Molecular Ecology and Conservation Genetics of Neotropical Mammals

Although all living beings modify their environment, human beings have acquired the ability to do so on a superlative space-time scale. As a result of industrialization and the use of new technologies, the anthropogenic impact has been increasing in the last centuries, causing reductions in the sizes or the extinction of numerous wild populations. In this sense, from the field of conservation genetics, various efforts have been made in recent decades to provide new knowledge that contributes to the conservation of populations, species, and habitats. In this book, we summarize the concrete contributions of researchers to the conservation of the Neotropical mammals using Molecular Ecology techniques. The book is divided into three major sections. The first section provides an up-to-date review of the conservation status of Neotropical mammals, the applications of the molecular markers in its conservation, and the use of non-invasive and forensic genetic techniques. The second and third sections present, respectively, a series of case studies in various species or taxonomic groups of Neotropical mammals. Foreword Acknowledgments Contents Chapter 1: Introduction 1 Overall Framework 2 Overview of Chapters References Part I: Background and Technical Notes Chapter 2: A Review of the Conservation Status of Neotropical Mammals 1 Introduction: The Worldwide Loss of Biodiversity 2 The Current Situation in the Neotropics 3 Unequal Efforts in Conservation Genetics 4 Effective Conservation Responses References Chapter 3: The Use of Molecular Markers in Neotropical Mammal Conservation 1 Introduction 2 Forensic DNA, Poaching, and Illegal Traffic 3 Inbreeding, Mating Systems, and Dispersal Patterns 4 Phylogeography and Identification of Conservation Units and Evolutionarily Significant Units 5 Gene Flow and Biological Corridors 6 Rewilding and Reintroduction 7 Ex-situ Conservation 8 Cryptic Species 9 Next-Generation Sequencing and Conservation Genomics 10 Environmental and Ancient DNA References Chapter 4: Non-invasive Sampling Techniques Applied to Conservation Genetic Studies in Mammals 1 Introduction 2 Sample Types and Sampling Techniques 3 The Most Commonly Used Molecular Markers 4 Limitations and Solutions for the Use of Genetic Non-invasive Sampling 5 Future Challenges for the Use of Genetic Non-invasive Sampling References Chapter 5: The Use of Forensic DNA on the Conservation of Neotropical Mammals 1 Wildlife Related Crimes 2 Wildlife DNA Forensics 2.1 DNA Samples 2.2 Genetic Markers 2.3 Data Analysis and Databases 3 Wildlife DNA Forensics Applied to Neotropical MAMMALS 3.1 Illegal Hunting in Brazil: Case 1 3.2 Illegal Hunting in Brazil: Case 2 3.3 Dolphin Love Charms in Brazil 3.4 Illegal Traffic of South American Camelids in Argentina 3.5 Hybrids Detection of South American Camelids 3.6 Illegal Traffic of Aotus in Colombia 4 Challenges and Future Directions References Part II: Case Studies at the Species Level Chapter 6: Effects of Sample Size in the Determination of the True Number of Haplogroups or ESUs Within a Species with Phylogeographic and Conservation Purposes: The Case of Cebus albifrons in Ecuador, and the Kinkajous and Coatis Throughout Latin Ameri 1 Introduction 2 Materials and Methods 2.1 Sampling Strategy 2.2 Laboratory Procedures 2.3 Phylogenetic Analyses 2.4 Genetic Heterogeneity 2.5 Spatial Genetic Structure 3 Results 3.1 The Case of C. albifrons in Ecuador 3.1.1 Nucleotide Substitution Model in C. albifrons 3.1.2 Phylogenetic Analysis with the mtCOI and COII Database in the Ecuadorian C. albifrons 3.1.3 Spatial Genetic Structure in the Ecuadorian C. albifrons 3.2 The Case of P. flavus in Latin America 3.2.1 Nucleotide Substitution Model in P. flavus 3.2.2 Phylogenetic Analysis with the Mitogenome Dataset from P. flavus in Latin America 3.2.3 Spatial Genetic Structure in P. flavus 3.3 The Case of the Coatis, Nasua and Nasuella in Latin America 3.3.1 Nucleotide Substitution Model in Coatis (Nasua and Nasuella) 3.3.2 Phylogenetic Analysis with the Mitogenome Dataset in Nasua and Nasuella in Latin America Haplogroups in N. nasua Haplogroups in N. narica Haplogroups in N. olivacea 3.3.3 Genetic Heterogeneity Between Haplogroups of Coatis 3.3.4 Spatial Genetic Structure in N. olivacea 4 Discussion 4.1 The Main Differences Between the Two Genetic Datasets Analyzed for the Primates and Carnivores Studied 4.2 The Case of C. albifrons in Ecuador 4.3 The Case of P. flavus in Latin America 4.4 The Case of the Coatis, Nasua and Nasuella in Latin America References Chapter 7: Genetic Diversity of Odocoileus virginianus veraecrucis (Goldman & Kellog 1940) and Other’s Subspecies in Mexico: Implications for Its Genetic Conservation 1 Introduction 1.1 Evolution of Odocoileus virginianus 1.2 Genetic Diversity Studies in Subspecies of O. virginianus 1.3 The Management of O. virginianus in Mexico 2 Material and Methods 2.1 Bibliometric Analysis 2.2 Description of the Deer Samples of O. v. veraecrucis 2.3 DNA Extraction and Amplification of the D-Loop Region 2.4 Phylogenetic and Molecular Evolutionary Analyses of O. virginianus Subspecies 3 Results 4 Discussion 4.1 Implications of Genetic Management of the Subspecies of O. virginianus in Mexico 5 Conclusions References Chapter 8: Current and Historical Genetic Structure of the White-Footed Tamarin (Saguinus leucopus) 1 Introduction 2 Materials and Methods 2.1 Study Area and Sampling 2.2 DNA Extraction 2.3 Genotyping 2.4 Data Analyses 2.4.1 Population Genetic Structure 2.4.2 Demographic Changes 2.5 Data Availability 2.6 Ethical Note 3 Results 3.1 Genetic Diversity and Population Structure 3.1.1 Microsatellites 3.1.2 Mitochondrial DNA 3.2 Demographic Shifts 4 Discussion 4.1 Nuclear Genetic Variation 4.2 Mitochondrial Genetic Variation 4.3 Historical Demography 4.4 Implications for Conservation References Chapter 9: Aquatic Mammals of the Amazon: A Review of Gene Diversity, Population Structure and Phylogeography Applied to Conservation 1 Introduction 2 Methodology 3 Results 3.1 Family Iniidae 3.2 Family Delphinidae 3.3 Family Trichechidae 3.4 Family Mustelidae 3.4.1 Giant Otter 3.4.2 Neotropical Otter 4 Discussion 5 Conclusion References Part III: Case Studies at other Taxonomic Levels Chapter 10: Molecular Ecology Approaches to Study Neotropical Bats 1 Introduction 2 Genetic Variation in Neotropical Bats 2.1 Genetic Diversity 2.2 Genetic Differentiation 2.3 Genetic Distance: Plylogenetic and Phylogeographic Studies 3 Conservation and Management of Neotropical Bats 4 Understanding and Inferring Species Behavior 4.1 Diet 4.2 Social Structure and Behavior 5 Recent Methodological Advances and Future Research Directions 5.1 Use of Non-invasive Sampling to Study Neotropical Bats 5.2 Next-Generation Sequencing Technologies Applied to Neotropical Bats’ Conservation 5.3 Molecular Epidemiology References Chapter 11: Using Genetic Diversity Estimates in the Assessment of the Conservation Status of Neotropical Primates 1 Background and Goals 2 Genetic Data Collection and Analysis 3 What Did We Find? 4 What Did We Learn from Our Assessment Based on Genetic Data? 5 Why Should We Use Genetic Data to Inform Conservation Policy and Management? References Chapter 12: Conservation Genetics in the Neotropical Carnivorous Mammals: A Systematic Review 1 Introduction 2 Methods 2.1 Literature Search and Criteria for Inclusion 2.2 Assessment of Conservation Impact 2.3 Neotropical Carnivorous Mammals in Numbers 2.4 Conservation Genetics Using Graph Theory 2.5 Sampling Effort and Protected Areas 3 Results 3.1 Assessment of Conservation Impact 3.2 Neotropical Carnivorous Mammals in Numbers 3.3 Conservation Genetics Using Graph Theory 3.4 Sampling Effort and Protected Areas 4 Discussion References Chapter 13: Conservation Genetics of Rodents in Argentina 1 Introduction 2 The Conservation Status of Rodents in Argentina 3 Species Identification and Delimitation 4 DNA Barcoding 5 Phylogeography 6 Landscape Genetics: Identifying Units for Conservation 7 Environmental and Landscape Drivers of Population Structure 8 Genomic Perspectives References Chapter 14: Conservation Genetics of Sigmodontinae and Caviomorph Rodents: A Neotropical Perspective 1 Introduction 2 Sigmodontinae and Caviomorph Rodents 3 Phylogeography of Sigmodontinae Rodents 3.1 Amazon Region 3.2 Pampa Region 3.3 Atlantic Forest 3.4 Patagonia Region 3.5 Andean Region 3.6 Yungas Region 3.7 Final Remarks 4 Studies on Conservation Genetics of Ctenomys 4.1 Ctenomys flamarioni 4.2 Ctenomys “chasiquensis” 4.3 Ctenomys lami 4.4 Ctenomys australis 4.5 Ctenomys ibicuensis 4.6 Ctenomys minutus 4.7 Final Remarks 5 Ecotoxicology as a Tool for Conservation Genetics 6 Summary and Conclusions References Chapter 15: Concluding Remarks References Index