecular Species Identification 17.3.2 Molecular Sex Identification 17.3.3 Population Analyzes 17.4 Concluding Remarks – Implications to Neotropical Wildlife Conservation References Chapter 18: Environmental and Invertebrate-Derived DNA: A Powerful Approach for Surveying and Monitoring Biodiversity 18.1 Introduction – eDNA and iDNA for Monitoring Biodiversity 18.2 Environmental Samples 18.2.1 Water Samples 18.2.2 Soil Samples 18.2.3 Alternative Sources of DNA to Assess the Biodiversity and Species Ecology 18.3 Invertebrate-Derived DNA (iDNA) 18.4 Challenges and Perspectives 18.4.1 Methodological Concerns 18.4.2 Conservation Remarks References Part VI: Conservation Genomics Chapter 19: Conservation Genomics of Neotropical Carnivores 19.1 Introduction 19.2 Neotropical Carnivores 19.3 Genomic Resources for Neotropical Carnivores 19.4 Genomic Studies of Neotropical Carnivores and Their Implications for Conservation 19.4.1 Jaguars (Panthera onca) 19.4.2 Pumas (Puma concolor) 19.4.3 Small Cats of the Genus Leopardus 19.4.4 Otters (Mustelidae: Lutrinae) 19.4.5 Canids 19.5 Current Challenges and Future Directions References Chapter 20: Challenges with Conservation Genetics and Genomics in Neotropical Forest 20.1 Brief History of Deforestation in the Neotropics and Loss of Biodiversity 20.2 Genetic Diversity Discoveries in Neotropical Trees and Proposals for Conservation and Mitigation 20.3 New Approaches Using Conservation Genomics in Neotropical Forests for Conservation Purposes 20.4 Future Implications for the Conservation of Neotropical Forests with a Genomic Approach References Chapter 21: Integrating Genomic and Cytogenetic Data to Study the Evolutionary History of Arapaimas and Arowanas in the Neotropics 21.1 Introduction 21.2 The Neotropical Bonytongues 21.3 Osteoglossidae Biogeography 21.4 Integrating Genomic and Cytogenetic Data in Neotropical Arapaima 21.5 Neotropical Arowanas Phylogeography 21.6 Concluding Remarks References Part VII: Science Learning and Conservation Chapter 22: Environmental Education on Practices for Biodiversity Conservation 22.1 Introduction 22.2 Environmental Education in Conservation Units: Research and Projects in the Neotropics 22.2.1 The Thematic Chambers of Environmental Education 22.2.2 The Itatiaia National Park Goes to School (PNIVE) 22.2.3 Primates of Itatiaia Project 22.3 Lived Experiences in Nature and Their Importance in Building a Relationship with Nature 22.4 Final Considerations References Chapter 23: Phenotypic Plasticity of Plants in Formal and Non-formal Education: Genetics in Everyday Life 23.1 Introduction 23.2 Why Should We Promote the Public Appreciation for Botany? 23.3 A Brief Overview of Genotypes and Phenotypes 23.4 Plants Expressing Phenotypic Plasticity 23.5 Is Phenotypic Plasticity an Adaptive Response in Plants? 23.6 Epigenetics and Plant Phenotypic Plasticity 23.7 Science Learning Activities: Phenotypic Plasticity in Boldos 23.7.1 What Are Boldos? 23.7.2 How Did Everything Begin? 23.7.3 The Experimental Design 23.7.4 What Do We Learn from This? 23.8 Final Considerations References Correction to: Phylogeography for Neotropical Species Conservation: Lineages Through Time and Space Index